Open-source software for exploring and analyzing large, high-dimensional image-derived data.
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Updated
Mar 12, 2024 - Python
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
A pixel classification based multiplexed image segmentation pipeline
A curated list of awesome cytodata resources
Python package for processing image-based profiling data
Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
Image-based Profiling Handbook
High-dimensional phenotyping to define the genetic basis of cellular morphology
slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.
Running cellprofiler on eddie3 / SGE clusters
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
Tutorial for single cell analysis of nuclear translocation measured by timelapse imaging
Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
Image-based analysis of cardiac fibroblast datasets to uncover proprietary drug impact on reversing fibrosis
Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6, unet and classify
Tools for Processing Results from CellPainting Assay
Singularity-based linux container with CellProfiler 4 pre-installed into it.
R scripts to clean/analyse CellProfiler output, forked from
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