A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay.
Large-scale image sets acquired by automated microscopy of perturbed samples enable a detailed comparison of cell states induced by each perturbation, such as a small molecule from a diverse library. Highly multiplexed measurements of cellular morphology can be extracted from each image and subsequently mined for a number of applications.



This microscopy dataset includes 919 265 five-channel fields of view, representing 30 616 tested compounds, available at "The Cell Image Library" (CIL) repository. It also includes data files containing morphological features derived from each cell in each image, both at the single-cell level and population-averaged (i.e., per-well) 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 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, such as 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.
Imaging Platform.
Mark-Anthony
MA
Bray
Chemical Biology and Therapeutics Science Program.
Sigrun M
SM
Gustafsdottir
Imaging Platform.
Mohammad H
MH
Rohban
Imaging Platform.
Shantanu
S
Singh
Imaging Platform.
Vebjorn
V
Ljosa
Imaging Platform.
Katherine L
KL
Sokolnicki
Center for the Development of Therapeutics.
Joshua A
JA
Bittker
Chemical Biology and Therapeutics Science Program.
Nicole E
NE
Bodycombe
Chemical Biology and Therapeutics Science Program.
Vlado
V
Dancík
Center for the Development of Therapeutics.
Thomas P
TP
Hasaka
Chemical Biology and Therapeutics Science Program.
Cindy S
CS
Hon
Chemical Biology and Therapeutics Science Program.
Melissa M
MM
Kemp
Chemical Biology and Therapeutics Science Program.
Kejie
K
Li
Chemical Biology and Therapeutics Science Program.
Deepika
D
Walpita
Chemical Biology and Therapeutics Science Program.
Mathias J
MJ
Wawer
Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA, 02142.
Todd R
TR
Golub
Chemical Biology and Therapeutics Science Program.
Stuart L
SL
Schreiber
Chemical Biology and Therapeutics Science Program.
Paul A
PA
Clemons
Chemical Biology and Therapeutics Science Program.
Alykhan F
AF
Shamji
Imaging Platform.
Anne E
AE
Carpenter
D002460:Cell Line; D002477:Cells / Q000187:drug effects / Q000648:ultrastructure; D006801:Humans; D007091:Image Processing, Computer-Assisted; D054852:Small Molecule Libraries
D054852:Small Molecule Libraries
U2OS; cellular morphology; high-content screening; image-based screening; phenotypic profiling; small-molecule library