Supporting data for "A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay"

Dataset type: Imaging
Data released on December 05, 2016

Bray MA; Gustafsdottir SM; Ljosa V; Singh S; Sokolnicki KL; Bittker JA; Bodycombe NE; Dančík V; Hasaka TP; Hon CS; Kemp MM; Li K; Walpita D; Wawer MJ; Golub TR; Schreiber SL; Clemons PA; Shamji AF; Carpenter AE (2016): Supporting data for "A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay" GigaScience Database.


Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each treatment. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications.
This microscopy dataset includes 919,874 five-channel fields of view representing 30,616 tested compounds. The images are available at The Cell Image Library repository. All additional data files are available from GigaDB, including; morphological features derived from each cell in each image, both at the single-cell level and population-averaged (i.e., the per-image level); the image analysis workflows that generated the morphological features are also provided. Quality-control metrics are provided as metadata, indicating fields of view that are out-of-focus (blurry) or containing highly fluorescent material or debris. Lastly, chemical annotations are supplied for the compound treatments applied.
Because computational algorithms and methods for handling single-cell morphological measurements are not yet routine, the dataset serves as a useful resource for the wider scientific community applying morphological (image-based) profiling. The dataset can be mined for many purposes, including small-molecule library enrichment and chemical mechanism-of-action studies, including target identification. Integration with genetically-perturbed datasets could enable identification of small-molecule mimetics of particular disease- or gene-related phenotypes that could be useful as probes or potential starting points for development of future therapeutics.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 28327978)

Related datasets:

doi:10.5524/100200 IsPreviousVersionOf doi:10.5524/100351 (It is a more recent version of this dataset)

There is a new version of this dataset available at: DOI: 10.5524/100351

Additional information:

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
U2OS cell line9606HumanhumanHomo sapiens Sex:female [PATO:0000383]
Disease status:osteocarcoma
Displaying 1-1 of 1 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
tabular dataUNKNOWN4.95 MB2016-08-02
tabular dataUNKNOWN18.12 KB2016-08-02
md5sum valuesTEXT22.05 KB2016-11-15
Scriptarchive14.61 KB2016-08-02
U2OS cell lineMixed archiveTAR379.07 MB2016-08-02
U2OS cell lineMixed archiveTAR330.92 MB2016-08-02
U2OS cell lineMixed archiveTAR337.22 MB2016-08-02
U2OS cell lineMixed archiveTAR363.61 MB2016-08-02
U2OS cell lineMixed archiveTAR371.13 MB2016-08-02
U2OS cell lineMixed archiveTAR344.36 MB2016-08-02
Displaying 1-10 of 418 File(s).
Funding body Awardee Award ID Comments
National Science Foundation CAREER DBI-1148823 Anne E Carpenter (for publishing costs)
Date Action
December 5, 2016 Dataset publish
December 13, 2016 External Link added :
January 9, 2018 Manuscript Link added : 10.1093/gigascience/giw014
April 27, 2022 Manuscript Link updated : 10.1093/gigascience/giw014