US20100017030A1 - Systems and methods for the automated pre-treatment and processing of biological samples - Google Patents

Abstract

Systems and methods in accordance with embodiments of the present invention allow for the automatic control and scheduling of a staining apparatus for biological samples on slides present within the apparatus. In some embodiments, the actions of a robot coupled to the staining apparatus, which performs some of the staining tasks on the individual slides in accordance with their respective protocols, may be prioritized and scheduled. In some embodiments, the scheduling may result in increasing or maximizing the throughput of slides. In some embodiments, robot scheduling ensures that the individual slides are processed substantially within the tolerances specified by their respective protocols. In some embodiments, the robot scheduler may respond to spontaneous user actions and adaptively schedule or re-schedule robot actions.

Description

CROSS REFERENCES TO RELATED APPLICATIONS
• This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which claims priority to Provisional Patent Application 60/697,591, filed on Jul. 7, 2005 and Provisional Patent Application 60/697,813, filed on Jul. 7, 2005, all of which are herein incorporated by reference in their entirety.
• This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which is a continuation of U.S. patent application Ser. No. 11/229,098, filed on Sep. 16, 2005, which is a continuation-in-part of U.S. patent application Ser. No. 10/741,628, filed on Dec. 19, 2003, which claims priority to U.S. Provisional Application No. 60/435,601, filed on Dec. 20, 2002, all of which are herein incorporated by reference in their entirety. This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which is a continuation of U.S. patent application Ser. No. 11/229,098, filed on Sep. 16, 2005, which is a continuation-in-part of U.S. patent application Ser. No. 10/731,316, filed on Dec. 8, 2003, which claims priority to U.S. Provisional Application No. 60/435,601, filed on Dec. 20, 2002, all of which are herein incorporated by reference in their entirety.
• This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which is a continuation-in-part of U.S. patent application Ser. No. 11/119,417, filed on Apr. 30, 2005, which is a continuation-in-part of international application PCT/DK2003/000877, having an international filing date of Dec. 15, 2003 and designating the United States of America, which claims priority to U.S. Provisional Application No. 60/435,601, filed on Dec. 20, 2002, all of which are herein incorporated by reference in their entirety. This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which is a continuation-in-part of U.S. patent application Ser. No. 11/156,760, filed on Jun. 20, 2005, which is herein incorporated by reference in its entirety.
• This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which is a continuation-in-part of the following international applications: PCT/DK2003/000877, having an international filing date of Dec. 15, 2003 and designating the United States of America; PCT/DK2003/000911, having an international filing date of Dec. 19, 2003 and designating the United States of America; PCT/US2003/040518, having an international filing date of Dec. 19, 2003 and designating the United States of America; PCT/US2003/040591, having an international filing date of Dec. 19, 2003 and designating the United States of America; PCT/US2003/040520, having an international filing date of Dec. 19, 2003 and designating the United States of America; PCT/US2003/040974, having an international filing date of Dec. 19, 2003 and designating the United States of America; PCT/US2003/040519, having an international filing date of Dec. 19, 2003 and designating the United States of America; PCT/US2003/041022, having an international filing date of Dec. 22, 2003 and designating the United States of America; and PCT/US2003/040880, having an international filing date of Dec. 22, 2003 and designating the United States of America; all of which international applications claim priority to U.S. Provisional Application No. 60/435,601, filed on Dec. 20, 2002, all of which applications are herein incorporated by reference in their entirety. This application is a continuation of U.S. patent application Ser. No. 11/338,522, filed on Jan. 23, 2006, which is a continuation-in-part of PCT/US2005/006383, having an international filing date of Feb. 28, 2005 and designating the United States of America, which claims priority to U.S. Provisional Application 60/549,889, filed on Mar. 2, 2004, all of which are herein incorporated by reference in their entirety.
• U.S. patent application Ser. No. 11/227,270, filed on Sep. 16, 2005, is herein incorporated by reference in its entirety.
• This application is also related to European Patent Office Application 03076463.3 filed on May 14, 2003. Each of the above-referenced patent applications is incorporated herein by reference, in its entirety. Each of the patent application publications corresponding to the above-referenced international applications is also incorporated herein by reference in its entirety, said patent application publications being, namely: international patentapplication publication WO 2004/057307 A1, international patentapplication publication WO 2004/057308 A1, international patentapplication publication WO 2004/058950 A1, international patent application publication WO 2004/059287 A2, international patent application publication WO 2004/058404 A2, international patent application publication WO 2004/059284 A2, international patentapplication publication WO 2004/059288 A2, international patentapplication publication WO 2004/059441 A2, and international patentapplication publication WO 2004/059297 A1.
FIELD OF THE INVENTION
• This disclosure relates to preparation of biological samples and in particular, to systems and methods for the automated, continuous flow, pre-treatment and processing of biological samples.
BACKGROUND
• In this disclosure, the term “staining” is used to refer to the process by which certain parts of a sample are treated in order to reveal or highlight characteristics of the sample. As a result of staining, characteristics sought to be revealed may acquire a different color, either in the optic range or in another electromagnetic range, such as the ultra-violet range. In some instances, staining may lead to a detectable change in properties, such as a change in the fluorescent, magnetic, electrical, or radioactive properties of the sample. To obtain a staining a sample may undergo a series of treatment steps referred to as a treatment protocol. A typical treatment protocol may include any or all of washing; binding of reagents to the specific parts of the sample; any activation of the reagents; and each treatment step may include a plurality of individual treatments.
• Sample processing in immunohistochemical (“IHC”) applications, for example, and in other chemical and biological analyses may involve one or a number of various processing sequences or treatment protocols as part of an analysis of one or more samples. Typically, such treatment protocols are defined by organizations or individuals requesting analysis, such as pathologists or histologists attached to a hospital, and may be further defined by the dictates of a particular analysis to be performed.
• In preparation for sample analysis, a biological sample may be acquired and presented on a slide or other carrier usually in some form of preservation. As one example, a sample such as a layer or slice of skin may be preserved in formaldehyde and presented on a slide with one or more paraffin or other chemical layers overlaying the sample. Samples preserved with paraffin may undergo deparaffinization, a process by which paraffin layers overlaying the sample are removed. In addition, the target or sample may be restored to a condition where it is suitable for staining operations—a process known as target retrieval.
• Immunologic applications, for example, may involve processing sequences or treatment protocols that comprise steps such as deparaffinization, target retrieval, and staining, especially for in-situ hybridization (“ISH”) techniques. Previously, these steps have generally been performed manually, potentially creating a time-intensive treatment protocol and necessitating personnel to be actively involved in the sample processing. Attempts have been made to automate sample processing to address the need for a less manually burdensome and expedient sample processing operation. However, prior sample processing automation efforts have been extremely limited in scope and have been deficient in several aspects, such as, for example, the following: the lack of sufficient control and monitoring of sample processing; the lack of information sharing regarding processing treatment protocols and process status, especially for individual samples; the lack of diagnostic capabilities; and the lack of real-time or adaptive capabilities for continuous multiple sample processing.
• Conventional apparatuses have also not provided for sample pre-treatment. Biological samples, such as tissue samples, are usually prepared before the staining can be performed and may be subjected to a pre-treatment process depending upon the type of staining process that is to be performed on the tissue. Pre-treatment processes are generally carried out manually in a laboratory and may include deparaffinization or target retrieval. In addition, pre-treatment processes may also require immersion of the slide in a buffer, or in other types of processing liquids, for some predetermined amount of time and at a specific temperature. Manual sample preparation is cumbersome because pre-treatment steps are often subject to stringent constraints and are sensitive to minute variations in experimental conditions. Consequently, small deviations in the pre-treatment protocol may lead to improper pre-treatment and inaccurate results.
• Thus, there is a need for systems and methods to allow for the intelligent automatic real-time continuous processing of biological samples, so that once a carrier containing a sample, such as a slide, has been prepared and introduced into an apparatus, it is processed in accordance with specified treatment protocols, in conformity with any constraints, and, with minimal, or no further user-intervention.
• There is also a need for systems that automate the scheduling of sample processing to maximize throughput and that allow users to track and monitor the status of slides in the apparatus. Additionally, because of the sensitive nature of the process, there is a need to provide feedback to users about processing related errors, or a lack of resources in sufficient time for corrective action to be taken. Moreover, there is a need to collect both slide and apparatus related information and share the collected information so as to improve efficiency and allow automatic interaction with other information processing systems.
SUMMARY
• In some embodiments of systems, methods and apparatus according to the present invention the automatic pre-treatment of the biological samples on slides or other similar carriers or substrates in an automatic staining apparatus is performed, so that the entire processing of the biological samples may be performed automatically in a single physical apparatus.
• Some embodiments of the present invention also include a method comprising steps for adaptively scheduling robot tasks in a time interval, for a robot coupled to a stainer. In some embodiments, the robot treats slides that are coupled to the stainer according to a treatment protocol using reagents in reagent bottles or fluid containers coupled to the stainer. In some embodiments, the steps in a method to adaptively schedule robot tasks in a time interval comprise creating a robot task list comprising all robot tasks that are ready for execution within the time interval, calculating a robot task priority for each robot task in the robot task list, sorting the robot task list in descending order of robot task priority, and adding robot tasks starting from the top of the sorted robot task list to a robot task execution queue until the robot is fully utilized in the time interval, or the robot task list is exhausted.
• In some embodiments, the robot tasks ready for execution comprise those robot tasks where no prerequisites for commencing robot task execution remain to be completed. In some embodiments, creating a robot task list comprising all robot tasks that are ready for execution within the time interval further comprises determining slides that may spoil if a new treatment protocol step is not performed within the time interval, determining if robot tasks associated with the new treatment protocol step for each slide may be performed within the time interval, and substituting a task of applying buffer to a slide for each slide for which robot tasks associated with the new treatment protocol step cannot be performed within the time interval.
• In some embodiments, creating the robot task list further comprises adding robot tasks that have been generated as a result of contemporaneous events to the robot task list. The contemporaneous events comprise one or more of introducing new slides into the stainer, adding or removing reagent bottles or fluid containers, and altering a priority assigned to one or more slide racks on which the slides are mounted. In some embodiments, the robot may performs tasks of many types comprising one or more of moving the robot to a position within the stainer, mixing reagents for a slide, applying a reagent to a slide from the reagent bottle or the fluid container, air blowing a slide, tipping a slide to a horizontal or a vertical position; and capturing an image of a slide. In some embodiments, applying a reagent to a slide from the reagent bottle or the fluid container further comprises one or more of applying a buffer to a slide, and applying deionized water to a slide.
• In some embodiments, the steps in a method for adaptively scheduling robot tasks in a time interval are performed autonomously by the stainer, which may exercise control over the robot and its operations. In some embodiments, the steps are repeatedly executed for successive time intervals starting from the time at which the stainer is first powered on. In some embodiments, the steps are executed concurrent with the performance of other stainer and robot tasks.
• In some embodiments, calculating a robot task priority for each robot task in the robot task list further comprises calculating a score for each robot task based on a mathematical function of sub-scores assigned to individual task parameters. In some embodiments, the individual task parameters further comprise the earliest start time for a task, the latest start time for a task, the time duration to execute the task, the location of the robot, the priority of the rack on which a slide associated with the task is mounted, and a predetermined relative priority for the robot task type. In some embodiments, a predetermined relative priority for a robot task may be one of high or low. In some embodiments, certain robot tasks may be designated highest priority and added directly to the top of the robot's execution queue.
• The foregoing summary does not purport to define the invention. Indeed, it should be understood that the foregoing and following descriptions are exemplary. These and other embodiments of the invention are more fully described below with respect to the following figures.
BRIEF DESCRIPTION OF THE DRAWINGS
• The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate a number of non-limiting embodiments of the invention and, together with the description, serve to explain the principles of the invention. In the figures, elements with similar functions are prefixed with the same numeric identifier, and individual instances are identified with a hyphenated ordinal suffix.
• FIG. 1A shows the top-view of an apparatus for the automatic pre-treatment and processing of biological samples.
• FIG. 1B shows a schematic of an exemplary robot head used in an apparatus for the automatic pre-treatment and processing of biological samples.
• FIG. 1C illustrates an exemplary overall process flow for a slide undergoing automatic pre-treatment and processing in a stainer.
• FIG. 1D illustrates an exemplary system for the automatic pre-treatment and processing of biological samples.
• FIG. 1E shows an exemplary system for the automatic pre-treatment and processing of biological samples.
• FIG. 1F illustrates exemplary software architecture for a system for automatic pre-treatment and processing of biological samples.
• FIG. 2A illustrates exemplary software architecture for the System Manager.
• FIG. 2B shows an exemplary menu hierarchy listing some functionality provided by the System Manager.
• FIG. 2C shows an exemplary user screen for the System Manager.
• FIG. 3A illustrates exemplary software architecture for the System Manager Server.
• FIG. 3B shows an outline of a logical data model for the System Manager Server.
• FIG. 3C shows an outline of a logical data model for the System Manager Server.
• FIG. 4A illustrates software architecture for the Stainer Control Software.
• FIG. 4B shows a block diagram of an exemplary stainer communications subsystem.
• FIG. 5A shows a block diagram of an exemplary API for control of stainer hardware sub-systems.
• FIG. 5B shows a block diagram of an exemplary stainer logic and schedulers module for control of stainer program threads
• FIG. 6A shows a block diagram of an exemplary robot scheduler.
• FIG. 6B shows a flowchart of an exemplary method for determining regular and time-critical task lists for a robotic head.
• FIG. 6C shows a block diagram of an exemplary fluidics scheduler.
• FIG. 6D shows a flowchart of an exemplary method for scheduling and allocating resources for a fluidics scheduler.
• FIG. 7 shows a block diagram of an exemplary applications programming interface (“API”) for control of stainer hardware functions.
• FIG. 8A shows a state transition diagram tracking slide state transitions for an exemplary state process thread.
• FIG. 8B shows a flowchart for a state process thread instance showing steps in an exemplary method for slide drawer and reagent rack processing.
• FIG. 9 shows a flowchart for a control thread instance showing steps in an exemplary method for container and waste-processing.
• FIG. 10 shows a flowchart for a control thread instance showing steps in an exemplary method for graphical user interface (“GUI”) and alert processing according to some embodiments of the present invention.
• FIG. 11 illustrates an exemplary GUI screen hierarchy for a stainer control software module.
• FIG. 12 shows an exemplary slide rack dialog screen according to some embodiments of the present invention.
• FIG. 13 shows an exemplary reagent rack dialog screen according to some embodiments of the present invention.
• FIG. 14 shows an exemplary cart dialog screen according to some embodiments of the present invention.
DETAILED DESCRIPTION
• Some embodiments of the present invention include a system and method for pre-treatment of biological samples. Various modifications to the embodiments described will be readily apparent to those skilled in the art and generic principles disclosed herein may be applied to other embodiments. The described examples are exemplary only and embodiments described herein are not intended to limit the present invention. As such, the inventions are to be accorded the widest scope consistent with the principles and features described herein.
• The present disclosure relates, in part, to the field of software and hardware for the control, management, tracking, monitoring, scheduling, and diagnosing of automatic biological sample processing systems. In some embodiments, systems, methods, and apparatus according to the present invention allow for the automatic pre-treatment of the biological samples on slides or other carriers or substrates (hereinafter referred to generally as slides) in an automatic staining apparatus (hereinafter referred to as a stainer) so that the entire processing of the biological samples may be performed automatically in a single physical apparatus.
• In some embodiments, a method for processing slides comprises introducing one or more new slides into a stainer, obtaining slide identification information for at least one of the one or more new slides, obtaining a treatment protocol sequence for the at least one of the one or more new slides from a database associated with the stainer using the slide identification information, and processing the new slide according to commands in a command list corresponding to the treatment protocol sequence for the at least one new slide of the one or more new slides. In some embodiments, one or more new slides are introduced into the stainer while the stainer is processing of any old slides previously presented to the stainer.
• In some embodiments, a treatment protocol sequence for the at least one new slide may be obtained from the database associated with the stainer by retrieving an individual slide record containing the treatment protocol sequence for the at least one new slide using the slide identification information on the at least one new slide.
• In some embodiments, processing the at least one new slide according to commands in a command list corresponding to the treatment protocol sequence for the at least one new slide further comprises creating a list of stainer commands corresponding to individual processing steps in the treatment protocol sequence for the at least one new slide and executing commands in the command list in order on the stainer on the at least one new slide. In some embodiments, processing the new slide according to commands in a command list corresponding to the treatment protocol sequence for the at least one new slide of the one or more new slides is performed autonomously by the stainer.
• In some embodiments, slide identification information for the at least one new slide may be obtained by reading a label containing the encoded slide identification information affixed to the at least one new slide. In some embodiments, slide identification may be obtained by reading a glyph that contains the encoded slide identification information. In some embodiments, slide identification information for the at least one new slide may be obtained by reading a radio frequency identification tag associated with the at least one new slide.
• In some embodiments, the database associated with the stainer may be accessed for other purposes including slide pre-processing, data entry, queries, and report generation concurrent with the processing of any old slides previously presented to the stainer. Slide pre-processing includes creating or updating slide records pertaining to slides in the database associated with the stainer and generating labels containing slide identification information for affixment to slides.
• In some embodiments, executing commands in the command list in order on the stainer on the at least one new slide further comprises determining if prerequisites for execution of a next command on the command list have been satisfied, taking corrective action if prerequisites for execution of the next command in order on the command list have not been satisfied, and executing the next command when prerequisites for execution of that command have been satisfied. In some embodiments, executing the next command when prerequisites for execution of that command have been satisfied further comprises applying a reagent to the at least one new slide and updating at least one database record in the database associated with the stainer to reflect the completion of execution. In some embodiments, determining if the prerequisites for execution of the next command on the command list have been satisfied further comprises obtaining information on reagents to be used in executing the next command and determining if an adequate quantity of the reagent is available.
• In some embodiments, taking corrective action if prerequisites for execution of the next command in order on the command list have not been satisfied further comprises alerting an operator about prerequisites for the next command that have not been satisfied and monitoring unsatisfied prerequisites for the next command for changes in status.
• In some embodiments, updating at least one database record in the database associated with the stainer to reflect the completion of execution further comprises updating at least one database record elected from a group consisting of a slide log to reflect the actions taken on the at least one new slide, a reagent log to reflect the actions taken on a reagent, and a stainer log to reflect the actions taken by the stainer.
• Some embodiments of the invention also include a method for performing operations over a network on at least one stainer of a plurality of stainers connected in a LAN, comprising establishing a network connection with the at least one stainer in the LAN, sending commands to the at least one stainer over the network connection, and receiving responses corresponding to commands sent to the at least one stainer over the network connection. In some embodiments, establishing a network connection with the at least one stainer is initiated from a device within the LAN.
• In some embodiments, establishing a network connection with the at least one stainer in the LAN further comprises establishing a network connection with an agent within the LAN, wherein the functions of the agent comprise relaying commands to, and responses from the at least one stainer, and relaying queries to, and returning responses from, a database associated with the plurality of stainers, wherein the database includes information including status information about stainers, slides, consumables, and treatment protocols associated with the plurality of stainers. In some embodiments, the agent is a software tool that also provides a defined interface for an external application through which operations may be performed on the at least one stainer over the network. In some embodiments, the external application is a laboratory information system.
• In some embodiments, the operations performed over the network on the at least one stainer include running diagnostic tests and retrieving diagnostic information. In some embodiments, the diagnostic information is used to automatically schedule service on the at least one stainer, if the diagnostic information indicates that such service is to be performed. In some embodiments, the operations performed over the network on the at least one stainer include performing one or more of software and firmware updates.
• In some embodiments, the operations performed over the network on the at least one stainer include obtaining information on stainer consumable usage. In some embodiments, information on stainer consumable usage could include aggregate stainer consumable usage for the plurality of stainers. In some embodiments, the information on stainer consumable usage includes reagent usage information and bulk fluid usage information. In some embodiments, the information on stainer consumable usage is used to make a determination regarding the ordering of additional supplies of one or more consumables. In some embodiments, the ordering of additional supplies of one or more consumables is done automatically. In some embodiments, the ordering of additional supplies of one or more consumables is based on an economic order quantity. In some embodiments, the ordering of additional supplies of one or more consumables is based on a predefined plan for the ordering of consumables subscribed to by an entity operating the stainer network.
• In some embodiments, the operations performed over the network on the at least one stainer include monitoring the status of slides being processed by the at least one stainer apparatus. In some embodiments, the operations performed over the network on the at least one stainer include obtaining a real-time estimate of the completion time of any of the slides being processed by the at least one stainer. In some embodiments, a real-time estimate of the completion time may reflect the effect of user actions or other unscheduled events such as the introduction or removal of reagent bottles from the stainer, or changing a priority of a slide rack in the stainer, or introducing new slides into the stainer.
• In some embodiments, the operations performed over the network on the at least one stainer include obtaining images of samples on slides being processed by the at least one stainer. In some embodiments, the images of the sample may be taken with an appropriate magnification and resolution. In some embodiments, the operations performed over the network on the at least one stainer include obtaining status information pertaining to slides that have not been loaded into the stainer. In some embodiments, all information exchanged with the stainer over the network connection, including all commands sent to the stainer over the network connection and all responses received over the network connection, are encrypted.
• Some embodiments of the present invention also include a method comprising steps for adaptively scheduling robot tasks in a time interval for a robot coupled to a stainer. In some embodiments, the robot treats slides that are coupled to the stainer according to a treatment protocol using reagents in reagent bottles or fluid containers coupled to the stainer. In some embodiments, the steps in a method to adaptively schedule robot tasks in a time interval comprise creating a robot task list comprising all robot tasks that are ready for execution within the time interval, calculating a robot task priority for each robot task in the robot task list, sorting the robot task list in descending order of robot task priority, and adding robot tasks starting from the top of the sorted robot task list to a robot task execution queue until the robot is fully utilized in the time interval, or the robot task list is exhausted.
• In some embodiments, the robot tasks ready for execution comprise those robot tasks where no prerequisites for commencing robot task execution remain to be completed. In some embodiments, creating a robot task list comprising all robot tasks that are ready for execution within the time interval further comprises determining slides that may spoil, if a new treatment protocol step is not performed within the time interval, determining if robot tasks associated with the new treatment protocol step for each slide may be performed within the time interval, and substituting a task of applying buffer to a slide for each slide for which robot tasks associated with the new treatment protocol step cannot be performed within the time interval.
• In some embodiments, creating the robot task list further comprises adding robot tasks that have been generated as a result of contemporaneous events to the robot task list. The contemporaneous events comprise one or more of introducing new slides into the stainer, adding or removing reagent bottles or fluid containers, and altering a priority assigned to one or more slide racks on which the slides are mounted. In some embodiments, the robot may performs tasks of many types comprising one or more of moving the robot to a position within the stainer, mixing reagents for a slide, applying a reagent to a slide from the reagent bottle or the fluid container, air blowing a slide, tipping a slide to a horizontal or a vertical position; and capturing an image of a slide. In some embodiments, applying a reagent to a slide from the reagent bottle or the fluid container further comprises one or more of applying a buffer to a slide, and applying deionized water to a slide.
• In some embodiments, the steps in a method for adaptively scheduling robot tasks in a time interval are performed autonomously by the stainer, which may exercise control over the robot and its operations. In some embodiments, the steps are repeatedly executed for successive time intervals starting from the time at which the stainer is first powered on. In some embodiments, the steps are executed concurrent with the performance of other stainer and robot tasks.
• In some embodiments, calculating a robot task priority for each robot task in the robot task list further comprises calculating a score for each robot task based on a mathematical function of sub-scores assigned to individual task parameters. In some embodiments, the individual task parameters further comprise the earliest start time for a task, the latest start time for a task, the time duration to execute the task, the location of the robot, the priority of the rack on which a slide associated with the task is mounted, and a predetermined relative priority for the robot task type. In some embodiments, a predetermined relative priority for a robot task may be one of high or low. In some embodiments, certain robot tasks may be designated highest priority and added directly to the top of the robot's execution queue.
• Some embodiments of the invention also include a method for dynamically allocating at least one of a plurality of resources coupled to a stainer in response to a resource allocation request by a task comprising determining a requested fraction of the at least one of a plurality of resources, computing a utilization factor of the at least one of a plurality of resources at several potential allocation time instants, adding the requested fraction of the at least one of a plurality of resources to the utilization factor at each potential allocation time instant to obtain a projected utilization factor, and allocating the at least one of a plurality of resources at the first time instant at which the projected utilization factor for the at least one of a plurality of resources is one or less.
• In some embodiments, computing a utilization factor of the at least one resource at several potential allocation time instants further comprises determining resource utilization factors for the at least one resource by all tasks executing or scheduled to be executing at the several potential allocation time instants. In some embodiments, the plurality of resources coupled to a stainer comprise one or more of fluid conduits coupled to the stainer, one or more valves coupled to the stainer controlling access to the fluid conduits, one or more reagent mixers coupled to the stainer, and power available to processing tank heaters coupled to the stainer.
• In some embodiments, the stainer may generate additional resource allocation requests corresponding to actions to be taken prior to allocating the at least one resource to a task. In some embodiments, the actions to be taken prior to allocating the at least one resource to a task may include flushing a fluid conduit or a reagent mixer coupled to the stainer.
• Some embodiments of the invention provide a GUI to allow user input and control of the apparatus. Some embodiments of the present invention include a system for the software simulation of the operation of the sample processing system apparatus. Such a system allows testing, debugging, and performance tuning of the sample processing system apparatus, hardware, and software.
• In some embodiments, one or more optical and/or electronic sensors may be used to retrieve slide-related information, including high resolution images of samples on the slides. In some embodiments, these images may be indexed, stored, and retrieved for processing and analysis. In some embodiments, images of the samples may be captured, indexed, and stored at various stages of the processing.
• A detailed description of embodiments of the present invention follows, with reference to the accompanying drawings. In the figures, elements with the same numeric identifier have similar function, and individual instances are identified with a hyphenated ordinal suffix.
• FIG. 1A shows the top-view of anexemplary stainer1000 for the automatic pre-treatment and processing of biological samples. As shown inFIG. 1A,exemplary stainer1000 includesslide drawers1040 that containslides1045, which may contain biological samples needing treatment. In some embodiments, slides1045 are mounted on individual holders hinged to sliderack handle1070, which allowindividual slides1045 to be maneuvered to a horizontal or vertical position. In some embodiments, theslide rack handle1070 may allow theslides1045 to be tipped vertically or horizontally. In some embodiments, theslide rack1065 may be placed in one of a plurality ofslide drawers1040, which is slid intostainer1000. In some embodiments, processing tanks (not shown) may be present beneath theslides1045. In some embodiments, the processing tanks may be temperature controlled. Processing tanks may be filled with fluid, drained, and/or flushed using fluids supplied by the fluidics component of fluidics, LAN, andpower connections1025. In some embodiments, slides1045 may be immersed in the fluid present in a processing tank in accordance with some methods for the pretreatment of biological samples. In some embodiments,stainer1000 also containsrobot1032.
• As shown inFIG. 1B,exemplary robot head1010 may include one or more of aprobe10, optical orelectronic sensing device25,syringe pump1015,air nozzle124,air cylinder39 andslide tipping tool38. In some embodiments,probe10 may be used to aspirate a precise quantity of reagent fromreagent bottle1080 for application to slide1045. (FIGS. 1A and 1B). In some embodiments,robot1032 may be directed toreagent mixer1050 so that reagents aspirated fromreagent bottle1080 byprobe10 may be mixed inreagent mixer1050 to create new or custom reagents. In some embodiments,robot1032 may be directed to probewash station1055 to permitprobe10 to be washed.Washing probe10 prevents reagent contamination and residue build-up inprobe10. In some embodiments, the aspiration and release of reagents may be controlled bysyringe pump1015.
• As schematically illustrated inFIG. 1B, therobotic head1032 may also be provided with anair nozzle124 for blowing air ontoslide1045 in orderdry slide1045 or to blow away liquid.Robot head1010 may also include a variety of other components, including, but not limited to aslide tipping tool38, for actuating slide rotation, that may be coupled to anair cylinder39. In some embodiments, slide tippingtool38 may operate onslide1045 to tip the slides from a vertical to a horizontal position and vice versa.
• In some embodiments,robot head1010 may include an optical orelectronic sensor25, which may be moved to various positions withinstainer1000 through action of therobot1032. In some embodiments, optical orelectronic sensor25 can include a camera, which may be a Charge Coupled Device (“CCD”) camera. In some embodiments, the camera may be a high resolution camera capable of taking pictures of the samples on the slides at an appropriate magnification. In some embodiments, the captured image may be analyzed for reagent analysis or other analyses. In some embodiments, the camera may be used 1) as an area locator, 2) to locate a tissue area, or 3) to apply reagent based on location and area. In some embodiments, data captured by electronic oroptical sensor25 may be associated with the location ofrobot1032, and/or with the location of electronic oroptical sensor25, and/or with the location ofslide1045 orreagent bottle1080.
• In some embodiments, when aslide1045 is in a horizontal position, a precise quantity of reagent may be applied to slide1045 using aprobe10 andsyringe pump1015 mounted onrobot1032. In some embodiments, a separate conduit may be used to apply a buffer to slide1045 in a horizontal position.Robot1032 is capable of moving in two-dimensions usingX axis mechanism1035 andY axis mechanism1030. The movement and positions ofrobot1032 may be tracked. Additionally, in some embodiments a docking or homing station with a known reference position may be provided forrobot1032.Robot1032 may dock or be commanded to dock at the homing station when it is idle, prior to tracking its movements, for calibration purposes, and/or to prevent, correct, and minimize tracking errors.Robot1032 also contains aZ head1010 that is capable of being moved in the Z (vertical) dimension (perpendicular to the page). In some embodiments, the movement ofrobot1032 and timing of reagent application may be controlled by a scheduler (not shown inFIG. 1A) that coordinates the movement ofrobot1032 and reagent and buffer application based on treatment protocol constraints.
• In some embodiments, a plurality ofreagent racks1060 hold individual labeledreagent bottles1080, which may be both humanly and electronically readable to identify the contents ofreagent bottles1080. In some embodiments, the identifiers may take the form of an Infoglyph™ and may be read using a camera orother sensing apparatus25 mounted beneathZ head1010. In some embodiments, slides1045 may also be labeled with identifiers, including an Infoglyph™, which may contain information about the slide. Other systems for reading information, for example transponders, radio frequency identification (“RFID”) receivers, magnetic readers, optical character recognition (“OCR”) techniques etc. may also be utilized.
• Reagents may be aspirated fromreagent bottles1080 usingsyringe pump1015 and probe10, then mixed with other reagents usingreagent mixer1050, if specified by the protocol, before being applied to theslides1045. In some embodiments, the quantity of reagent applied to aslide1045 may be controlled precisely by controls operating onsyringe pump1015. In some embodiments,syringe pump hardware1015 may be motor driven, so that rotating the motor in a forward direction causes fluid to be aspirated into the syringe, and rotating the motor in a reverse direction drives the fluid back out of the syringe. In some embodiments, commands tosyringe pump1015 to aspirate and/or dispense reagent may be driven by a configuration table, which details the steps thatsyringe pump1032 follows to perform the task at hand.
• In some embodiments, sensors (not shown) may be present in or introduced intoreagent bottles1080 to detect the level of reagent remaining inreagent bottle1080. In some embodiments, an operator may be alerted if a reagent level falls below a certain threshold. In some embodiments,reagent mixer1050 may be capable of mixing a wide variety of reagents including mixing small and large volumes of reagents, mixing reagents with different viscosities and densities, and mixing nearly immiscible reagents. In some embodiments, gases formed during the mixing process are allowed to escape throughexhaust1075. Probewash station1055 allowsprobe10 to be washed to remove any residues, to prevent residue build-up, and to prevent contamination of reagents and samples.
• In some embodiments,stainer1000 may also include fluidics, Local Area Network (“LAN”) andpower connections1025, which includes controls and connections for fluidics, for networking and for power. As shown inFIG. 1E, some embodiments ofstainer1000 may include a fluidics subsystem with afluidics cart1295 with labeled electronicallyreadable containers1299 that store bulk fluids such as for example, slide buffers, fluids for flushing conduits, probe cleaning fluids, de-ionized water etc. In some embodiments, fluids may be delivered to locations, such as processing tanks, withinstainer1000 at appropriate points in time using conduits (not shown) fromfluid containers1299 onfluidics cart1295. In some embodiments, multiple conduits may be provided for fluid delivery and the conduits allocated to fluids, based on resource allocation and scheduling algorithms in accordance with treatment protocol-related constraints. In some embodiments, fluids drained fromstainer1000 may be held in a separate labeledfluidics container1299 influidics cart1295 for bio-hazardous material.
• Some embodiments of the invention may also provide LAN connections to allowstainer1000 to communicate with other devices, including remote devices, other stainers, other laboratory instruments, laboratory and third party information systems, and computers within LAN1223.LAN connections1025 allow stainer1000 to send and receive status information including information aboutslides1045, process-status, treatment protocols, reagents, fluids, diagnostics, and other information that may be requested by remote users. In some embodiments, a touch-control panel1020 may be provided to allow users to interact directly withstainer1000.Touch control panel1020 may provide a GUI along with menu screens and help screens to facilitate user-interaction and control ofstainer1000. Additionally, in some embodiments,stainer1000 may also include an embedded computing system with processors, memory, hard drives, graphics and other electronic sub-systems (not shown) that allow software, firmware, and other program code to be run and executed onstainer1000.
• FIG. 1C illustrates an exemplaryoverall process flow1100 for a single run of a system for the automatic pre-treatment of biological samples. It should be noted thatsteps1120 through1135 depicted in exemplaryoverall process flow1100 occur in the sequence shown for a single slide. In general, steps1120 through1135 may be performed concurrently for different slides.
• The system is turned on instep1110, following which it goes through an initialization process instep1115. In some embodiments, the initialization process may include booting upstainer1000, running initial stainer diagnostics, establishing network and database connections, determining reagent and bulk fluid types and levels, movingrobot1032 to the homing station and other actions. In some embodiments, an operator may be alerted regarding possible diagnostic issues or other matters during the initialization phase.
• After System Initialization has been completed, patient and/or slide data may be entered by an operator instep1120. In some embodiments, the data may be retrieved electronically from another computer system, over a network, from a Laboratory Information System (“LIS”), or from another laboratory instrument. Patient data may include a patient identifier, sample related data, other identifying information and may include information regarding a medical provider or other services to which results data may be sent. Slide data may include a slide identifier and a treatment protocol associated with the slide. In some embodiments, slide data may be printed on a label in a machine readable format such as an Infoglyph™ and applied to aslide1045 containing the sample.
• Instep1125, slides1045 andreagent bottles1080 are loaded intostainer1000. In some embodiments, a slide or reagent drawer is closed afterslides1045 have been loaded and slide and reagent labels may be read and any errors reported. For example, Infoglyph™ labels on theslides1045 andreagent bottles1080 may be read by acamera25 mounted under Z-head1010 (FIGS. 1A and 1B). Instep1130, theslides1045 are processed according to the treatment protocol associated with the slide. Biological samples on aslide1045 are often preserved using paraffin based agents. Samples onsuch slides1045 may be subjected to a process of deparaffinization before aslide1045 may be processed. Deparaffinization involves immersingslides1045 into processing tanks where a series of fluids may be sequentially introduced and removed for predetermined periods of time (potentially for about 5 or 10 minutes). The process is intended to first remove from the tissue sample the paraffin in which it was mounted, then remove the paraffin solvent, then through a series of reagents progressively re-hydrate the sample. Deparaffinization and target retrieval processes are performed onboard stainer1000 with theslides1045 in a vertical orientation, immersed within their individual processing tanks that can be filled and emptied with various reagents. In some embodiments, the reagents may be heated to an appropriate temperature to permit effective treatment of theslides1045.
• In some embodiments, if deparaffinization or target retrieval is to be performed, the processing tanks beneath theslides1045 are filled with the appropriate solution and theslides1045 are lowered into the processing tank and immersed in the solution for an appropriate amount of time. Different fluids may then be introduced into processing tanks into which slides1045 have been lowered according to the deparaffinization or target retrieval protocol.Slides1045 may then be raised and the processing tanks drained. Deparaffinization is an initial slide processing step and generally performed only once, when slide pre-treatment is commenced. When the deparaffinization and target retrieval processes are complete theslides1045 can be tipped back to a horizontal position and lowered down onto temperature controlled platforms to perform the staining phase.
• A treatment protocol associated with a slide specifies the sequence of reagents, types of reagents, quantities, duration of exposure, temperature and other parameters related to the treatment of a slide. In some embodiments, theslide1045 may be placed on a temperature controlled rack to ensure it is maintained at the correct temperature as specified in a treatment protocol. In some embodiments, software may check to ensure that all the reagents specified in a treatment protocol have been loaded prior to initialization of that protocol. An operator may be alerted if reagents specified for processing aslide1045 are not present.
• Once the processing of loadedslides1045 has been completed, instep1135, slides1045 andreagent bottles1080 may be unloaded. In some embodiments,reagent bottles1080 may be swapped and/or new reagents added whileslides1045 are being processed. In some embodiments,new slides1045 may be introduced for processing in aslide drawer1040 that is currently unused, orreagent bottles1080 introduced and/or removed, whileslides1045 in anotherslide drawer1040 are being processed. Processing on suchnew slides1045 introduced intostainer1000 may begin even while processing on other slides previously presented to the stainer is in progress. In some embodiments,steps1120 through1135 may be repeated until all slides1045 have been processed.
• It should be noted that althoughsteps1120 to1135 are performed sequentially with respect to a single slide,stainer1000 may perform the steps concurrently on different slides. For example, an operator may be entering slide data, while aslide rack1065 is being loaded and slides on anotherslide rack1065 are undergoing processing.
• Instep1140, the system may be shut down. In some embodiments, during shutdown processing tanks may be drained and hazardous waste purged into appropriate containers. Additionally, all processing tanks and fluid conduits may be cleaned and flushed, heating elements turned off, valves depressurized, and all drawers and doors closed. Finally, instep1150, the system may be powered off.
• In some embodiments, atsteps1115 through1140 in exemplaryoverall process flow1100, aSystem Log1160 may be generated to keep track and maintain a log with details of events at each step, as shown inFIG. 1B. For example, details of system initialization such as the results of any system diagnostic tests may be stored in the log generated duringstep1115. In some embodiments, the system log may be used to verify proper system functioning, pinpoint process errors, or used for quality assurance purposes. In some embodiments, the logs for each step depicted inFIG. 1B may also be stored separately or, associated with stainer objects such asslides1045, orreagent bottles1080. For example, actions performed on anindividual slide1045 may be recorded in individual slide logs, which describe every action undertaken on theslide1045.
• FIG. 1D illustrates anexemplary system1200 for the automatic pre-treatment of biological samples.FIG. 1E also shows an exemplary system for automatic pretreatment of biological samples. A description of embodiments of a system for the automatic pretreatment of biological samples will now be made with reference toFIGS. 1D and 1E.
• As shown inFIG. 1D,exemplary system1200 can consist of one or more stainers1000, such as exemplary stainer1000-1 and1000-2 with coupledbulk fluid carts1295 containing bulk fluids used by the stainers. In some embodiments, additional stainers may be added toexemplary system1200 as shown by the dashed line depicted inFIG. 1D between stainers1000-1 and1000-2. As shown inFIG. 1E, eachstainer1000 makes use of a number of bulk fluids to perform the pretreatment and staining tasks. In some embodiments, these fluids can be stored externally incontainers1299 influid cart1295. In some embodiments, a fluid level sensor may be provided with eachfluid container1299 on afluidics cart1295 and read periodically by the coupled stainer1000. In some embodiments, power may be supplied to eachstainer1000 through an Uninterruptible Power System (UPS)1298, which may also be monitored by its coupled stainer1000 to detect power-line fluctuations, or an impending loss of power.
• In some embodiments, the stainers, such as exemplary stainers1000-1 and1000-2 may be networked in LAN1223 and may communicate with other system components usingnetwork hub1250. In some embodiments,stainers1000 may contain embedded computing systems that allow software, firmware, and other program code to be stored, updated, compiled, and executed on the stainer. In some embodiments these programs may be able to interact and exchange data and control information with programs running on computing devices1230-1 and1230-2. In some embodiments, information may be exchanged between computing device1230-1 andlaboratory devices1296 and1297. In some embodiments, data may also be exchanged betweenlaboratory devices1296 and1297 anddatabase1220.
• Network hub1250 may also provide a network connection to a Wide Area Network (“WAN”)1270 throughnetwork bridge1260. In some embodiments,WAN1270 can be the Internet. In some embodiments, the network connection tonetwork hub1250 may be wireless. In some embodiments, the wireless networking function may allownetwork hub1250 to support the IEEE 802.11b and/or IEEE 802.11g and/or other wireless networking protocols, and serve as a Wireless Access Point (WAP). In some embodiments, communication between thestainers1000 and/or withremote users1280 throughWAN1270 may also occur using standard communications protocols such as TCP/IP, or any other communications protocol. In some embodiments, a remote user orremote device1280 may query or communicate with anystainer1000 throughWAN1270. In some embodiments, communication betweenstainers1000 and/or communication overWAN1270 may be encrypted.
• In some embodiments ofsystem1200, stainers1000 may also be coupled to one or more computing devices1230 containing removable media drives capable of readingremovable media1240.Removable media1240 may be a floppy disk, CD-ROM, DVD-ROM, DVD+RW, DVD-RW, or any other computer readable media. In some embodiments, computing devices1230 may contain network and communication ports including, but not limited to, USB, Ethernet, Serial, and/or Parallel ports to allow communication withstainers1000 andWAN1270 throughnetwork hub1250 and/ornetwork bridge1260 using appropriate communication devices, methodologies, and communication protocols. In some embodiments, computing device1230 may also contain one or more of processors, memory, hard disks, graphics cards, and display and data entry devices. Examples of computing device1230 include PCs, Workstations, Laptops, Handhelds, or any other mobile computing devices capable of being used insystem1200.
• In some embodiments, computing device1230-1 may be able to run software, such as a server, that coordinates the actions of theindividual stainers1000, obtains status ofstainers1000, and obtains and updates slide and process related information. Computing device1230-1 may also be coupled to printer1210-1 anddatabase1220. In some embodiments,database1220 may contain system related information including stainer, patient, slide, treatment protocol, fluid and/or reagent related information. In some embodiments, computing device1230-1 may query stainers1000-1 and/or1000-2 for status or other information andupdate database1220. In some embodiments, a system log such assystem log1160 may be generated by stainers1000-1 and1000-2 and stored indatabase1220. In some embodiments, printer1210-1 coupled to computing device1230-1 may also be used to print reports generated by computing device1230-1. In some embodiments,stainer1000 may back-up stainer, process and slide related information on storage media on computing device1230-1.
• In some embodiments, computing device1230-2 may run software to allow users to enter data related tosystem1200 intodatabase1220. In some embodiments, software running on computing device1220-2 may allow users to configure and manage stainers1000-1 and1000-2. In some embodiments, users may enter data including identification data forslides1045,reagent bottles1080, andbulk fluid containers1299 using software running on computing device1230-2. In some embodiments, printer1210-2 coupled to computing device1220-2 may be used to print the slide, bulk fluid container, and/or reagent container labels.
• In some embodiments, portions of programs or data related to the control and/or monitoring ofstainers1000 may reside onremovable drive1240. In some embodiments, programs running on computing device1230-2 may provide stainer, slide, and process related information to users using an appropriate GUI. In some embodiments, users may be able to control the actions of one or more ofstainers1000 using programs running on computing device1230-2.
• In some embodiments, computing device1230-3 may also run other laboratory information systems (LIS)1222.LIS1222 may use, store, and update data indatabase1221 and also request information from stainer related applications running on computing device1230-1 or from thestainers1000 directly. In some embodiments,LIS1222 running on computing device1230-3 may store patient records and other lab related data. In some embodiments, a user may import patient data and slide orders into the System Manager fromLIS1222 through an intermediate interface called an “LIS Agent.” In some embodiments, the LIS Agent may facilitate the exchange of data between thestainer1000 and related software systems, software running on computing devices1230-1 and1230-2, anddatabase1220, on one hand andLIS1222, on the other hand. In some embodiments, the LIS Agent may include software that provides a bidirectional interface to receive and send data to other software such as software running onstainers1000, computing devices1230, orlaboratory devices1296 or1297. In some embodiments software running on computing device1230-1 could include the LIS Agent as a module.
• For example, information about reagent and/or bulk fluid usage could be analyzed by software running on computing device1230-1 or1230-2 and supplies ordered usingLIS1222 through the LIS Agent whenever the inventory level falls below a certain threshold. In some embodiments, re-ordering of supplies through LIS Agent may take place according to a prearranged subscription plan. In some embodiments, software running on computing device1230-1 or1230-2 may track diagnostic messages and/or error codes fromstainers1000 and automatically schedule service through the LIS Agent. In some embodiments, software running on computing device1230-1 or1230-2 may use stainer and slide related information to perform accounting functions, including the generation of invoices and reports. In some embodiments, software running on computing device1230-1 or1230-2 may use stainer and slide related information stored indatabase1220 to generate cost and usage statistics relating to the operation of the stainers. In some embodiments, invoices and reports generated by software running on computing device1230-1 or1230-2 may be sent toLIS1222 through the LIS agent. It should be noted thatsystem1200 is exemplary only and additional stainers, computers, lab devices, and other components may be added to the system in order to perform methods and achieve objects and functionality of the system.
• FIG. 1F illustrates exemplary software architecture for a system for automatic pre-treatment of biological samples. The architecture shown inFIG. 1F is exemplary and for descriptive purposes only and other configurations of the software may be used to achieve the same or similar functions. As shown inFIG. 1F,exemplary software architecture1300 for a system for the automatic pre-treatment of biological samples may include Stainer Control Software (“SCS”)1310, System Manager Server (“SMS”)1320, and System Manager1330 (SM). In some embodiments, multiple instances ofSCS1310, each running on individual stainers, may interact with multiple instances ofSM1330 throughSMS1320.
• In some embodiments,SCS1310 may be resident on and run directly stainer1000 using its embedded computer system. In some embodiments,SMS1320 may be resident and executed on exemplary computing device1230-1 and maintain andupdate database1220. In some embodiments,SM1330 may be resident and executed on computing device1230-2. In some embodiments,SMS1320 andSM1330 may be resident on different computing devices. At any point in time, multiple instances ofSM1330 may be active and interact withdatabase1220 throughSMS1320.SCS1310 controls the staining instrument hardware on associated stainer1000 so that the hardware may perform the operations of pre-treating and staining ofslides1045 that are introduced into the machine. In some embodiments,SCS1310 software may communicate withSMS1320 over TCP/IP on system LAN1223 in order to obtain information aboutslides1045 and reagents onstainers1000.
• In some embodiments, slide programming of aslide1045 may be done usingSM1330. Slide programming includes associating a treatment protocol with aslide1045 and affixing an electronically readable label to the slide. Once aslide1045 is electronically scanned and recognized bystainer1000 its treatment protocol information is downloaded fromSMS1320 and, if the fluids for the treatment protocol are present, thestainer1000 can automatically process the slide. In some embodiments,SCS1310 controls the function ofstainer1000 and monitors level sensors associated withbulk fluid containers1299 inbulk fluid cart1295 to determine if enough fluid is available to complete certain tasks.
• In some embodiments,SCS1310 also supports a full simulation mode and can be run on a computer without any actual stainer hardware present. In thismode SCS1310 simulates stainer hardware actions accurately and produces final results that are similar to results achieved using actual stainer hardware. In some embodiments, an accelerated simulation capability is also provided. The accelerated simulation capability, which uses time compression techniques, permits the debugging, validation, and performance tuning of stainer hardware and processes in a few minutes. The debugging, validation, or performance tuning processes would normally take several hours for each run on a conventional stainer. In some embodiments,SCS1310 may run in simulation mode while executing on astainer1000 but without exercising any stainer hardware (other than the embedded computing system) or using any fluid or reagents. The simulation capability may also be used by the adaptive scheduler to determine optimal operation.
• In some embodiments,SCS1310 may perform some or all of the actions insteps1115 and1130, as related in the description ofoverall process flowchart1100. When slide processing in a particular drawer is started,SCS1310 locks theslide drawer1040. In some embodiments, once staining has been completed theslide rack1065 can be elevated to the load position and theslide rack1065 can be marked complete. In some embodiments, the operator may be notified visually and aurally that theslide rack1065 has completed and theslide drawer1040 is unlocked to permit the operator to remove the rack.
• In some embodiments,SCS1310 uses a non-deterministic scheduling system to allow different staining processes to happen in parallel withindifferent slide drawers1040. The scheduling subsystem ofSCS1310 may continuously evaluate tasks to be performed, and makes decisions about the order of tasks based on priority. If errors occur during processing, for example if a reagent is not available an operator can be alerted. In some embodiments,SCS1310 may direct the application of a buffer to theslide1045 to prevent spoilage of the sample while an operator loads the reagent.SCS1310 may also be run in a utility mode that allows technicians and operators to perform routine maintenance on the machine.
• In some embodiments,SMS1320 may serve as a data handling and processing center for theSM1330 andSCS1310. In some embodiments,SMS1320 may communicate withSCS1310 andSM1330, handle database interaction, and perform support functions for each instance ofSM1330 andSCS1310. In some embodiments,SMS1320 may handle all SCS and SM data and messaging communications. In some embodiments,SMS1320 can accept requests fromSM1330 and send out status reports in response. Additionally,SMS1320 can also receive requests fromSCS1310 and send out status reports in response. In some embodiments,SMS1320 may connect to and control a database system, such asdatabase system1220, in order to satisfy the incoming requests. To facilitate diagnostics,SMS1320 may act as an agent, proxy, or intermediary for support connections to all instances ofSCS1310 andSM1330 that are coupled toSMS1320. In some embodiments,SMS1320 may run on a computing device1230-1, which in some instances may be a server.
• In some embodiments, data and configuration parameters that affect the operation of the entire system may be maintained under the control ofSMS1320. In some embodiments,SMS1320 may have an associated backup and restore utility that allows for automatic backups. In some embodiments,SMS1320 may also automatically backup its database to hard disks on any or all ofstainers1000, when stainers1000 are operating. Accordingly, in the event of catastrophic failure ofSMS1320, one of its components, or of its database, a ready backup can be made available thus limiting any down-time of the laboratory. In addition,stainer1000 may use its copy of (backed up)database1220 to complete the processing of slides already instainer1000 at the time of the failure. In some embodiments,SMS1320 may automatically search LAN1223 and auto-discoverstainers1000. In some embodiments, different TCP/IP ports may be used to segregate control, status, and diagnostic messages.
• SM1330 may also run on one of computing devices1230. In some embodiments,SM1330 may provide functionality for slide programming. For example, users may input one or more of patient demographic information, block information like tissue type and preparation, and treatment protocol related information into one or more records that may be stored in a database, such asexemplary database1220. In some embodiments,SM1330 may also provide an interface to add and edit other auxiliary information such as Tissue Types, Tissue Preparations, Reagent Compatibility, Users, and user-customizable fields.
• In some embodiments,SM1330 may also have a stainer-monitoring window showing a list ofstainers1000 and general status information, with options to allow a user to retrieve more detailed information about the status of stainers. For example, detailed slide status views may show slides pending, slides in a particular stainer, and slides that have completed the staining process and have been removed from machines. In some embodiments,SM1330 may generate detailed reports related to slide processing, case history, and reagent usage in response to operator requests.
• In some embodiments,SM1330 may provide an interface to program and edit treatment protocols and detection systems. Treatment protocols define a complete sequence of steps to process a slide, whereas detection systems are templates that are complete except for the primary antibody and enzyme block. Additionally,SM1330 may allow for the management of reagents, including reagent inventory, reagent usage, and reagent properties such as incompatibility, expiration date, and reagent category. Custom reagents, specified by users, can be added to the reagent list. In addition, embodiments ofSM1330 may allow the specification of “just-in-time” mixing of reagents, for reagents with a very short shelf life.
• FIG. 2A illustratesexemplary software architecture1400 for thesystem manager1330.Users1415 may interact withSM1330 through auser interface1420, which may include menu screens and other features to help users to log in, request information, enter commands, change configuration parameters, update status information, and/or navigate through the system. In some embodiments,SM1330 communicates withSMS1320 using astatus communication module1445.
• In some embodiments,status monitoring module1435 allowsusers1415 to request status information fromstainers1000 throughuser interface1420, such as whether astainer1000 is active, operating normally, or has requested service or time-critical attention.Status communication module1445 provides communication functionality to transmit such requests to stainers. Additionally,status communication module1445 provides functionality to informstainer1000 throughSCS1310 about system configuration changes. In some embodiments,SMS1320 may relay requests and responses betweenstatus communication module1445 andSCS1310. In some embodiments,SMS1320 may perform additional processing on requests and responses prior to relaying the information to its destination. In some embodiments, the functionality ofstatus monitoring module1435 may be restricted to status communications of a general nature where information may be exchanged without regard to confidentiality, security, accessibility, and/or privacy issues.
• In some embodiments,user1415 may invoke a separate data review andmanipulation module1430 to request data from thestainers1000 orSMS1320 usinguser interface1420 throughsecurity module1425. For example, users may request a list ofslides1045 that have been programmed and labeled by the user, but have not appeared on anystainer1000; a list ofstainers1000 that are being served bySMS1320; a list ofslides1045 that are being processed by astainer1000; a list ofslides1045 that have completed the prescribed staining protocol and have been removed fromstainer1000; all information about aparticular slide1045 including case demographic information, slide ID, location, and estimated completion time; a list of all reagents on a specified stainer; status information on a specified reagent, such as expiration date, location, volume, and when placed onstainer1000; as well as other information.
• In some embodiments,security module1425 offers a one-call function to determine if currently a logged inuser1415 has the appropriate privileges to invoke a particular function. Additionally, in order to accurately correlate user activities with tasks performed,security module1425 may be provide a “named user” functionality in which user actions are logged using user login information. In some embodiments, users may also be assigned to a named group and security privileges can be allocated and maintained based on the named group. Membership in a group may confer upon and limit a user to the privileges of that group.
• An administrator-level user may be assigned full privileges to create users, assign users to groups, reset passwords, and set global system parameters usingsystem configuration module1410. Administrator-level users may also set access parameters for sensitive data or protected functions. A function may be deemed protected if modification of its configuration, or of data related to the function, may adversely affect the operation of software; or if data related to or accessible through the function is to be protected from some users. For example, patient privacy laws may require that only certain users be granted access to sensitive patient information. In some embodiments,security module1425 may call a check access function before allowing users access to protected functions.
• FIG. 2B shows anexemplary menu hierarchy1500 listing some functionality provided by theSystem Manager1330 throughUser Interface1415. In some embodiments, menu choices available to users may be provided through icons, tabs, drop down or pull down menus, or using various GUIs. As shown inFIG. 2B, a user may navigate fromMain Screen1510 through top level menus includingtabs menu1511,login menu1552,system menu1555,administration menu1560, andhelp menu1575.
• In some embodiments,main screen1510 displays other windows when a user selects a menu item, and also displays icons or tabs for discrete windows that implement portions of the workflow. For example, tabs may be provided to access screens that allow user interaction with process information relating to new slides, pending slides, stainers, and completed slides. In some embodiments, a container window is created within which other windows may be displayed. For example,main screen1510 may be a container that holds the individual tab windows, so that individual tab windows are child-windows and displayed within the parent main screen container. In some embodiments, main screen also allows application startup and initialization. In some embodiments, on application startup a configuration file may be accessed and the system configuration parameters may be read from the file. For example, network configuration parameters, which indicate how to connect to theSMS1320, may be read from a configuration file.
• In some embodiments,tab menu1511 may be provided in the form of a set of tabs along an edge of a GUI window. Clicking on a tab can allow users to view the underlying information. For example, users who select the new slides tab may be shown a data entry interface to enter information about a new slide and the pending slide tab can show pending slides1045, which have been entered into the system but have not been processed by stainers. In some embodiments, portions ofmain screen1510 and lower level screens may be hidden from a user or otherwise disabled bysecurity module1425, if the user does not have the privileges for access functions provided on that screen. In some embodiments, a user profile for each user may be stored indatabase1220 that allows the user's GUI preferences to be restored whenever the user logs in to any computer1230 running an instance ofSM1330.
• Login screen1552 may provide log in related functions such as allowing users to log in and to set login scripts and a login environment. In some embodiments,system menu1555 may allow a user to set display or GUI options, change the user's password, and to log out fromSM1330. In some embodiments,help menu1575 may allow a user to get assistance using the software, including accessing a software manual, searching for terms, and/or by connecting to online help that may be provided remotely. In some embodiments, anadministration menu1560 may allow a user with appropriate privileges to create, retrieve, or alter information pertaining to reagents throughreagent menu1562. For example, a user may enter a new reagent into the system.
• In some embodiments, atreatment protocol menu1565 allows a user to specify rules including, for example, rules for primary antibodies, specimen preparation, target retrieval fluids, and custom treatment protocols. For example, a user may define the fluids, quantities, and temperature for a certain target retrieval process. In some embodiments, the primary antibody rules menu allows users to display and edit the treatment protocol rules for primary antibodies. Configuration menu1567 permits configuration of system parameters, including slide label configuration; adding or changing users, groups, and user profiles; and changing or updating network settings. For example, slide label configuration allows the format of information printed on machine-readable labels that are affixed toslides1045 to be specified. In some embodiments, a retrieveupdate menu1569 allows users to retrieve any software updates to the SM or other system components.
• In some embodiments, user actions such as the creation of a new slide record may cause a database to be updated throughSMS1320. In some embodiments, user actions may be logged for traceability and accounting purposes. In some embodiments, a “wizard” providing a fast and easy way to perform commonly executed tasks may be provided.
• FIG. 2C shows an exemplary user screen1700 for theSystem Manager1330.Tabs Menu1511 appears at the top of the screen allowing users to select between tabs for:New Slides1710, Pending1715,Stainers1720, and Completed1725. As shown inFIG. 3B,Stainers Tab1720 has been selected and various stainers, such as1000-1-1000-4 that are part of LAN1223 are shown on the left hand panel of the screen. Users may select any one of theindividual stainers1000 shown in the left hand panel to obtain additional information about the stainer. Exemplary user screen1700 indicates that stainer1000-5, named “Pilot19“has been selected by the user and details of stainer1000-5 appear on the screen. The status ofslides1045 on aslide rack1065 in stainer1000-5 is shown by columns with icons for theindividual slides1045, as inexemplary column1730. In some embodiments, icons forslides1045 may be color coded to indicate their status within astainer1000. A slide rack column without slide icons indicates thatcorresponding slide rack1065 is empty. At the bottom of each column, acounter1732 displays the elapsed time on each non-empty rack.
• User Interface1700, as shown inFIG. 2C, also contains areagent display column1735, which shows icons forreagent bottles1080 in stainer1000-5. A reagent display column without icons forreagent bottles1080 indicates that the correspondingreagent rack1060 is empty. In some embodiments, the icons may be color coded to indicate whetherreagent bottle1080 is full, empty or is to be replaced.Fluid display panel1760 shows the status of variousbulk fluid containers1299 on stainer1000-5.Dialog box1740 displays messages related tostainer1000 including alerts, warnings, or status related information to the operator.Print report button1750 allows the operator to print various reports pertaining tostainer1000,slide1045,reagent bottle1080, orbulk fluid container1299 status. Displayslide list button1770 allows details ofindividual slides1045 to be displayed. Selection of one of the tabs intab menu1511 can cause user interface screens for the option chosen to appear. It should be noted that the screen shown is exemplary only and other configurations of screens and user interfaces are possible.
• FIG. 3A illustrates exemplary software architecture1600 forsystem manager server1320. As shown inFIG. 3A,exemplary SMS1320 includes a systemmanager communication module1615 for communication withSM1330 and astainer communication module1630 for communication withSCS1310. In some embodiments,SMS1320 performs data handling and processing for theSM1330 andSCS1310, and may also process and handle data and messaging communications betweenSCS1310 andSM1330. In some embodiments,SMS1320 can accept inputs fromSM1330 and/orSCS1310 and output status reports in response. In some embodiments,SMS1320 can also connect to and controldatabase system1220 including maintainingdatabase system1220 and performing any other database functions.
• In some embodiments,SMS1320 may run as an operating system service. A service application is designed to be always available and provides services to other applications, which may access the provided services over a network such as LAN1223. For example, on Microsoft Windows based operating systems,SMS1320 can run as a Window XP Service application so that users need not be logged into Windows XP for theSMS1320 to be operational. In addition, as shown inFIG. 1F, multiple instances ofSM1330 andSCS1310 may interact with asingle SMS1320 and its associated database system.
• Systemmanager communication module1615 andstainer communication module1630 can communicate with multiple individual instances ofSM1330 andSCS1310 respectively. In some embodiments, instances ofSM1330 andSCS1310 running onstainers1000 and computing devices respectively that are part of LAN1223 can communicate withSMS1320 through systemmanager communication module1615 andstainer communication module1630 respectively. For example,stainer communication module1630 may retrieve Slide Detail Data, Slide Protocol data, and/or Global Stainer Configuration data fromdatabase system1220 usingdatabase module1620 and send the data to stainer1000 in response to a request fromstainer1000. Systemmanager communication module1615 may also process and forward a request for Stainer Status, Slide Status, Stainer Error or Exception Conditions, and/or Slide Log data fromSM1330 to astainer1000, process and relay the response ofstainer1000 back toSM1330, and update appropriate records indatabase system1220 usingdatabase module1620.
• Database module1620 can respond to requests to retrieve and to store data pertaining to slide1045,reagent bottle1080, status, and other data.Database module1620 has information about the logical organization of data tables and queries to fulfill requests for data storage or retrieval fromdatabase system1220. In some embodiments, the data may reside in a Microsoft Access database format, or in another commercial database system format. In some embodiments, such as in aWindows2000 or Windows XP implementation ofSMS1320, the operating system may support Active Data Objects thus providing native support for the Access database format. In some embodiments, User Interfaces toSMS1320, as well as all database tables indatabase system1220 that provide or deal with user accessed or updated information may be localized to support local languages and/or data formats. In some embodiments, certain data tables may include pre-assigned data such as reagent and treatment protocol names.
• In some embodiments, messages exchanged between systemmanager communication module1615 andSM1330 andstainer communication module1630 andSCS1310 may be encrypted over LAN1223. In some embodiments, the exchanged messages can be plain text internal to the modules to facilitate debugging of network communications. In some embodiments, all database transactions may be encrypted to maintain privacy, confidentiality, and security of information in the database. In some embodiments, a log of all data requested from and written todatabase system1220 can be maintained.
• In some embodiments, data and configuration parameters that affect the operation of the entire system can be maintained bySMS1320. In some embodiments,SMS1320 may have a backup and restore utility that can allow for automatic backups on a user-specified, predetermined, or default schedule. In some embodiments,SMS1320 may search the LAN1223, auto-discoverstainers1000 and make connection to discovered stainers1000. In some embodiments,SMS1320 can also allowstainers1000 requesting access to connect to it. In some embodiments, different TCP/IP ports may be used to segregate control, status, and diagnostic messages.
• In some embodiments,support module1610 handles the initiation of outbound support connections to manufacturer or service provider support centers and acts as the proxy for support communications with thestainers1000 andSM1330. In some embodiments,support module1610 may interact with asoftware support tool1635. Software support tool may allow third party applications to accessSMS1320 via a predefined or standard interface.Support module1610 permits both automated call out on a periodic basis as well as on-customer-demand call out for support. In some embodiments, a dial-up modem line to an Internet service provider or a direct network connection to the Internet may be used to access manufacturer or service provider support centers.
• In some embodiments,support module1610 andsoftware support tool1635 provide a general means for a facility operating one ormore stainers1000 to interact with the external world. By appropriately configuringsupport module1610 andsoftware support tool1635, the operator of a stainer facility can receive support and/or exchange information securely and seamlessly with support centers, hospitals, customers, physicians, patients, and other related entities.
• To alleviate security concerns, the support system can be configured to initiate support calls only from within the customer's site. This allows a support call to be placed from a facility without opening an inbound port in the facility's firewall. The existence of an inbound port in a network firewall may present a security hazard in some situations. Accordingly, some embodiments of the present invention allow support calls to be placed even in environments where only outbound network connection requests are allowed. Outbound network connection requests are generally more secure and are more likely to be supported by network managers. In some embodiments, all external network communications may be encrypted with a strong encryption algorithm.
• In some embodiments,support module1610 may act as a proxy, or an intermediary between a support technician (or automated support center modules) and end-use software, such asSCS1310 orSM1330. In some embodiments,support module1610 may also directly respond to and/or relay certain commands toSCS1310 orSM1330, so that a support technician can also investigate support issues.
• In some embodiments, whensupport module1610 has connected to a support center, the support module may be asked to login to the support center using a previously provided or default customer number and indicate whether the request is a periodic or on-demand type. The support module can then accept commands from support center software or from a support technician via the support center. For example, in a periodic support call, the support center may issue commands to the support module to obtain system running operational information, including diagnostic files, system configuration information, system logs, and reagent usage statistics. In some embodiments, the transmission of patient-related or other private or protected data may not be allowed via automated support connections. As another example, the support center may transmit or make software updates ready for download bysupport module1610.
• In some embodiments, when a customer has initiated an on-demand support call, via a dialog on any client, the support module may wait until a support technician connects and is ready to initiate commands. For example, a customer who is receiving support from a technician over the phone may invoke thesupport module1610 through an appropriate interface. Whensupport module1610 connects to the support center, the support technician or a support center software module can take command of the connection and may then issue commands to obtain more information about theSMS1320 and other software components. When the support session is finished, the support center technician or software can issue a command for the support module to disconnect. In some embodiments, the support module may use an inactivity timer, which can cause the session to be terminated after a preset time length without activity.
• FIG. 3B andFIG. 3C show portions of an outline for an exemplary logical data model forSystem Manager Server1320 showing some of the data tables, data fields, and data records. In some embodiments, data used bySMS1320 may be normalized and organized as a relational database. In some embodiments, the structure ofdatabase1220 used bySMS1320 may be based onlogical data model1800. As shown inFIG. 3B andFIG. 3C, exemplary SMSLogical Data Model1800 indicates the logical organization and inter-relationships between various data tables used bySMS1320. It should be noted that the tables and organization depicted inFIGS. 3B and 3C are exemplary only and other tables, records and fields may be added or deleted, or the logical data model otherwise modified.
• Exemplary Slide Table1810 is indexed by primary key Slide ID, which uniquely identifies eachslide1045. Slide Table1810 may also contain identifier CaseID, which is the index to a record in the Slide Case table1812 that contains the case demographic information.Many slides1045 onstainer1000 may correspond to the same case. The FromLIS field in the Slide Case table1812 can hold an indicator of whether the case information came from anLIS system1222, or via an LIS Agent.
• In some embodiments, the LIS Agent may act as an interface between SMS and external customer-supplied LIS software. In some embodiments of the present invention, the LIS Agent can perform actions analogous toSM1330 in its capability to enter data into and retrieve data fromSMS1320 and its associated database. In some embodiments, the LIS Agent may be provided additional capabilities, including the capability to interact with thestainers1000, and other components ofsystem1200. In some embodiments, LIS Agents may be customized to interact with specific LIS systems. In some embodiments, LIS Agents may also be used to interface to other laboratory instruments, such asexemplary instruments1296 and/or1297.
• The PreTreat field indicates whether aslide1045 is to undergo deparaffinization, target retrieval or other pretreatment steps. Treatment Type and Treatment ID fields contain links indicating the treatment type name for which this slide was programmed. For example, the Treatment Type field could refer to a standard test such as the HercepTest, CD30, or a custom named test. The Panel ID field is an index to Panel table1880 and identifies the panel by which aslide1045 was added. Panel table1880 holds information on panels, which are groups ofslides1045 that can be added tostainer1000 together. If aslide1045 has a custom treatment protocol then the panel identified by PanelID, may only contain thatslide1045. Tissue Type ID field links to Tissue Type table1824 and indicates the tissue type of a specimen. Tissue Type table1824 is a lookup table for the various types of tissue samples that can be stained. In some embodiments, records in Tissue Type table1824 may be initialized for standard tissue types, but end-users may add more tissue types.
• A slide record in Slide Table1810 may also contain a tissue preparation identifier (“TissuePrepID”), which is an index to Tissue Prep Table1826. Tissue Preparation Table1826 is a lookup table for various types of specimen preparations. In some embodiments, records in Tissue Prep table1824 may be initialized for standard preparation types, but end-users may add more preparation routines. In Tissue Prep table1824, a Depar field indicates if deparaffinization has been specified for the tissue sample, while the HIER field and the EnzymePT field indicate if target retrieval or enzyme pretreatment respectively have been specified.
• In some embodiments,Slide Record1810 may also contain a Primary Antibody ID field (“PrimaryABID”), which is an index to PrimaryAB Table1852. Primary AB Table1852 contains information about the standard incubation times for a primary antibody, as well as information about which detection system and target retrieval to use. In some embodiments, Primary AB Table1852 contains a DetectionSystemID field, which is an index to Detection System Steps Table1864. Detection System Steps Table1864 has information regarding reagent details and command for each step of the treatment protocol associated with the primary antibody.
• Slide Steps Table1814, indexed by the Slide ID and StepNum fields, indicates the command and Reagent ID for each processing step of a particular slide. For example, the command field may hold a processing command such as “Dispense Reagent,” where the reagent in question is identified by the contents of the Reagent ID field. The step number (“StepNum”) field keeps track of the current step number. The event sequence at each step may be logged and written to SlideLog Table1816. Slide Log Table1816 holds the entire slide event log generated by a stainer. The slide log contains information about the type, quantity, and time of application of reagents.
• Slide record1810 may also include a Stainer ID, which is an index to Stainer Table1818, which contains details about individual stainers. Stainer table1818 holds information aboutstainers1000 coupled to LAN1223 for aSystem Manager1330. In some embodiments, when anew stainer1000 is added to LAN1223,stainer1000 may auto-discoverSM1330 and send out its serial number and IP address, which is recorded in the database bySMS1320. Stainer Table1818 includes information about the name of eachstainer1000, the IP address, the number ofslide racks1065 on thestainer1000, number ofslides1045 in eachslide rack1065, rack type, and rack number (“RackNum”). In some embodiments, the contents of the Status Code field indicate the current status ofstainer1000, which could be one of running, idle, waiting for user intervention, error, or offline. Alerts generated by astainer1000 are stored in Stainer Alerts table1820 and are indexed by Stainer ID and a unique message identifier (“MsgID”) for each message generated. A help identifier field (“HelpID”) holds an error code that can be looked up using the on-line help menu provided bySystem Manager1330. In some embodiments, the contents of HelpID field may be used by a support center technician or an automatic debugging tool to detect and correct problems in offendingstainer1000.
• Stainer ID, Rack Type, and RackNum are indexes to a Rack State Table that indicates the state of eachslide rack1065 including its priority and estimated completion time. Stainer ID, Rack Number, and Slot Number are used to indicate the precise location of the programmedslide1045 once it is introduced intostainer1000. Whenslide1045 is introduced intostainer1000, the label onslide1045, which bears machine readable encoded information, can be read and the location ofslide1045 recorded bySMS1320. In some embodiments, the location of theslide1045 may be calculated from the location (for example, the X, Y, co-ordinates) ofrobotic head1010 at the time when the slide label is initially read.SM1330 may then querySMS1320 to obtain the slide information fromdatabase1220.
• Slide record also contains a User ID field, which is an index to UserInfo Table1828 and identifies the user that programmed the slide. In some embodiments, the system may automatically generate the data for a user, such as user name, user phone number and other fields based on information associated with a user's log-in record. User Groups Table, also indexed by UserID, contains information about the group to which a user belongs. In some embodiments, a user may be allowed or denied access to certain software function based on user group membership.
• The Current Status field indicates ifslide1045 has been programmed (associated with a treatment protocol), if it has been placed instainer1000, ifslide1045 is in-process (the first step of the treatment protocol sequence has commenced), if processing has been completed butslide1045 is still instainer1000, or if processing forslide1045 has been completed andslide1045 has been removed fromstainer1000. The Current Status field identifies the specific step in the process flow with which aslide1045 is currently associated. The Final Result field indicates whether theslide1045 was processed according to treatment protocol, or was spoiled. Aslide1045 is deemed spoiled if for somereason slide1045 was not processed within the tolerances specified by the associated treatment protocol.
• As shown inFIG. 3C,logical data model1800 may also contain Reagent Bottle Table1858. In some embodiments, reagents are added tostainer1000 in machine-readable labeledreagent bottles1080 that are placed inreagent rack1060. The label on eachreagent bottle1080, on which information may be encoded, for example in the form of an Infoglyph™, includes a unique identifier corresponding to a bottle serial number that is stored in InterfaceNum. In some embodiments, the label may also contain information about the Bottle Size. In some embodiments, InterfaceNum may be include a bottle code that could serve as an index to Bottle Code Info Table1870, which may contain information about bottle size and fill volume.
• InterfaceNum also serves as an index to Reagent Bottle table1858 and allows determination of the lot number (“LotNum”) ofreagent bottle1080, kit identifier (“KitCode”), and reagent identifier (“ReagentID”). ReagentID is an index to Reagent Catalog Table1850 from which additional information about the reagent contained inreagent bottle1080 may be obtained. In some embodiments, when the label onreagent bottle1080 inreagent rack1060 is read, the position ofZ Head1010 on astainer1000 identified by StainerID may be used to calculate the slot position (“SlotID”) and rack number (“RackNum”) ofreagent bottle1080.
• ReagentID, which is specified along with Command in Slide Steps Table1814, identifies the reagent to be dispensed during the specified step StepNum. For the purposes of the database, reagents can include buffer, water, and air. Reagent Catalog Table1850 identifies the specific reagent from the ReagentID index, by both the Reagent Name and by a Reagent Catalog ID fields. The combination of the fields Reagent Catalog ID and Reagent ID indicates whether the reagent to be used may be taken from a general reagent stock, or if the reagent is drawn from a specified kit.
• When a kit is specified, the reagent in question belongs to the identified kit, to ensure the accuracy of test results. If a kit is to be used, the Reagent Catalog ID contains a “KitCode.” The KitCode is an index to Kit Table1868 and KitComps Table1866, which contain details pertaining to the specified kit. As noted earlier, Reagent ID specifies the actual reagent (from the kit) to be used. If no kit is specified and the reagent may be taken from general reagent stock, then the Catalog ID and Reagent ID have identical values. Kit details, indexed by KitCode, are specified in Kit Table1868 and Kit Comps Table1866. Kit Comps Table1866 specifies the components of each kit. In some embodiments,SMS1320 andSCS1310 have the capability of identifying a new kit and automatically generating and assigning a unique kit number toreagent bottles1080 when they are first introduced instainer1000, thus ensuring thatreagent bottles1080 in the kit are utilized as a group.
• When a reagent is aspirated for application to a slide, the Usage Date and Amount aspirated is updated in Reagent Bottle Usage Table1860. Quantity field in Reagent Bottle Table1858 is also updated. When the Quantity in Reagent Bottle Table1858 is zero or below a certain usable threshold, the bottle is designated as empty. An Empty Bottles Table1872 tracks empty bottles. In some embodiments, data in Empty Bottles table may be used to update lab inventory onLIS1222 and an order may be placed automatically for additional reagents. In some embodiments, an operator may be alerted and asked to replace the reagent bottle.
• Detection System Steps Table1864 is indexed by DetectionSystemID, which also appears in the PrimaryAB Table1852. A detection system can be generally used with a Primary Antibody reagent selection. Detection System Steps Table1864 contains information about manufacturer supplied and user-defined detection systems including the actual treatment protocol steps as well as treatment protocol placeholder steps. Placeholder steps may be filled in with selected primary antibodies as well as enzyme pretreatment information where applicable. Thus, using the PrimaryABID field from a slide record, treatment protocol-related information may be obtained by using appropriate tables indatabase1220. Detection System Table1862 contains information about the detection system including its name, whether the system is currently active, and any comments related to the detection system.
• In some embodiments, Reagent Category Table1854 may be used to look up reagent classifications. Such categories could include Primary Antibody, Secondary Antibody, Labeled Polymer, Chromogen, and Counterstain and Reagent Category Table1854 may be provided as part ofdatabase system1220.
• In some embodiments, Compatibility Table1856 provides information related to the compatibility of reagents. For example, some reagents may only work with mouse antibodies, or with rabbit antibodies, while others may work with both types of antibodies. Compatibility Table1856 provides information to indicate the compatibility or otherwise of reagents. In Compatibility Table1856, CompType field indicates if the reagent compatibility value pertains to species or enzyme compatibility, whereas the CompValue field uniquely identifies a particular category of compatibility. For example, if the CompType field indicates species compatibility then the CompValue field could indicate a code for a mouse, or a rat.
• In some embodiments, a Mix Table (not shown) may also be present that contains the quantity of constituent reagents to be mixed in order to produce a final mix reagent. In some embodiments, Mix Table may be provided tostainer1000 for its mixing calculations.
• The exemplary data model shown inFIG. 3B andFIG. 3C may be used to create tables indatabase system1220 to provide information, including information for system administrators, users, system components, diagnostic and maintenance software, support personnel and software,LIS1222 applications, and other in-house or third party applications that interact withsystem1200. Other tables including tables for holding system configuration parameters, administrative information or to support other functions may be provided.
• FIG. 4A illustrates exemplary software architecture for theStainer Control Software1310. In some embodiments,SCS1310 may run on a computing system embedded withinstainer1000 and control and coordinate the operations ofindividual stainer1000 with other system components. In some embodiments,SCS1310 may consist of a number of unique autonomous threads or sub-processes. Each thread performs specific tasks and manipulates a number of objects to control and monitor physical device states.
• As shown inFIG. 4A, exemplary architecture forSCS1310 includescommunication module1920, which interacts with embeddedcomputer communication hardware1910 onstainer1000, in order to communicate withSMS1320. In some embodiments,communication module1920 also receives information and messages from stainer logic andschedulers module1935 and may also exchange information withstainer API module1925. In some embodiments,stainer API module1925 provides an interface for control of stainer hardware at a high level. In some embodiments,stainer API1925 can translate the high level commands it receives into a sequence of lower level stainer hardware API module calls in order to accomplish the objects of the received command.
• FIG. 4B shows a block diagram of an exemplary stainer communications subsystem. As shown inFIG. 4B embodiments ofcommunication module1920 may includecommunications component2001 and computer communications andcontrol component2007.Communications component2001 may include two communication interfaces, stainer-server communications interface2002 for communication withSMS1320 anddiagnostic communications interface2030 for diagnostic communication related to SCS internal component modules.
• In some embodiments, stainer-server communications requests may be generated by internal processes withinSCS1310. Processes withinSCS1310 may queue communications requests withincommunications interface2002, which monitors and transmits the requests toSMS1320. When a response is received,communications interface2002 sends the response to the appropriate process. Examples of stainer-server communication can include requests for the following: stainer setup information; registering a newly detected slide; slide record information; slide log information; pending slide information; reagent information; reagent level status; rack queries; pretreatment information; deparaffinization information; target retrieval fluids list; list of all reagent kits; all reagents within a kit; list of all reagents; new reagent kit identifier information; list of bottle identifiers for a kit; and get server date-time.
• Stainer-server communications may also include database update requests and/or commands, such as remove reagent rack; reject slide rack; mark slide spoiled; mark slide complete; mark slide drawer open; set target retrieval fluid; set target retrieval or deparaffinization state; update slide state; update reagent state; set slide drawer state; set reagent drawer state; set bulk fluids cart container state; request a simulated reagent bottle (for simulation purposes); reset slide information; set slide drop zone (zone where reagents drop onto a slide); update total processed slide count; add/update an alert; delete an alert; delete all alerts; set kit bottle identifiers; and backup configuration files.
• The examples above are exemplary only and other commands and/or requests may be created and added. In some embodiments,SMS1320 may querydatabase1220 to obtain the requested information. In some embodiments,database1220 may be updated with information sent out bystainer1000, or anoperator using stainer1000.
• In some embodiments,diagnostic communications interface2030 may allow external applications to obtain diagnostics information related to hardware and components on astainer1000, when such access has been granted by the system administrator. In some embodiments, the diagnostic interface facilitates a low-level interface where machine status can be queried and various diagnostic commands executed.Diagnostic interface2030 may be used by a manufacturer or service provider to assist local users in diagnosing and/or correcting problems onstainer1000, applying software updates and patches, providing technical support, and to ensure the smooth operation ofsystem1200. In some embodiments, a Software Support Tool (“SST”) may be provided to facilitate interaction withstainer1000 throughdiagnostic interface2030.
• In some embodiments, acommunications protocol interface2004 may provide functionality for communication protocols, such as the TCP/IP communications protocol, to effect communication with other system components.Port management sub-module2008 may allow communication ports to be configured to send and/or receive specific types of messages and may direct messages to the appropriate communications port. In some embodiments, different TCP/IP ports may be used to segregate control, status, and diagnostic messages. Embodiments ofcommunications component2001 allow transactions to be cached and re-transmitted if a communications link has been lost. Accordingly, a system may process all failed, pending, and/or unsent communications requests once the link is restored. In some embodiments,communications component2001 may be capable of automatic reconnection. In some embodiments, computer communications control sub-module2007 contains communicationhardware device drivers2008 that control anddirect communications hardware1910 to take actions to effect the actual transmission of data.
• In some embodiments,stainer API module1925 consists of a group of functions and procedures that perform the process of pre-treating and staining slides1045. In some embodiments, methods performed byStainer API1925 are high level in nature and may rely upon many lower level objects to perform their tasks. For example, stainer API may directrobot1032 to aspirate a specific reagent. As a result,stainer hardware API1930 may directrobot1032 to probewashing station1055, to allowprobe10 to be washed prior to reagent aspiration. The probe washing command in turn may translate a command into a sequence of even smaller steps performed by multiple individual components onstainer1000.
• Stainerhardware API module1930 controls low-level functionality on various devices and components withinstainer1000. For example, stainerhardware API module1930 may poll sensors to ensure that all reagent rack doors are closed prior to commencing operation onstainer1000.
• In some embodiments, bothstainer API module1925 andStainer Hardware API1930 can also simulate the actions of each of the devices in their control. For example,Stainer API1930 may model the time taken byprobe10 to apply reagent to a slide, and/or the decrease in available volume of fluid inreagent container1080. The completion time and/or buffer availability information may be sent quickly tocommunication module1920, for onward transmission toSM1330. The simulation of the actions of system components allowsstainer API1925 andstainer hardware API1930 to operate in a simulation mode, where no physical actions are actually taken by system components. In some embodiments,stainer API1925 can return results based on its simulation model toSMS1320 andSM1310, which may be unaware thatstainer API1925 is operating in a simulation mode and continue to perform their usual functions. In a simulation mode, the system may be debugged and new procedures tested quickly without risk to or use of system components and expensive reagents. In some embodiments, an accelerated simulation mode may be available, wherein an entire simulation run may be executed in a very short time.
• In some embodiments, exemplary stainer logic andschedulers module1935 contains the logic and decision criteria to trigger, initiate, suspend, report, or terminate actions performed bystainer1000. In some embodiments, stainer logic andschedulers module1935 also performs automated background tasks such as waste pull and monitoring. In some embodiments, logic for the control and coordination of robotic and fluidic schedulers instainer1000 may also be contained within this component. In some embodiments,robotic head1032 onstainer1000 is moved to ensure that reagents are applied to or removed from aslide1045 substantially within the time period specified by a treatment protocol. In some embodiments, a robotic scheduler controls the movement ofrobotic head1032 to ensure that treatment protocol-related constraints are met. In some embodiments, bulk fluids used bystainer1000 are stored incontainers1299 onfluidics cart1295 and can be delivered to processing tanks withinstainer1000 at appropriate points in time. In some embodiments, the conduits conveying the fluids to the processing tanks may be limited and shared by several fluid containers. Accordingly, the allocation of conduits is scheduled to ensure that all fluids are ready for delivery at an appropriate time, and that the conduits are adequately flushed to eliminate residues. In some embodiments, a fluidics scheduler controls the allocation of the conduits to fluids.
• Exemplary configuration module1915 holds configuration settings forstainer1000 including device types, positions, speeds, accelerations, set points, etc. Other SCS modules may request operating parameters fromconfiguration module1915. For example, stainer logic andschedulers module1935 may request the speed ofrobotic head1032 fromconfiguration module1915 to calculate a viable schedule for movement ofrobotic head1032.
• Exemplary startup sequencer1945 orchestrates stainer1000 through a safe and orderly startup when it is powered on. In some embodiments, the system can enter a normal running mode after successful completion of the startup sequence. In some embodiments,startup sequencer1945 may perform one or more of the following functions: system initialization including language selection; preparation of internal data structures and the GUI; checking the operating system and firmware versions and characteristics; locking all loaded drawers; checking and performing tests on motion controller hardware and electronic boards in the stainer; homing the robot; washing the probes; rinsing processing tanks; connecting to a specifiedSystem Manager Server1320 or locatingSMS1320 on LAN1223; synchronizing date and time with other system components; and starting the schedulers. In some embodiments, exemplaryuser interface module1940 provides operational information updates to the built in LCD display and to accept operator input.
• FIG. 5A shows the interactions of an exemplary Stainer Applications Programming Interface (“API”)2000 for control of functions ofstainer1000. In some embodiments,stainer API1925 provides a high-level system control and monitoring interface to perform operations for slide processing and pretreatment. In some embodiments,stainer API1925 may serve as an interface forrobotic scheduler2010 andfluidic scheduler2020 to invoke and exchange information with routines indiagnostic interface2030.
• In some embodiments,stainer API module1925 provides a mechanism to accessdiagnostic interface2030, which may be part ofcommunications module1920.Diagnostic interface2030 facilitates access to hardware onstainer1000, where machine and component status can be queried and various commands related to diagnostics executed. In some embodiments,diagnostic interface2030 may exchange data and control information withsupport module1610 to facilitate remote monitoring, diagnosis, and support of functions and operations ofstainer1000.
• Robotic scheduler2010 andfluidic scheduler2020 work throughstainer API1925, which also handles all interfaces to the low level devices throughstainer hardware API1930. For example, in some embodiments,robotic scheduler2010 may look ahead to determine the robotic head's next rendezvous (the location and point in time where therobotic head1032 may be utilized next) and may elect to park therobotic head1032 close to that location by issuing an appropriate command throughstainer API1925.
• In some embodiments stainerAPI1925 provides access to several routines and functions that are useful for operations relating to the processing and pretreatment ofslides1045. Some of these routines may invoke other routines provided bystainer hardware API1930. In some embodiments,stainer API1925 may provide an image acquisition and glyph decoding routine to detect theslides1045 and decode information on theslides1045. The image acquisition and glyph decoding routine causes glyphs on labels affixed toslides1045 or reagents to be read and decoded. In some embodiments, data read from the labels may be sent toSMS1320 along with slide or reagent location information, and an appropriate slide or reagent record indatabase1220 may be updated. In some embodiments, image acquisition and glyph decoding routine may cause a picture of theslide1045 to be taken by a camera underZ Head1010, and the image may be stored as part of the slide or reagent record. In some embodiments, the image taken by the camera may be processed using image processing routines to extract information from the glyph, or to determine if a slide or reagent is present.
• In some embodiments, forslides1045 to be stained,slide rack1065 is lowered until theslides1045 are resting on platforms. Embodiments ofstainer API1925 may also provide an elevator control function to unlatch andlower slides1045 to a staining or pretreatment position. Elevator control function may also allowslide rack1065 to be raised to a latch position in preparation for the opening of a drawer. During normalstaining operations SCS1310 may control temperature and humidity and ensure operator safety in part by locking a front cabinet door on the stainer. Access to a locking function throughstainer API1925 may be provided to lock the front cabinet door. In some embodiments,stainer API1925 may also provide access to routines to control and stabilize the temperature of aslide1045 during staining, and to control the temperature of reagent containers in reagent racks. In some embodiments, slides1045 are tipped vertically to enter the pre-treatment processing tank. Embodiments ofstainer API1925 may provide a routine to tipslides1045 to a vertical position. Embodiments ofstainer API1925 may also provide access to routines for filling, emptying, and heating processing tanks associated with eachslide drawer1040.
• In some embodiments stainerAPI1925 may also provide access to routines to air blow a slide, or to rinseslides1045 with buffers or water. Routines accessed throughstainer API1925 may themselves invoke other routines. For example, a slide rinse routine may invoke functions to move the robot to a start rinse position over a particular slide; activate the rinse tool and water pump; move the robot to an end rinse position; and retract the rinse tool. In some embodiments, a buffer rinse allows slide samples to be overlaid with a buffer, which prevents sample deterioration or degradation. In some embodiments, a buffer rinse may be used onslides1045 between pretreatment and staining, or when a reagent is unavailable, or when the reagent cannot be applied to theslide1045 within the time allotted by a treatment protocol. Applying buffer to a slide sample preserves the sample until resources such as a reagent orrobot1032 for the next operation are available.
• Stainer API1925 may also provide access to reagent aspiration and dispense routines, wherein a specified amount of reagent may be aspirated from a reagent bottle or the system mixer intoprobe10. In some embodiments,robotic scheduler2010 may be presented with a series of slide dispense tasks, which it prioritizes and sorts.Robotic Scheduler2010 may then access the reagent aspiration and dispense routine throughstainer API1925 to perform the specified aspiration and to dispense the specified reagent amount fromprobe10 onto aslide1045 or into the system mixer. In some embodiments, the reagent aspiration and dispense routine may in turn call an on-demand reagent mixing routine, which allows a reagent to be created on demand by mixing its constituent reagents in a system mixer. In some embodiments, after the reagent has been mixed, aspirated, and dispensed, the reagent aspiration and dispense routine may cause the mixer to be rinsed, emptied, and dried.
• Routines to empty all bottles that belong to a reagent kit when the kit has been designated as empty are also accessible throughstainer API1925. In some embodiments, when any bottle in a kit has been designated “empty,” all bottles belonging to the kit are replaced. A kit may be seen logically as a discrete integrated unit, so that operations such as accepting a kit or discarding a kit are performed on the entire kit. Accordingly, in some embodiments, when a bottle within a kit no longer contains a minimum aspiration amount of reagent, the bottle and all bottles belonging to the kit are marked as empty. To prevent usage of reagents remaining in other bottles, the system may be directed to empty all bottles belonging to the kit. Reagents aspirated for the purpose of emptying bottles in a kit may be dumped into waste containers. After each reagent is dispensed on to a slide,reagent probe10 is washed to prevent carry over from one reagent to the next. Embodiments ofstainer API1925 may also provide access to a probe wash routine to move the robot to probewash station1055,lower probe10 intoprobe wash station1055, wash theprobe10 using de-ionized water inprobe wash station1055, and dispose of wash waste.
• Stainer API1925 provides routines to perform the exemplary operations described and other additional operations. Operations performed in response to invocation ofstainer API1925 routines may request and use parameters fromconfiguration module1915. In some situations, a single operation may also involve calls to a number of individual hardware interface routines usingstainer hardware API1930.
• FIG. 5B shows a block diagram of exemplary stainer logic andschedulers module1935 for control of stainer program threads. The various exemplary threads operate on objects including slide drawers object2162, reagent racks object2164, slidesobject2166, and reagents object2168. It should be noted that the program threads shown are exemplary only and that other program threads may be added or the program thread structure and logic modified according to some embodiments of the present invention.
• In some embodiments, the state of each object, which may correspond to the state of an underlying physical object, is maintained in a field within a data structure and may be controlled bystate process thread2120. Device drivers that interface with a physical object may be responsible for updating the virtual object corresponding to the physical object. For example, a device driver may poll a sensor on aslide drawer1040, determine that it is open, and make a request to update the status of the slide drawer object. Device drivers are also responsible for executing actions on physical objects that may be desired by SCS components. For example,slide drawers1040 may be locked prior to processing a request to read glyphs on slide objects2166. Accordingly, astainer API1925 call to read glyphs may result in multiplestainer hardware API1930 calls, for example to lockslide drawers1040, moverobot1032, read, and decode glyphs etc.Stainer hardware API1930 calls may in turn invoke device driver routines that interact with hardware components onstainer1000 to effect the physical action. For example, a slide drawer driver may instruct slide drawer hardware to lock aslide drawer1040.
• In some embodiments, slide drawers and reagent racks may rely upon thestate process thread2120 to perform steps in operations triggered by operator actions such as opening or closing a drawer, or inserting or removing a reagent rack. When aslide drawer1040 is opened a field within a data structure associated with theslide drawer object2162 may be updated to indicate that theslide drawer1040 is open. In some embodiments, the field indicating the state of the object may also be held within a record for the object indatabase1220. For example, state data information pertaining to slideobject2166 may be held in a record within slide table1810 and could include current process step number as per the treatment protocol associated with the slide. Information to perform operations may also be passed toschedulers2195, which may includerobotic scheduler2010 andfluidic scheduler2020. In some embodiments,schedulers2195 may run as separate threads.
• In some embodiments,system thread2110 provides automatic background processing for waste pull, container level, and electronic board communications and status monitoring.System thread2110 manages and processes all waste pull requests and ensures that different systems requesting waste pulls get adequate time. In some embodiments,system thread2110 also monitors all sensors oncontainers1299 onfluidics cart1295, and provides information about fluid level states oncontainers1299 to other stainer logic sub-components and to thestainer GUI1940. Devices that are monitored by thesystem thread2110 include all on-board communications and the front door interlock controller. In some embodiments,System Thread2110 also has the ability to log various sensor conditions at periodic intervals.
• In some embodiments, upon launching,system thread2110 loads a list of all input and output addresses and/or ports and initializes sensors.System thread2110 may then enter a continuous loop. In some embodiments, on every iteration of the loop,system thread2110 processes waste pull requests, handles priority waste pulls, monitors input-output ports and on-board communications, and reads sensors oncontainers1299 onfluidics cart1295. In some embodiments, readings of the cart sensors may be averaged over a time period to diminish the effect of fluid motion.
• In some embodiments,state process thread2120 processes event driven states for the slide drawers, reagent drawers, slides1045, and reagents. In some embodiments,state process thread2120 periodically calls eachslide drawer object2162,reagent rack object2164,slide object2166, andreagent object2168 to process any pending events, and may accept a value returned from each process call. The value returned from the process call is used to trigger actions usingcontrol thread2130. In some embodiments, eachslide drawer object2162 and eachreagent rack object2164 may operate as an autonomous process that is independent from processes for other drawers and racks. In some embodiments, upon initializationstate process thread2120 loads specified objects into a list before entering a continuous loop. In some embodiments,state process thread2120 may process states for all of the objects in a list, during every iteration of the loop. If an object returns a code requesting allocation during iteration,state process thread2120 may requestcontrol thread2130 to execute on the allocation. For example, a reagent specified for a particular treatment protocol step may be allocated to aslide1045 based on a request to controlthread2130 bystate process thread2120. Allocation establishes a logical connection between the allocated object and the requesting object and may be one of a sequence of steps performed before physical actions corresponding to the allocation are manifested in a stainer.
• In some embodiments,control thread2130 handles reagent allocation executions,stainer GUI1940 updates and interactions, and provides an interface to frequently accessed objects. In some embodiments,control thread2130 handles all reagent allocation requests and performs a periodic reallocation. In some embodiments,control thread2130 also supplies data touser interface1940 and triggers all user interface updates. For example, user actions on astainer panel1020 are recorded byuser interface1940 and passed back tocontrol thread2130, which makes the change in the specified object. Uponinitialization control thread2130 loads lists of objects and enters a continuous loop. On each loop iteration,control thread2130 checks for allocation requests and processes the allocation requests. For example, if a reagent allocation request has been made,control thread2130 allocates the reagent appropriately, and the request may be passed toSchedulers2195 for prioritization and scheduling. In addition, on each iteration of theloop control thread2130 may also update GUI objects with the actual states of the real objects in the system and vice versa.
• In some embodiments,UPS thread2140 connects to and monitors any coupled Uninterruptible Power Supplies (UPS)1298 for power failures. In some embodiments,UPS thread2140 also handles timing considerations when the line power fails and notifies other logic sub-components when it is time to shutdown heaters and/orstainer1000 itself. In some embodiments,UPS thread2140 connects to and periodically monitors a coupledUPS1298 for line status information. IfUPS1298 reports that line power has failed, theUPS thread2140 can start monitoringUPS1298 battery power and can direct the shutdown of processing tank heaters andstainer1000 itself when theUPS1298 battery power falls to a critical level. In some embodiments, a log entry may be made just prior to shutdown. On startup,UPS thread2140 may direct UPS objects to connect to any coupledUPS1298 and the connections are continuously monitored.
• In some embodiments,heater thread2150 provides a single point interface for all slide drawer processing tank heaters. In some embodiments, the single point interface provided byheater thread2150 is used in the event that UPSthread2140 detects a line power loss in order to provide a single shutdown point for all heaters. In some embodiments, all processing tank heater enable and disable requests are fed throughheater thread2140. Upon startup,heater thread2140 fills its internal lists with the actual heater input/output enable addresses and initializes data structures and flags before entering a continuous loop. In some embodiments, external processes desiring to enable or disable a heater may access processing tank heater enable flags provided byheater thread2140. On eachiteration heater thread2140 turns on those processing tank heaters that have their flag enabled, and turns off those processing tank heaters whose flags are not enabled. In some embodiments,heater thread2140 may also be used to effect allocation of limited power resources coupled tostainer1000 to heaters to load balance the demand on power resources effected by heating tasks.
• FIG. 6A shows a block diagram showing interactions between components of anexemplary robot scheduler2010. The SCS schedulers, includingrobotic scheduler2010 andfluidics scheduler2020, are responsible for conducting staining (robot) operations and pre-treatment (fluidics) operations onstainer1000. In some embodiments,robot scheduler2010 may use a dynamic algorithm that continually readjusts the staining tasks that are executed, based on system changes, user actions, and a continuous feedback loop. Embodiments offluidics scheduler2020 may also use a dynamic algorithm capable of continually monitoring system changes and scheduling new pretreatment tasks as they are requested. Features provided by the dynamic, self-adjusting scheduling algorithm facilitate the continuous processing of slides. In some embodiments,robotic scheduler2010 andfluidic scheduler2020 are instantiated as autonomous threads onstainer1000 startup and continuously operate to control actions ofstainer1000.
• In some embodiments,robot scheduler2010 manages the coordination ofrobot1032 actions, including aspiration and mixing of reagents, for the staining of eachslide1045 within the dynamic environment instainer1000.Robot scheduler2010 analyzes impending steps for each slide, as defined by the treatment protocol for the slide, then intersperses the steps across allslides1045 and scores (prioritizes) them. In some embodiments,stainer1000 may contain multiple slide drawers, each of which can containseveral slides1045, and each of theseslides1045 may have its own individual treatment protocol necessitating an individually tailored pretreatment and/or reagent application schedule. From the viewpoint ofrobotic scheduler2010 actions are performed on each of theslides1045 instainer1000 within a specified period of time, and in a specific sequence.
• In some embodiments,robot scheduler2010 ensures thatrobot1032 has enough time to rinseprobe10, aspirate and/or mix reagents, travel to the location of aslide1045, and apply the reagent to slide1045. This sequence of tasks is repeatedly performed for eachslide1045 present in the stainer.Robot scheduler2010 therefore looks ahead in time for a certain period, and prioritizes or scores tasks that are performed in that period. Ifrobot scheduler2010 determines that a task may be performed at a later time, the task may be pushed down and re-scored during the next period. In some embodiments,robot scheduler2010 can work on the highest scored task first and then proceed to other tasks in order of priority. In some embodiments, the highest scored task may be the most time critical task. In some embodiments, ifrobot scheduler2010 determines thatrobot1032 does not have sufficient time to aspirate and apply reagent to aslide1045, a buffer may be applied to slide1045 to preserve the sample and the task marked to be re-scored during the next period.
• In some embodiments, the speed at whichrobot1032 can perform actions and number of slide slots provided instainer1000 are matched to ensure that the spoiling of slide samples on account of treatment protocol violations is extremely rare or non-existent. In the unlikely event thatrobot1032 is unable to perform its actions within the specified period or incubation tolerance for a treatment protocol step (for example, due to a transient mechanical problem), the violation is logged, but processing ofslides1045 is continued. When the processing ofslides1045 in aslide rack1065 containing spoiledslide1045 has been completed, a qualified technician can review the log to determine the nature and seriousness of the treatment protocol step tolerance violation, and also view the resulting stained sample to determine if the results are acceptable.
• In some embodiments,robot scheduler2010 can continually monitor all system events and re-adjust schedules in response to any changing events to allow allslides1045 to complete properly. In some embodiments, scoring and scheduling may be performed in accordance with algorithms described below. In some embodiments,robot scheduler2010 andfluidics scheduler2020 may operate to maximize throughput ofstainer1000, as measured by the total number ofslides1045 successfully processed in a given period of time. In some embodiments,robot scheduler2010 may recompute schedules to respond to dynamic changes in the load ofstainer1000 such as may occur when new slide racks are loaded and rack priorities are changed. In some embodiments,robot scheduler2010 may handle expected and unexpected failures and errors by trying to isolate affected subsystems and saveslides1045 from spoiling.
• As shown inFIG. 6A, embodiments ofrobotic scheduler2010 may includecollect tasks module2210, scoretasks module2220,schedule tasks module2240, and executetasks module2250. In some embodiments,collect task module2210 interfaces withcontrol thread2130 to obtain a list of all pending robot tasks. Robot tasks include all tasks that utilizerobot1032 or tools associated with the robot, such as reading a reagent label using the camera, tipping a slide, or dispensing reagent on aslide1045 usingsyringe pump1015 andprobe10. In some embodiments, tasks that are to be performed within the next time interval are identified and collected while all the others are filtered out.
• In some embodiments, scoretasks module2220 calculates a numerical score for each collected task based on several predefined categories, such as rack priority, incubation expiration time, or reagent availability. In addition, each category may be ranked by its relative importance. Once scored, the tasks are sorted in descending order of task scores, so that high scoring tasks are prioritized and appear at the top of the sorted list.
• In some embodiments,schedule tasks module2240 selects and groups tasks to be performed in the next time interval, and generates additional tasks for thesyringe pump1015,probe10, ormixer1050 subsystems in the context of their current state. In some embodiments,schedule tasks module2240 may optimize the slide staining process by reducing idle delays. In some embodiments scheduletasks module2240 may operate to increase responsiveness and flexibility so that tasks may be re-scheduled under the dynamically changing conditions. Executetasks module2250 interfaces with theStainer API module1925 to physically execute scheduled tasks. In some embodiments, executetasks module2250 may preempt scheduled tasks with other time-critical tasks due for immediate execution.
• In collect task routine2211, a list of all currently pending robot tasks gathered from the top of each subsystem queue is obtained fromcontrol thread2130. In some embodiments,objects2160 may be associated withslides1045, slide drawers, reagents, and reagent racks. For example,slide object2166 pertaining to aslide1045 may include queues of pending tasks associated with the slide. Likewise,slide drawer object2162,reagent object2168, andreagent rack object2164 may include queues of pending tasks associated with slide drawers, reagents, and reagents racks respectively. In some embodiments, queues may be implemented as first-in first-out lists. For example a slide queue might contain a task to dispense reagent, and a slide drawer queue might contain a task to read all slide labels in the rack.
• In some embodiments, checkreagent routine2212, checkmixer routine2214, and checksyringe routine2216 are used to filter out tasks associated with reagents, mixers, and syringes respectively, where prerequisites for the tasks are lacking. Thus, tasks whose prerequisites cannot be satisfied because of reagent, syringe, or mixer unavailability are filtered out. For example, if reagent A is not present inreagent rack1060 then a task requiring reagent A may be filtered out. Filtering ensures that the list of tasks submitted for scoring, sorting, and scheduling are those that can run to completion if scheduled. In some embodiments, data associated with a task could include the task's earliest execution time, latest execution time, task command, and task status.
• In some embodiments, collect task routine2211 may classify tasks as time-critical or regular tasks. Time-critical tasks may execute at specific times and have tight tolerances. Regular tasks are not time-critical and their tolerances are considerably more generous. In some embodiments, collect task routine2211 may also create, use and update lists of time critical and regular tasks available for scheduling. In some embodiments, buffer and water rinse tasks may be classified as time-critical. A buffer rinse protects samples onslide1045 from drying out therefore applying or re-applying a buffer rinse at specified intervals is considered time-critical. Accordingly, if a buffer solution onslide1045 is near its expiration time and there is insufficient time for dispensation of the next reagent, a new buffer rinse task may be created.
• In some embodiments, scoretasks module2220 calculates a numerical score that is used to prioritize potentially executable tasks for execution. In some embodiments, tasks submitted for scoring are analyzed taking into account the type of each task (e.g. rinse or dispense), their spatial properties such as slide location, temporal properties such as reagent incubation period expiration, other properties such as rack priority, and properties relating to system or subsystem state such as the reagent currently in a syringe.
• In some embodiments, task and subsystem properties are classified into separate scoring categories with individual importance rankings. For example, for buffer and water rinse tasks the earliest and latest time of rinse application with respect to current system time may be accorded a high weight, the user selectable rack priority may be weighted normal, and the location of aslide1045 instainer1000 may be accorded a low weight. In some embodiments, the high, normal, and low weights correspond to actual numerical values from which a score may be calculated. For example, to score rinse tasks with respect to reagent incubation time, a scoring routine may compute different scores based on whether the earliest rinse time for the sample has passed. Thus, before the earliest rinse time the newly computed sub-score may be given by:
• $\mathrm{NewSubScore}=\frac{\mathrm{CurrentSubScore}}{2}-\frac{\mathrm{EarliestRinseTime}-\mathrm{CurrentTime}}{\mathrm{NormalizingFactor}}$
• whereas, after the earliest rinse time has passed, the newly computed sub-score may be given by:
• $\mathrm{NewSubScore}=\mathrm{CurrentSubScore}-\frac{\mathrm{EarliestRinseTime}-\mathrm{CurrentTime}}{\mathrm{NormalizingFactor}}$
• As can be seen from the example above the priority of the rinse task may be significantly higher after the earliest rinse time has passed.
• In the scoring process multiple sub-scores from the categories relevant to each type of task are weighed by their relative ranking and combined into a single composite numerical score for each task. For example, in some embodiments,timing routine2230, priority routine2232 (which, includes location routine2234), andreagent routine2236 may calculate sub-scores related to the various task properties. The overall score obtained by combining the weighted individual sub-scores ultimately determines when the task can be scheduled and executed in relation to other competing tasks. For example, an overall score may be computed using the following equation.
• 
  OverallScore=(SubScore1*WeightingFactor1)+ . . . +(SubScoreN*WeightingFactorN)
• It should be noted that the computations above are exemplary only and other functions, including step functions, quadratic or higher order functions, or combinations of superimposed functions may also be used to compute the sub-scores and overall score. In some embodiments, the effect of the scores onstainer1000 may be modeled using the simulation capabilities ofStainer API Module1925 andStainer Hardware API1930 prior to actual use.
• In some embodiments, time-critical tasks are not passed through any filters, they are immediately advanced toscoring module2220 usingtiming routine2221,priority routine2222, andlocation routine2224 and an overall score calculated. In some embodiments, the overall scores are sorted usingsort routine2226 and the prioritized task list immediately advanced to execute routine2251 within executemodule2250. In some embodiments, the scoring of time-critical tasks may be based primarily on the execution time of each task. For example, time critical buffer and water rinse tasks may be scored using a different set of categories and the sub-scores may be weighed differently. Thus, for time-critical tasks, the earliest time of rinse application with respect to current run time may be accorded a high priority.
• Sorting routine2238 sorts tasks based on their overall scores and submits the prioritized task list for scheduling. In some embodiments,scheduler tasks module2240 examines the sorted list of tasks and schedules actual tasks and generates any prerequisite tasks. In some embodiments,scheduler tasks module2240 may process the sorted task list starting at the highest scoring task but then select one which can be executed immediately or whose preparatory tasks are capable of immediate commencement. In some embodiments, tasks directed to common functions may be grouped together usingreagent routine2241, mixing routine2242, orother routines2244 to minimize the generation and execution of additional tasks. For example, a reagent dispense task may use the syringe, use a specified quantity of a reagent of specific type, and may specify thatprobe10 be washed and the reagent aspirated before dispensing can take place. In some embodiments, preparatory tasks may be performed just in time in order to minimize potential delays such as waiting for the correct reagent or mix. Performing preparatory tasks just in time also avoids locking the scheduler into a specific sequence of actions ahead of time. In some embodiments, just in time scheduling may rely on a prediction of how long each task may take to execute. In some embodiments, parameters affecting task durations may be determined at the time of calibratingstainer1000 and stored in memory.
• In some embodiments, executetask module2250 executes time-critical and regular tasks using time-critical routine2251 and regular routine2252. In some embodiments, scheduled tasks submitted for execution may be turned into lower level commands issued to stainer1000 to perform physical actions. In some embodiments, translation of high level tasks to lower level tasks may be accomplished by calling appropriate functions withinstainer API module1925, which may encapsulate and abstract lower level functionality. In some embodiments, the scheduled execution of a regular task can be preempted at any time, if a time-critical task requests an immediate execution.
• FIG. 6B shows a flowchart of an exemplary method for determining regular and time-critical task lists. As shown inFIG. 6B, the algorithm loops continuously and the next task is processed instep2305. Instep2310, the task is examined to check whether it pertains to aslide1045 bypassing pre-treatment. Instep2325, the task may be further examined to check whether it pertains to a buffer about to expire and, if this is the case, then a new buffer rinse task is created instep2365 and the buffer rinse task is classified as time-critical instep2370. If the task is not aslide1045 bypassing pretreatment then it is examined instep2315 to determine if it is a rinse task. If the task is a rinse task then is classified as time-critical instep2370.
• In some embodiments, if the task is not a rinse task, then instep2320 it is examined to determine whether it is a dispense task. If instep2330, the dispense task is determined to relate to a sample whose buffer is about to expire and for which reagent may not be applied in time then, in step2355 a new buffer rinse task is created and the buffer rinse task is classified as time-critical instep2370. If the dispense task does not pertain to a sample whose buffer is about to expire then reagent availability is determined instep2340, followed bysyringe1015 availability instep2345 andmixer1050 availability instep2350. If all of these objects are available (or, if themixer1050 is not used by the task) then the task is added to the regular task list instep2375. If any of the objects is unavailable then the task is postponed, instep2360. Once a task has been processed, the algorithm returns to step2305 to process the next task on the sorted list.
• FIG. 6C shows a block diagram of anexemplary Fluidics Scheduler2020. In some embodiments,fluidics scheduler2020 may be an autonomous process and implemented as one or more threads, which run in a continuous loop within the context ofSCS1310. In some embodiments, a fluidics scheduler thread may run independently but may query other components for the data to create schedules and to coordinate task execution related to the schedules. In some embodiments,stainer1000 may have a limited set of conduits to convey fluids to and from the bulk fluids cart, or to remove waste from the stainer. Additionally, conduits and chambers withinstainer1000 may be periodically flushed to ensure that there is no reagent or fluid cross-contamination. Embodiments offluidics scheduler2020 operate to ensure that the conduits are available to fluids in a manner that ensures that fluids can be delivered to or removed from appropriate locations instainer1000 at appropriate points in time.Fluidics scheduler2020 allows the time-sharing of conduit resources to facilitate various operations performed bystainer1000.
• In some embodiments, the fluidics subsystem may have multiple conduits each of which may be controlled by multiple individual valves and pumps. Accordingly, fluidics scheduler may create and implement schedules permitting multiple actions to be taken in parallel, such as directing fluids along different fluid paths simultaneously. In some embodiments, individual control systems associated with the conduits may be inherently parallel. For example, a valve may stop the flow of fluid in one conduit, while another conduit is simultaneously removing waste fluid from the stainer. Therefore, in some embodiments,fluidics scheduler2020 may direct the execution of individual actions by coordinating a dynamic collection of autonomous threads, each responsible for executing distinct individual tasks.
• In some embodiments, a single run throughfluidics scheduler2020 may consist of checking eachslide drawer object2162 for a pending pretreatment request, generating a sequence of fluidics actions for each such request, and then directing the execution of any sequenced action when its scheduled time has arrived.Fluidics scheduler2020 may then loop back and repeat the cycle above.
• In some embodiments,slide drawer object2162 may provide information related to aslide drawer1040 including drawer identification information, drawer state, drawer pretreatment related information, drawer pretreatment sequence, drawer deparaffinization treatment protocol steps, drawer target retrieval treatment protocol steps, pending tasks, and processing tank fluid level which may be used byfluidics scheduler2020 in making scheduling decisions. In some embodiments, a schedule may include task related information such as an identifier, task originator, task command, task status, source and destination containers, fluid type, task start time, and duration. In some embodiments,fluidics scheduler2020 may use a list of shared fluidics resources, and interface withstainer API module1925 and stainer logic andschedulers module1935. In some embodiments, exemplary task commands could include pause, fill processing tank, empty processing tank, incubate in processing tank, heat processing tank, cool processing tank, flush processing tank, replenish processing tank and wait in processing tank. In some embodiments, commands may be executed by appropriate calls tostainer API module1925. Each command may perform numerous lower level individual steps to carry out the command. For example, an empty processing tank command requiring a fluid transfer, may cause valves to be opened, the pump to be started, the pump stopped when fluid transfer has completed, and the valves closed when the action has terminated.
• To illustrate the operation offluidics scheduler2020 an exemplary sequence of operations is described. For example, when a rack of slides is newly loaded intostainer1000 and determined to require deparaffinization,fluidics scheduler2020 obtains the treatment protocol steps and uses them to generate a comprehensive sequence of fluidics states. Accordingly, a five minute incubation ofslides1045 in a processing tank filled with solvent fluid may be part of a sequence. The incubation step is mapped into three distinct fluidics states: filling the processing tank from a solvent bottle, incubating theslides1045 for the specified five minute duration and draining the processing tank contents. During the period when the two fluid transfer phases are in progress, other processing tanks cannot use the conduit that is being used to effect the fluid transfer. However, the processing tanks may make use of any free conduits to perform other fluidic transfers. In some embodiments, some conduits may have dedicated functions. For example, one conduit may be dedicated for solvents, another for alcohol, and a third for water. Other resources such as the processing tank heating system, which may be used during the five minute incubation period, are nonexclusive-use resources. Thus, a number of processing tanks may be heated simultaneously. After sequences have been generated resource conflicts are resolved to create a schedule. In some embodiments, fluidics scheduler may ensure that the pretreatment process is not interrupted after it has been commenced.
• As shown inFIG. 6C,exemplary fluidics scheduler2020 includes generatesequences module2405,schedule sequences module2410, generatetasks module2425, collecttasks module2430, executetasks module2435, updatesequences module2440, and monitorprocessing tanks module2450. In some embodiments, executetasks module2435 inexemplary fluidics scheduler2020 may also generate several fluid transfer task execution threads2470-1 through2470-N to direct the performance of tasks scheduled for execution.
• In some embodiments, generatesequences module2405 interfaces with stainer logic andschedulers module1935 and examines activeslide drawer objects2162 to determine whether there are pending requests for pretreatment or processing tank rinse. If a pending request exists then generatesequences module2405 may use the appropriate treatment protocol to generate a sequence of steps for scheduling and execution. In some embodiments, the sequence of steps may relate to deparaffinization and/or target retrieval. An exemplary sequence of steps generated by generatesequences module2405 may include information such as steps related to processing tank filling and draining, processing tank rinses, whetherslides1045 are tipped during the process, and the resources for each step in order to provide the scheduler with sufficient information to make decisions. An exemplary sequence may include steps such as: fill processing tank with target retrieval fluid; turn on the processing tank heater and heat for 1 minutes; turn off heater and cool for J minutes; drain processing tank to waste; fill processing tank with water; incubate in water for K minutes; and drain processing tank to waste.
• In some embodiments,schedule sequences module2410 schedules drawer pretreatment sequences in order to optimize the use of shared fluidics resources. In some embodiments,schedule sequences module2410 may develop a schedule in order to reduce the duration of pretreatment phase for each drawer. Sequences may be run in parallel if they use different resources, or use the same resources at different time intervals. In some embodiments, currently executing fluidics sequences may get priority with respect to claims on shared resources.
• In some embodiments, utilization factors may be associated with each resource. When a resource may be shared its utilization factor is increased proportionately upon every allocation. When a resource is exclusive its utilization factor is 1 (100% utilization) whenever it is allocated. In some embodiments, each shared resource requested by the scheduled sequence may be checked at critical points by calculating its total utilization factor. In some embodiments, if a resource allocation would cause the utilization factor for a resource to exceed 100% at any point in time, the sequence being scheduled may be time shifted to resolve the conflict. Schedule sequence module operates iteratively and is based in part upon time at which pretreatment requests were made by each drawer.
• In some embodiments,schedule sequences module2410 obtains all sequences already scheduled and in progress. Next, shared resource data is initialized by initialize resources routine2415 based on the sequences already in progress. In some embodiments, each new sequence submitted for scheduling is examined for any shared resource conflicts by checking each resource usingcheck resource routine2420 iteratively. If another conflict is found, the sequence is time shifted again by an appropriate amount and all shared resources are rechecked. The process continues until a conflict free schedule is generated. In some embodiments, time shift amounts are calculated precisely to coincide with the points in time at which the utilization factors of the shared resources change. In some embodiments, shared fluidics resources could include fluidics paths (including bottle and processing tank valves, routing valves, pumps, and conduits), processing tanks, and heaters. In some embodiments, the scheduling process is repeated for each newly generated sequence.
• In some embodiments, generatetasks module2425 generates executable tasks from newly scheduled sequences. In some embodiments, generatetasks module2425 translates the sequence for each newly scheduled drawer from a format suitable for scheduling into a list of tasks with a format suitable for execution. The output of generatetasks module2425 could include actual task commands, a scheduled start time, a fluid id, and source and destination information.
• In some embodiments,collect tasks module2430 creates a list of ready-to-execute pretreatment tasks for all active slide drawer objects2162. In some embodiments, all slide drawer objects and their associated fluidics tasks may be monitored to identify ready-to-execute tasks, which are those tasks whose scheduled time has arrived.
• Executetasks module2435 can execute scheduled tasks. Fluid transfer tasks can be executed indirectly by interfacing withstainer API module1925 via dynamic task execution threads direct the performance of physical actions on valves and pumps. Other tasks, such as incubation, may be executed directly by starting their countdown timers. In some embodiments, task execution module may spawn several individual fluid transfer task execution threads2470-1 through2470-N that may execute in parallel to direct simultaneous fluid transfers along different paths. In some embodiments, each task submitted for execution is examined. For non-transfer tasks, where physical actions are not taken, the start of a new state may be recorded. In some embodiments, for tasks with physical actions, the applicable function instainer API module1925 may be invoked. In some embodiments, to execute a fluid transfers, task execution module may dynamically launch an appropriately initialized task execution thread. Each task execution thread can cause performance of lower-level actions by calling an appropriate function instainer API module1925.
• In some embodiments, fluidics transfer functions provided bystainer API module1925 may have a set of locks to prevent more than one task execution thread from gaining access to exclusive resources such as valves and pumps.
• In some embodiments, task execution threads2470-1 through2470-N may each execute a fluidics transfer thus allowing multiple simultaneous or overlapping fluidics transfers instainer1000. In some embodiments, threads2470-1 through2470-N may directly interact withstainer API module1925 to perform any lower level actions. Errors caused by equipment failure, or other external events encountered while executing an API function may also be handled by task execution threads2470-1 through2470-N. In some embodiments, errors may be handled by retrying the fluid transfers, pausing, or halting further processing tank processing, or disabling the processing tank.
• In some embodiments, updatesequences module2445 monitors timers, such as incubation timers instainer1000, records the completion of non-fluid transfer tasks, updates tasks and sequences as they complete, and detects conditions for rescheduling. When tasks complete, the task sequences for the drawers that originated the completed tasks are updated to reflect the actual machine state so that completed tasks are not repeatedly performed. Accordingly, updatesequences module2445 examines all currently executing tasks and updates the originating sequence to reflect completed tasks. In some situations, a task that cannot be completed because of abnormal conditions may be rescheduled.
• In some embodiments, exemplary monitorprocessing tanks module2450 executes non-scheduled, periodic actions and tasks such as monitoring processing tank levels and temperatures, and replenishing evaporated target retrieval fluid with de-ionized water to preventslides1045 from drying. In some embodiments, deviations from the acceptable incubation tolerances may be logged by monitorprocessing tanks module2450. In some embodiments, the level of target retrieval fluid in the processing tanks undergoing heating is also periodically monitored. For example, when the level of de-ionized water in a processing tank drops due to evaporation, it is replenished with more de-ionized water in order to preventslides1045 from drying out. In some embodiments, the transfer of de-ionized water to the processing tank may be accomplished through a task thread, which may interface withstainer API1925.
• FIG. 6D shows aflowchart2500 of an exemplary algorithm for scheduling and allocating resources forfluidics scheduler2020. In some embodiments, task pretreatment states are checked instep2505. States that have already been performed or that are currently in progress are skipped. If a task pretreatment state indicates that the task is not in progress, then each shared resource requested by that task is checked iteratively. The proportion of the next resource used by the task is calculated instep2510 and added to the utilization factor of the resource instep2520. If the utilization factor now exceeds 100% instep2525, then instep2530 the allocation of the resource is re-scheduled for the next point in time at which the resource utilization factor changes.Steps2525 and2530 are repeated until the allocation of the resource can be scheduled without conflict according to some embodiments of the algorithm. If the resource has been scheduled without conflict then steps2510 through2535 are repeated until all resources have been allocated. If the allocation of the resources has not caused a time shift in the original start time of the task then the algorithm returns to step2505 to process the next task. If a time shift to task start time has occurred as a result of resource conflicts, then instep2550 the task start time is updated to reflect the time shift and the algorithm returns to step2505 to process the next task
• In some embodiments,system thread2110,state process thread2120,control thread2130,robotic scheduler2020,fluidic scheduler2030,heater thread2140,UPS thread2150 and objects described above may be elements ofstainer logic component1935.
• FIG. 7 shows a block diagram of anexemplary API7000 for control of hardware sub-systems onstainer1000. Stainer hardware API may provide an interface to actual hardware components onstainer1000 that execute the physical tasks. Embodiments ofstainer hardware API1925 provide a commondevice base interface7075 and an object architecture that permits device decoupling. Commondevice base interface7075 allows external modules to view all hardware devices as sharing some common functionality. For example, from the viewpoint of an external module all devices may be seen to support a “LoadParameters” method, by which devices may load configuration defaults. Device decoupling ensures that software system functionality is unaffected by changes to hardware types and that the effect of any hardware changes is localized and limited to lower level components. Actual physical control over hardware onstainer1000 is exercised by several hardware device drivers7080. Thus, a call tostainer hardware API1930 may result in several device driver invocations to instruct hardware components onstainer1000 to take actions in consonance with parameters supplied to the call tostainer hardware API1930.
• In some embodiments,stainer hardware API1930 effects control over real world hardware by using actual device API objects that are tied to the underlying hardware. For example, exemplarystainer hardware API1930 may include objects related to the implementation of functionality such as digital and analog I/O object7010,robot object7020,syringe pump object7030,glyph decoder object7040,frame grabber object7050, andUPS object7060. A device object may contain data reflecting the state of the underlying hardware, and a functional interface indicating and allowing access to the underlying hardware. For example,robot object7010 may hold data indicating the current position ofrobot1032. In addition,robot object7010 may provide access to a “move_to(X,Y,Z)” function, which, if invoked, would culminate inrobot1032 moving to the position represented by the co-ordinates (X,Y,Z).
• In some embodiments,stainer hardware API1930 also uses a virtual device object for each actual device API object to provide a mechanism to interface with and support multiple types of hardware device types at run-time, by creating the correct derived object for the actual hardware device type in use. At run-time, a call tostainer hardware API1930 is translated to the actual hardware device type call using the interface specified by the virtual device object for that device type. Accordingly,exemplary stainer API1925 may include virtual device objects such as virtual digital and analog I/O7015,virtual robot7025,virtual syringe pump7035,virtual glyph decoder7045,virtual frame grabber7055, andvirtual UPS7065. In some embodiments, the objects above and others (not shown) may be part ofvirtual machine7005.
• IfSCS1310 is in a simulation mode, then the device call is intelligently simulated prior to the actual hardware call, usingsimulation module7070. In some embodiments, actual hardware is not exercised in simulation mode; insteadsimulation module7070 may return parameters to calling routines based on the underlying hardware that would normally have executed the actions of the API call. In some embodiments, all API calls are routed both to the simulator and to the actual device so thatsimulation module7070 can assist in diagnosing hardware behavior.
• In some embodiments, digital and analog I/O object7010 and associated virtual digital & analog I/O object7015 provide an interface to read or set system input and/or output facilitating control and monitoring of various devices in the system. An instance of the appropriate digital and analog I/O object may be created for each input and/or output present in the system. Access to an input or output may be provided through a digital/analog I/O object. In some embodiments, a master controller may handle the sending of digital and analog data to various boards in the system. In some embodiments, routines may be provided to control access to individual inputs and outputs, verify values written to, or read from an input or output, and to return the name and location of a specific input or output.
• In some embodiments,robot object7020 andvirtual robot object7025 may facilitate control of robot motion related functions, such as the motion ofexemplary robot1032.Virtual robot object7025 may define a minimal interface to facilitate control of robot motion related functions. If different kinds of robots are supported then one of these objects is created for each robot type. The decision on which one to use is controlled by configuration and selected at load time. In some embodiments,robot object7020 may provide control of robot movement in all three directions and of the air blower coupled to the robot.
• In some embodiments,syringe pump object7030 provides an interface to access and control the syringe pump, such asexemplary syringe pump1015, which facilitates the moving of reagents fromreagent bottles1080 onto theslides1045 being processed. Virtualsyringe pump object7035 may define a minimal interface for access and control of the syringe pump. If different kinds of syringe pump devices are supported then an object instance is created for each type of syringe pump, and the correct object may be selected and instantiated at run time when accessing and loading system configuration parameters.
• In some embodiments,glyph decoder object7040 provides an interface for decoding glyph type encodings, including InfoGlyphs™. Glyph decoding is the process of decoding the glyph in an image that may have been taken by a camera mounted onrobot1032 and acquired by a frame grabber. In some embodiments, after an image has been acquired using the frame grabber, the image is scanned and decoded byglyph decoder object7040. In some embodiments, decoding may be accomplished by sending image data to a decode library. In some embodiments, the decode library may be furnished by a third party provider. In some embodiments, the image may be filtered before it is sent to the library. In some embodiments, filtering may compensate for the effects of vibration, robot motion and other environmental factors. In some embodiments, any data decoded from the glyph image is returned to the calling process. Virtualglyph decoder object7045 defines a minimal interface for decoding glyph type encodings. If different kinds of glyph decoders are supported then an object instance is created for each type of glyph decoder.
• In some embodiments,frame grabber object7050 provides an interface to access and control the image acquisition system. In some embodiments, frame grabber object may provide an interface to a sensory hardware board that can acquire images from the camera located on therobot head1032. In some embodiments, frame grabber hardware may be configured to return images of a given size and format. In some embodiments, an acquired image may be stored in a bit-mapped format in previously allocated frame-buffer memory and made available to the calling routine. In some embodiments, the acquired images may be checked to prevent duplicates. In some embodiments,virtual object7055 may define a minimal interface. If different kinds of frame grabbers are supported then an object instance is created for each type of frame grabber.
• In some embodiments,UPS object7070 provides an interface to access and control thesystem UPS1298 to determine if a power fail state has occurred, to monitor line parameters, and to handle various timing parameters for power reduction, shutdown and user alerts.Virtual UPS object7075 may define a minimal interface. If different kinds ofUPS devices1298 are supported then an object instance is created for each type of UPS.
• FIG. 8A shows a state transition diagram tracking slide state transitions for exemplarystate process thread2120. As shown inFIG. 8A, upon initialization instep8010,state process thread2120 loads specifiedslide objects2166 into a list and enters a continuous loop. During each iteration of the loop,state process thread2120 may transitionmultiple slide objects2166 from one state to another to reflect the processing status of the underlying slides1045. Accordingly, the state ofslide object2166 may move from state empty8015, which reflects that no slide is present, to state pending8020 when aslide1045 is introduced into the rack. After processing has started, aslide1045 may move todeparaffinizing state8025, followed bytarget retrieving state8030, andstaining state8035. During any of these states, if aslide1045 requests fluids or reagents to be allocated,control thread2130 is informed so that additional actions may be commenced. After staining is complete, theslide1045 moves to completedstate8040. In some embodiments, each state may have sub-states to reflect individual processes within the states. Treatment protocol errors result in aslide1045 ending in a finalspoiled state8050. In some embodiments, aslide1045 spoiled due to treatment protocol errors may continue to move through states normally but may be marked spoiled only at the conclusion of the staining process. Continuing to process aslide1045 normally allows an operator to make an informed decision regarding the slide sample based on a visual inspection, the actual final state of theslide1045, the slide log, and the seriousness of the reported deviation from treatment protocol.
• FIG. 8B shows aflowchart8100 for a state process thread instance showing steps in an exemplary method for slide drawer and reagent rack processing. In some embodiments, exemplarystate process thread2120 may be a part of stainer logic andschedulers module1935. As shown inFIG. 8B,state process thread2120 may start instep8105. Instep8110,state process thread2120 may go through an initialization routine during which it loadsslide drawer objects2162 andreagent rack objects2164 into lists.
• In some embodiments,state process thread2120 may enter a continuous loop following the initialization step during which it periodically processes pending events associated with the loadedslide drawer2162 and reagent rack objects2164. For example, instep8115, exemplarystate process thread2120 may examine slide drawer objects for pending events. If a resource allocation request, such as a pretreatment fluid request, associated with aslide drawer object2162 is pending instep8120, thenstate process thread2120 may trigger the allocation instep8125 usingcontrol thread2130. Next, instep8130state process thread2120 may examinereagent rack objects2164 for pending events. If a resource allocation request, such as a read glyph request, associated with areagent rack object2164 is pending instep8135, thenstate process thread2120 may trigger the allocation of the resource instep8140 usingcontrol thread2130. In some embodiments, the processing of eachslide drawer object2162 and eachreagent rack object2164 may be an autonomous process that is independent from processes for other drawers and racks. If a shutdown is requested instep8145, thestate process thread2120 terminates instep8150, otherwise it may return to step8110 for the next iteration of the loop.
• FIG. 9 shows a flowchart for a control thread instance showing steps in an exemplary method for container and waste-processing. In some embodiments, upon starting instep9005,system thread2110 proceeds toinitialization step9010 where it loads a list of all input and output addresses and/or ports and initializes sensors. In some embodiments,system thread2110 may then enter a continuous loop. On each loop iteration,system thread2110 processes: bottle sensors instep9015; hazardous waste pull requests instep9020; waste pull requests instep9025; monitors input-output ports and on-board communications instep9030; and processes logging tasks instep9040.
• In some embodiments, instep9015,system thread2110 monitors all sensors oncontainers1299 onfluidics cart1295, and provides information about fluid level states oncontainer1299 to other sub-components ofstainer logic module1935 and to thestainer GUI1940. In some embodiments, the readings of the bottle sensors may be averaged over a time period to diminish the effect of fluid motion and obtain a more accurate fluid level reading.
• Instep9020, hazardous waste pull requests are processed. Hazardous waste pull involves the removal of hazardous waste from stainer processing tanks followed by deposition of the waste into hazardous waste containers in the fluidics cart. Instep9025, normal (non-hazardous) waste requests are processed. In some embodiments,system thread2110 manages and processes all waste pull requests and ensures that different systems requesting waste pulls get adequate time.
• Instep9030, thesystem thread2110 also monitors all system boards for loss of communication. Instep9035, if an error such as a communication loss is detected, then the error condition may be logged and the board reset instep9045. In some embodiments, instep9040,system thread2110 may log various sensor conditions at periodic intervals. If system thread detects a shutdown request instep9050, then the thread terminates instep9060, otherwise it returns to step9015 for the next iteration of the loop. In some embodiments,system thread2110 may run in the background while performing waste pull, container level monitoring, and electronic board communications and status monitoring functions.
• FIG. 10 shows aflowchart10000 for a control thread instance showing steps in an exemplary method for Graphical User Interface (“GUI”) and alert processing according to some embodiments of the present invention. In some embodiments,control thread2130 handles reagent allocation, stainer GUI updates and interactions, and server and time updates.
• In some embodiments,control thread2130 starts instep10305 and performs initialization routines instep10310 before entering a continuous loop. In some embodiments, initialization routines may include loading lists of objects. On each loop iteration,control thread2130 checks for requests associated with the objects and processes the requests.
• Instep10315,control thread2130 may check for pending allocation requests. For example, a pending reagent allocation may have been triggered bystate process thread2120 in response to a pending request associated with aslide object2166. If an allocation request is pending, the allocation may be performed instep10340.Control thread2130 can then check for alert requests in step320 and may update the GUI accordingly instep10325. Instep10330, server and time updates can be processed. If a shutdown request is detected instep10335, then instep10350control thread2140 terminates and performs termination related tasks, otherwise it proceeds to step10315 where it commences another iteration.
• FIG. 11 illustrates an exemplaryGUI screen hierarchy11000 for theStainer Control Software1310 according to some embodiments of the present invention. Each stainer, such asexemplary stainer1000, can have SCSmain screen11040 from which a user may navigate to other screens. In some embodiments, SCSmain screen11040 may provide a snapshot of the status ofstainer1000. For example, SCSmain screen11040 may provide a graphical depiction ofslide racks1065,reagent racks1060, andfluid cart1295 with colors used to display the status ofslides1045, reagents inreagent bottles1080, andfluid containers1299. In some embodiments, an estimated remaining process time may be displayed for each rack that is currently in use. In some embodiments, the SCS main screen may be automatically returned to from other sub-screens after a defined period of user input inactivity.
• In some embodiments, each graphical icon may act as an entry point to a more detailed lower level screen. Thus, SCSmain screen11040 may allow a user access to sliderack screen11010, which in turn links to slidedetail screen11005. In some embodiments,slide rack screen11010 may display anindividual slide rack1065 and provide a user with additional options to obtain details ofslide rack1065 or to accessslide detail screen11005.
• SCSmain screen11040 may also provide a link toreagent rack screen11020, which in turn links toreagent detail screen11015.Reagent rack screen11020 may display details of reagent racks and provide a user with additional options to obtain details ofreagent rack1060 or to accessreagent detail screen11015. In some embodiments,cart dialog screen11030, which provides access tocontainer detail screen11025, may be accessed from SCSmain screen11040.Cart dialog screen11030 may display details of the fluidics cart and provide a user with additional options to obtain fluidics cart related details or to accesscontainer detail screen11025.
• SCSmain screen11040,slide rack screen11010,slide detail screen11005,reagent rack screen11020,reagent detail screen11015,cart dialog screen11030, andcontainer detail screen11025 may represent typical screens that can be accessed by SCS operators during normal operation ofstainer1000. In some embodiments, SCSmain screen11040 receives GUI updates fromcontrol thread2130. Asslide object2166,slide drawer object2162,reagent object2168, and reagent racks object2164 change states, the GUI corresponding to SCSmain screen11040 can be updated to display the current state.
• Tools screen11045 provides access toutility screen11055, which allows access to a MATtest dialog screen11065, subsystemtest dialog screen11070, andstainer configuration screen11075. In some embodiments, screens below tools screen11045 provide access to stainer related diagnostic, configuration, test, cleaning and administrative functions, and may be utilized when stainer1000 is in an idle mode. In some embodiments, an operator may be requested to enter a tool access password to gain access to dialogs and screens belowtools screen11045. In some embodiments, successful access totools screen11045 and lower level screens may takestainer1000 out of a normal run mode and place it in an idle state in preparation for further user commands. Tools screen11045 also provides access to astainer cleaning menu11060 and ashutdown screen11080. In some embodiments,alert screen11035 may be a pop-up screen that may pop-up or flash whenever stainer1000 issues an operator alert. In some embodiments, at every screen, a contextsensitive help screen11050 allows an operator to access help relevant to the function that the operator is performing.
• FIG. 12 shows exemplary sliderack dialog screen11010 according to some embodiments of the present invention. As shown inFIG. 12, slide rack dialog screen displaysiconic representations12010 forslides1045 in one of the slide racks12045. Anexemplary label12020 indicates that theslides1045 displayed inFIG. 12 belong to sliderack3. In some embodiments, the slide icons may be color coded to indicate slide status and shaded areas without an icon may indicate empty rack positions. Details of eachslide1045 are shown inslide detail area12015 and additional details about aparticular slide1045 may be obtained by selecting that slide. Sliderack dialog screen11010 provides an operator with options to: cancel a rack ofslides12025; set slides tohigh priority12030; set slides tonormal priority12035; or set slides tolow priority12040.
• In some embodiments, a set oficons12050 provide access to other screens from any screen in a stainer. For example, the wrench icon provides access totools screen11045; the question mark icon provides access to contextsensitive help screen11050 for sliderack dialog screen11010; an exclamation icon provide access toAlerts dialog screen11035; and a hand icon provides access to a stainer stop dialog screen ifstainer1000 is currently actively processing slides. In some embodiments, standard GUI components, such as those available in Microsoft Windows, may be used to display the information held inslide object2166,reagent object2168,slide drawer object2162, andreagent rack object2164. In some embodiments,stainer1000 may provide a touch screen on the front panel from which a user may access the various screens.
• FIG. 13 shows an exemplary reagentrack dialog screen11020 according to some embodiments of the present invention. As shown inFIG. 13, reagentrack dialog screen11020 displays anicon13020 indicating the status of one of reagent racks13050. For example,FIG. 13 shows details forreagent rack2. Additionally, icons forindividual reagent bottles13010 may indicate the status of individual bottles onreagent rack1060 and may provide an access point for an operator to get reagent bottle details. In some embodiments, the icons for the bottles may be color coded to indicate the bottle status. In some embodiments,details13040 of the content of each bottle in thereagent rack1060 may be displayed. Icon set12050 may provide access to other screens forstainer1000.
• FIG. 14 shows an exemplarycart dialog screen11030 according to some embodiments of the present invention. As shown inFIG. 14,cart dialog screen11030 may display icons forcontainers14030 on the fluidics cart. In some embodiments, ahazardous materials icon14040 may flag aparticular container1299 onfluidics cart1295 as containing hazardous materials. In some embodiments, for eachcontainer1299 influidics cart1295container position indicator14010 anddescription14020 details the contents of the container. In some embodiments, a dialogbox containing messages14050 and14060 may provide an operator with information regarding the quantity of fluid remaining.
• An improved method and apparatus for pre-treatment of biological samples have been disclosed and described according to some preferred exemplary embodiments. Those skilled in the art can now appreciate, from the foregoing description, that the broad techniques of the embodiments of the present invention can be implemented in a variety of forms. Therefore, while the embodiments of this invention have been described in connection with particular examples thereof, the true scope of the embodiments of the present invention should not be so limited since many variations and equivalents of the method and the apparatus may be carried out without departing from the scope of the invention.
• Further, methods described herein according to embodiments of the invention may conveniently be implemented using program modules, hardware modules, or a combination of program and hardware modules. Such modules, when executed, may perform the steps and features disclosed herein, including those disclosed with reference to the exemplary flow charts shown in the figures. The operations, stages, and procedures described above and illustrated in the accompanying drawings are sufficiently disclosed to permit one of ordinary skill in the art to practice the invention. Moreover, there are many computing elements, programming languages and tools, and operating systems that may be used in practicing embodiments of the instant invention and, therefore, no detailed computer program could be provided that would be applicable to these many different systems. Each user of a particular system will be aware of the language, hardware, and tools that which are most useful for that user's needs and purposes.
• The above-noted features and aspects of the present invention may be implemented in various environments. Such environments and related applications may be specially constructed for performing the various processes and operations of the invention, or they may include a general-purpose system or computing platform selectively activated or reconfigured by program code to provide the functionality.
• Embodiments of the present invention also relate to computer readable media that include program instructions or program code for performing various computer-implemented operations based on the methods and processes of embodiments of the invention. The program instructions may be those specially designed and constructed for the purposes of the invention, or they may be of the kind well known and available to those having skill in the computer software arts. Examples of program instructions include, for example, machine code, such as produced by a compiler, and files containing a high-level code that can be executed by the computer using an interpreter.
• Other embodiments of the invention will be apparent to those skilled in the art from consideration of the specification and practice of the embodiments of the invention disclosed herein. It is intended that the specification and examples be considered as exemplary only, with a true scope and spirit of the invention being indicated by the following claims. As such, the invention is limited only by the following claims.

Claims (2)

1. A method comprising steps for adaptively scheduling robot tasks in a time interval for a robot coupled to a stainer, wherein the robot treats slides coupled to the stainer according to a treatment protocol with reagents in reagent bottles or fluid containers coupled to the stainer, the steps comprising:

creating a robot task list comprising all robot tasks that are ready for execution within the time interval;

calculating a robot task priority for each robot task in the robot task list;

sorting the robot task list in descending order of robot task priority; and

adding robot tasks starting from the top of the sorted robot task list to a robot task execution queue until the robot is fully utilized in the time interval or the robot task list is exhausted.

2-20. (canceled)

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