Human U2OS cells – compound-profiling Cell Painting experiment

Accession number BBBC022 · Version 1

Example images

Description of the biological application

Phenotypic profiling attempts to summarize multiparametric, feature-based analysis of cellular phenotypes of each sample so that similarities between profiles reflect similarities between samples. This image set provides a basis for testing image-based profiling methods wrt. to their ability to distinguish the effects of small molecules.

Images

The images are of U2OS cells treated with each of 1600 known bioactive compounds and labeled with six labels that characterize seven organelles (the “Cell Painting” assay).

This pilot experiment consists of 20 plates. Each plate has 384 wells and each well has 9 fields of view for a total of 69,120 fields of view. Each field was imaged in five channels (detection wavelengths), and each channel is stored as a separate, grayscale image file, so there are 345,600 image files in 16-bit TIFF format. The images were taken at 20X magnification (0.656 μm/pixel).

The images are provided in 100 zip archive files, one for each combination of plate and channel. There is a list of the URLs of all 100 files to facilitate downloading the entire image set in batch.

…20585w1.zip …20585w2.zip …20585w3.zip …20585w4.zip …20585w5.zip
…20586w1.zip …20586w2.zip …20586w3.zip …20586w4.zip …20586w5.zip
…20589w1.zip …20589w2.zip …20589w3.zip …20589w4.zip …20589w5.zip
…20590w1.zip …20590w2.zip …20590w3.zip …20590w4.zip …20590w5.zip
…20591w1.zip …20591w2.zip …20591w3.zip …20591w4.zip …20591w5.zip
…20592w1.zip …20592w2.zip …20592w3.zip …20592w4.zip …20592w5.zip
…20593w1.zip …20593w2.zip …20593w3.zip …20593w4.zip …20593w5.zip
…20594w1.zip …20594w2.zip …20594w3.zip …20594w4.zip …20594w5.zip
…20595w1.zip …20595w2.zip …20595w3.zip …20595w4.zip …20595w5.zip
…20596w1.zip …20596w2.zip …20596w3.zip …20596w4.zip …20596w5.zip
…20607w1.zip …20607w2.zip …20607w3.zip …20607w4.zip …20607w5.zip
…20608w1.zip …20608w2.zip …20608w3.zip …20608w4.zip …20608w5.zip
…20625w1.zip …20625w2.zip …20625w3.zip …20625w4.zip …20625w5.zip
…20626w1.zip …20626w2.zip …20626w3.zip …20626w4.zip …20626w5.zip
…20630w1.zip …20630w2.zip …20630w3.zip …20630w4.zip …20630w5.zip
…20633w1.zip …20633w2.zip …20633w3.zip …20633w4.zip …20633w5.zip
…20639w1.zip …20639w2.zip …20639w3.zip …20639w4.zip …20639w5.zip
…20640w1.zip …20640w2.zip …20640w3.zip …20640w4.zip …20640w5.zip
…20641w1.zip …20641w2.zip …20641w3.zip …20641w4.zip …20641w5.zip
…20646w1.zip …20646w2.zip …20646w3.zip …20646w4.zip …20646w5.zip

Metadata

The file BBBC022_v1_image.csv (35 MB) contains the metadata in CSV format, with the following fields:

Field nameExplanation
ImageNumbera number between 1 and 69,120 identifying the field
Image_FileName_OrigERname of image file for the con A channel
Image_FileName_OrigHoechstname of image file for the Hoechst 33342 channel
Image_FileName_OrigMitoname of image file for the MitoTracker Deep Red channel
Image_FileName_OrigPh_golginame of image file for the WGA/phalloidin channel
Image_FileName_OrigSytoname of image file for the SYTO 14 channel
Image_Metadata_ASSAY_WELL_ROLE"compound" or "mock"
Image_Metadata_BROAD_IDidentifies the compound
Image_Metadata_CLSID
Image_Metadata_CPD_MMOL_CONCconcentration of the compound
Image_Metadata_CPD_PLATE_MAP_NAMEname of plate map (stock plate)
Image_Metadata_CPD_SMILESstructure of the compound
Image_Metadata_CPD_WELL_POSITIONposition of well on the plate
Image_Metadata_PlateIDname of plate
Image_Metadata_SOURCE_COMPOUND_NAMEcompound name according to source
Image_Metadata_SOURCE_NAMEsource of compound
Image_Metadata_Sitesite number within well
Image_Metadata_Timetime the image was acquired (ms)
Image_PathName_OrigERpath to image file for the con A channel
Image_PathName_OrigHoechstname of image file for the Hoechst 33342 channel
Image_PathName_OrigMitopath to image file for the MitoTracker Deep Red channel
Image_PathName_OrigPh_golgipath to image file for the WGA/phalloidin channel
Image_PathName_OrigSytopath to image file for the SYTO 14 channel

Example rows from the file:

ImageNumber Image_FileName_OrigER Image_FileName_OrigHoechst Image_FileName_OrigMito Image_FileName_OrigPh_golgi Image_FileName_OrigSyto Image_Metadata_ASSAY_WELL_ROLE Image_Metadata_BROAD_ID Image_Metadata_CLSID Image_Metadata_CPD_MMOL_CONC Image_Metadata_CPD_PLATE_MAP_NAME Image_Metadata_CPD_SMILES Image_Metadata_CPD_WELL_POSITION Image_Metadata_PlateID Image_Metadata_SOURCE_COMPOUND_NAME Image_Metadata_SOURCE_NAME Image_Metadata_Site Image_Metadata_Time Image_PathName_OrigER Image_PathName_OrigHoechst Image_PathName_OrigMito Image_PathName_OrigPh_golgi Image_PathName_OrigSyto
1IXMtest_A01_s1_w22CA7BDF3-1425-4AE6-8E57-9C004D6F7FF2.tifIXMtest_A01_s1_w164FBEEF7-F77C-4892-86F5-72D0160D4FB2.tifIXMtest_A01_s1_w58DA6AF62-1799-4B85-BE17-744E12ADC245.tifIXMtest_A01_s1_w47457436C-5BE7-4DA2-B966-CCF64B9F0088.tifIXMtest_A01_s1_w3FD54227A-6BE4-460B-8E2C-54B8709F6E33.tifcompoundBRD-K98763141-001-06-88DA6AF62-1799-4B85-BE17-744E12ADC2458.85840119799373682404949170890782285609H-BIOA-002-1OC(=O)c1cccnc1Nc2cccc(c2)C(F)(F)FA0120585NIFLUMIC ACIDBiomol International Inc.1126754068376720585/20585/20585/20585/20585/
2IXMtest_A01_s2_w246FFAEE1-BEB6-4C81-913B-B979EC0C4BC3.tifIXMtest_A01_s2_w1AA6B1894-F561-42EE-9D1D-E21E5C741B75.tifIXMtest_A01_s2_w50F1562CD-EBCF-408E-9D8D-F6F0FDD746C8.tifIXMtest_A01_s2_w46657239A-5AFE-4C29-BB9B-49978EFE4791.tifIXMtest_A01_s2_w3A597237B-C3D7-43AE-8399-83E76DA1532D.tifcompoundBRD-K98763141-001-06-80F1562CD-EBCF-408E-9D8D-F6F0FDD746C88.85840119799373682404949170890782285609H-BIOA-002-1OC(=O)c1cccnc1Nc2cccc(c2)C(F)(F)FA0120585NIFLUMIC ACIDBiomol International Inc.2126754068626620585/20585/20585/20585/20585/
3IXMtest_A01_s3_w22AD5BD08-58A3-466D-A364-BE116BD98696.tifIXMtest_A01_s3_w108F3A6FF-A865-40A1-8488-9A5BA31605A9.tifIXMtest_A01_s3_w5489716D4-2D06-45BE-8D68-F2EEE857929D.tifIXMtest_A01_s3_w47B5F2FF6-A5A2-4101-AC2A-0A821FDE7445.tifIXMtest_A01_s3_w30B946780-C923-4A40-8EC5-16262CFF03A6.tifcompoundBRD-K98763141-001-06-8489716D4-2D06-45BE-8D68-F2EEE857929D8.85840119799373682404949170890782285609H-BIOA-002-1OC(=O)c1cccnc1Nc2cccc(c2)C(F)(F)FA0120585NIFLUMIC ACIDBiomol International Inc.3126754069062720585/20585/20585/20585/20585/

Recommended citation

"We used image set BBBC022v1 [Gustafsdottir et al., PLOS ONE, 2013], available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."

Copyright

CC0 To the extent possible under law, Anne Carpenter has waived all copyright and related or neighboring rights to BBBC022v1. This work is published from: United States.

This page last updated 2018-01-31