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TissueMAPS is a software framework for distributed analysis and interactive visualization of large-scale, high-dimensional microscopy image datasets.

Online documentation is available atdocs.tissuemaps.org.

TissueMAPS uses a distributed client-server model. The server exposesRESTful web services and clients interact with the server via theREST API using either the browser-based user interface or other client interfaces.

The easiest way to set up your own server for development and testing is to use either the pre-build container images available onDocker Hub or the pre-build virtual machines images forAmazon Web Services (AWS):

To run the containerizedTissueMAPS server, clone the repository and bring up the containers usingDocker Compose:

git clone https://github.com/tissuemaps/tissuemaps ~/tissuemapscd ~/tissuemapsdocker-compose up -d

To run aTissueMAPS server in a cloud virtual machine, launch a new instance from one of the sharedAmazon Machine Images (AMIs) using theElastic Compute Cloud (EC2) console. To find theTissueMAPS images, filter public AMIs in theFrankfurt region forAMI Name: TissueMAPS server (seeAWS documentation).

For further details and alternative installation options, please refer to theinstallation guide of the online documentation.

Once you have access to a running server instance, you can interact with it viaHTTP protocol.

The easiest way is to interact with the server is via the web-based user interface. To this end, point your web browser tohttp://localhost:8002 when running the server within a container. Otherwise, just point the browser to the public IP address of your cloud virtual machine. This will redirect you to the login page. Once you have authenticated yourself using your credentials, you will see a list of your existing experiments.

Alternatively, you could usecURL to access resources via the command line:

Authenticate with your credentials:

curl --data '{"username": "devuser", "password": "123456"}' --header "Content-Type:application/json" http://localhost:8002/auth

List your existing experiments using the receivedJSON web token (replaceXXX with the actual access token):

curl --header "Content-Type:application/json" --header "Authorization:JWT XXX" http://localhost:8002/api/experiments

TissueMAPS also provides a Python client that abstracts theHTTP interface and facilitas interaction with the server. You can install it via thepip Python package manager:

pip install tmclient

List your existing experiments using thetm_client command line tool:

tm_client -H localhost -P 8002 -u devuser -p 123456 experiment ls

Or using thetmclient Python package:

fromtmclientimportTmClientclient=TmClient(host='localhost',port=8002,username='devuser',password='123456')experiments=client.get_experiments()print(experiments)

Client code is licensed underApache 2.0 and server code underGNU Affero General Public License 3.0.

For more information please refer to thelicense section of the online documentation or theLICENSE.txt files in the individual Github repositories.