cellprofiler
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Open-source software for exploring and analyzing large, high-dimensional image-derived data.
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Aug 15, 2024 - Python
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
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Mar 9, 2025
Python package for processing image-based profiling data
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Mar 12, 2025 - Python
A pixel classification based multiplexed image segmentation pipeline
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Dec 5, 2023 - Jupyter Notebook
A curated list of awesome cytodata resources
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Nov 15, 2023
Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
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Feb 20, 2025 - Python
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
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Mar 17, 2025 - Python
Image-based Profiling Handbook
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Mar 21, 2024
High-dimensional phenotyping to define the genetic basis of cellular morphology
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Jan 24, 2023 - Jupyter Notebook
Running cellprofiler on eddie3 / SGE clusters
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Jun 24, 2021 - Python
slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.
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Oct 31, 2024 - Shell
Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
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Mar 13, 2025 - Jupyter Notebook
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Apr 25, 2024 - Jupyter Notebook
Tutorial for single cell analysis of nuclear translocation measured by timelapse imaging
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May 20, 2020 - R
Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6, unet and classify
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Aug 2, 2021 - Python
Tools for Processing Results from CellPainting Assay
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Nov 15, 2017 - Python
CellProfiler pipeline and ImageJ workflow developed for segmentation of H2B_FUCCI2a_MCF7 cell nuclei for per-nucleus and background fluorescence intensity measurement. Example workflows for downstream cell cycle analysis are also provided in this repository.
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Jan 28, 2025 - R
Singularity-based linux container with CellProfiler 4 pre-installed into it.
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Feb 15, 2022 - Shell
Analyzing Cell Painting results with Dask and Pandas - not yet ready for use by others
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May 24, 2018 - Python
Automated image analysis of colony formation assay experiments, using Cell profiler and R markdown
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Jul 6, 2017 - HTML
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