awesome-cytodata

A curated list of awesome cytodata resources

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Curated Resources

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A BaSiC tool for background and shading correction of optical microscopy imagesMethods
Illumination-correction method accounting for space- and time-dependent biases.
Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional NetworksMethods
End-to-end learning with CNNs to predict bioactivity of small molecules in unrelated assays using image-based profiles.
A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cellsApplications
Profiling the morphological changes induced in 1280 compounds in 12 knockout cell lines.
A map of directional genetic interactions in a metazoan cellApplications
Characterizing genetic interactions by integrating 21 phenotypic descriptors.
A multi-scale map of cell structure fusing protein images and interactionsApplications
Combining confocal imaging and mass spectrometry representations of proteins to predict physical proximity and characterize cellular organization.
Applications in image-based profiling of perturbationsReviews
Describe applications of image-based profiling including target and MOA identification, lead hopping, library enrichment, gene annotation and identification of disease-specific phenotypes

Access from GitHubGenetic Perturbations
3,456 cell painting profiles from CRISPR experiments knocking down 59 genes in A549, ES2, and HCC44 cells (
Bray et al. 2017Chemical Perturbations
Cell painting profiles from 30,616 compounds in U2OS cells (Center Driven Research Project
Bray et al. 2017Download from GigaDBChemical Perturbations
Access from public S3 bucket:).
Broad Bioimage Benchmark CollectionRaw Images
The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets. In addition to the images themselves, each set includes a description of the biological application and some type of "ground truth" (expected results).
Haghighi et al. 2021Chemical Perturbations
Cell painting matched to L1000 profiles in 4 experiments, including compound and genetic screens (
Human Protein AtlasRaw Images
Among other assays, the HPA performed confocal imaging of displaying the location of more than 2/3 of human proteins in cell lines.

Advanced Cell Classifier
A software package for exploration, annotation and classification of cells within large datasets using machine learning.
BioProfiling.jl
Toolkit for filtering and curation of morphological profiles in Julia.
CellProfiler
CellProfiler is a free open-source software for measuring and analyzing cell images.
CellProfiler Analyst
Interactive data exploration, analysis, and classification of large biological image sets.
Cytominer
Methods for image-based cell profiling in R.
EBImage
Image processing toolbox for R.

Showing a sample of 85 resources. View the full list on GitHub →