Cell Painting Gallery

Documentation for https://registry.opendata.aws/cellpainting-gallery

Citation

All the data will be released with CC0 1.0 Universal (CC0 1.0). However, please cite the appropriate resources/publications, listed below, when citing individual datasets. For example,

We used the dataset cpg0000 (Chandrasekaran et al., 2022), available from the Cell Painting Gallery on the Registry of Open Data on AWS (https://registry.opendata.aws/cellpainting-gallery/).

Available datasets

All datasets are generated using Cell Painting unless indicated otherwise.

The datasets are stored with the prefix indicated by the dataset name. E.g. the first dataset is located at s3://cellpainting-gallery/cpg0000-jump-pilot and can be listed using aws s3 ls --no-sign-request s3://cellpainting-gallery/cpg0000-jump-pilot/ (note the / at the end).

The datasets' accession numbers are the first seven characters of the dataset name. E.g. the accession number of the first dataset is cpg0000.

Dataset name Description Publication to cite IDR accession number
cpg0000-jump-pilot 300+ compounds and 160+ genes (CRISPR knockout and overexpression) profiled in A549 and U2OS cells, at two timepoints 3
cpg0001-cellpainting-protocol 300+ compounds profiled in U2OS cells using several different modifications of the Cell Painting protocol 6
cpg0002-jump-scope 300+ compounds profiled in U2OS using different microscopes and settings 7
cpg0003-rosetta 28,000+ genes and compounds profiled in Cell Painting and L1000 gene expression 5
cpg0004-lincs 1,571 compounds across 6 doses in A549 cells 4 idr0125
cpg0012-wawer-bioactivecompoundprofiling 30,000 compound dataset in U2OS cells 1,2 idr0016
cpg0015-heterogeneity 2,200+ compounds and 200+ genes profiles in U2OS cells 8 idr0016,idr0036, idr0033

Downloading from Cell Painting Gallery

See Folder Structure for a complete description of data organization in Cell Painting gallery. Note that for each dataset you can download just images, just extracted features and metadata, or both. Note also that many datasets contain separate batches and you may want a subset of available batches.

If you'd like to just browse the data, it's a lot easier to do so using a storage browser.

Publications using datasets in Cell Painting Gallery

First Author
Title
Year
Publication URL
Dataset Name in Gallery
1 Wawer Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling 2014 https://doi.org/10.1073/pnas.1410933111 cpg0012-wawer-bioactivecompoundprofiling
2 Bray A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay 2017 https://doi.org/10.1093/gigascience/giw014 cpg0012-wawer-bioactivecompoundprofiling
3 Chandrasekaran Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations 2022 https://doi.org/10.1101/2022.01.05.475090 cpg0000-jump-pilot
4 Way Morphology and gene expression profiling provide complementary information for mapping cell state 2022 https://doi.org/10.1101/2021.10.21.465335 cpg0004-lincs
5 Haghighi High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations 2022 https://doi.org/10.1101/2021.09.08.459417 cpg0003-rosetta
6 Cimini Optimizing the Cell Painting assay for image-based profiling 2022 https://doi.org/10.1101/2022.07.13.499171 cpg0001-cellpainting-protocol
7 Jamali 2022 In Preparation cpg0002-jump-scope
8 Rohban Capturing single-cell heterogeneity via data fusion improves image-based profiling 2019 https://doi.org/10.1038/s41467-019-10154-8 cpg0015-heterogeneity

Contributing to Cell Painting Gallery

See Folder Structure for the required folder structure of your data. See Upload for a complete description of how to upload to the Cell Painting gallery bucket.

Any data contributions to Cell Painting Gallery must be accompanied by a pull request to this repository with updates to this README to add your dataset to Available datasets and Publications.

Complementary Datasets

For other sources of publicly available Cell Painting datasets we encourage you to explore: