Human U2OS cells – compound-profiling Cell Painting experiment

Accession number BBBC022 · Version 1

Example Images

Hoechst 33342 staining con A staining Monoaster

Hoechst 33342 staining

con A staining

SYTO 14 staining

WGA + phalloidin staining MitoTracker Deep Red staining

WGA + phalloidin staining

MitoTracker Deep Red staining

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 name Explanation
ImageNumber a number between 1 and 69,120 identifying the field
Image_FileName_OrigER name of image file for the con A channel
Image_FileName_OrigHoechst name of image file for the Hoechst 33342 channel
Image_FileName_OrigMito name of image file for the MitoTracker Deep Red channel
Image_FileName_OrigPh_golgi name of image file for the WGA/phalloidin channel
Image_FileName_OrigSyto name of image file for the SYTO 14 channel
Image_Metadata_ASSAY_WELL_ROLE "compound" or "mock"
Image_Metadata_BROAD_ID identifies the compound
Image_Metadata_CLSID  
Image_Metadata_CPD_MMOL_CONC concentration of the compound
Image_Metadata_CPD_PLATE_MAP_NAME name of plate map (stock plate)
Image_Metadata_CPD_SMILES structure of the compound
Image_Metadata_CPD_WELL_POSITION position of well on the plate
Image_Metadata_PlateID name of plate
Image_Metadata_SOURCE_COMPOUND_NAME compound name according to source
Image_Metadata_SOURCE_NAME source of compound
Image_Metadata_Site site number within well
Image_Metadata_Time time the image was acquired (ms)
Image_PathName_OrigER path to image file for the con A channel
Image_PathName_OrigHoechst name of image file for the Hoechst 33342 channel
Image_PathName_OrigMito path to image file for the MitoTracker Deep Red channel
Image_PathName_OrigPh_golgi path to image file for the WGA/phalloidin channel
Image_PathName_OrigSyto path 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
1 IXMtest_A01_s1_w22CA7BDF3-1425-4AE6-8E57-9C004D6F7FF2.tif IXMtest_A01_s1_w164FBEEF7-F77C-4892-86F5-72D0160D4FB2.tif IXMtest_A01_s1_w58DA6AF62-1799-4B85-BE17-744E12ADC245.tif IXMtest_A01_s1_w47457436C-5BE7-4DA2-B966-CCF64B9F0088.tif IXMtest_A01_s1_w3FD54227A-6BE4-460B-8E2C-54B8709F6E33.tif compound BRD-K98763141-001-06-8 8DA6AF62-1799-4B85-BE17-744E12ADC245 8.85840119799373682404949170890782285609 H-BIOA-002-1 OC(=O)c1cccnc1Nc2cccc(c2)C(F)(F)F A01 20585 NIFLUMIC ACID Biomol International Inc. 1 1267540683767 20585/ 20585/ 20585/ 20585/ 20585/
2 IXMtest_A01_s2_w246FFAEE1-BEB6-4C81-913B-B979EC0C4BC3.tif IXMtest_A01_s2_w1AA6B1894-F561-42EE-9D1D-E21E5C741B75.tif IXMtest_A01_s2_w50F1562CD-EBCF-408E-9D8D-F6F0FDD746C8.tif IXMtest_A01_s2_w46657239A-5AFE-4C29-BB9B-49978EFE4791.tif IXMtest_A01_s2_w3A597237B-C3D7-43AE-8399-83E76DA1532D.tif compound BRD-K98763141-001-06-8 0F1562CD-EBCF-408E-9D8D-F6F0FDD746C8 8.85840119799373682404949170890782285609 H-BIOA-002-1 OC(=O)c1cccnc1Nc2cccc(c2)C(F)(F)F A01 20585 NIFLUMIC ACID Biomol International Inc. 2 1267540686266 20585/ 20585/ 20585/ 20585/ 20585/
3 IXMtest_A01_s3_w22AD5BD08-58A3-466D-A364-BE116BD98696.tif IXMtest_A01_s3_w108F3A6FF-A865-40A1-8488-9A5BA31605A9.tif IXMtest_A01_s3_w5489716D4-2D06-45BE-8D68-F2EEE857929D.tif IXMtest_A01_s3_w47B5F2FF6-A5A2-4101-AC2A-0A821FDE7445.tif IXMtest_A01_s3_w30B946780-C923-4A40-8EC5-16262CFF03A6.tif compound BRD-K98763141-001-06-8 489716D4-2D06-45BE-8D68-F2EEE857929D 8.85840119799373682404949170890782285609 H-BIOA-002-1 OC(=O)c1cccnc1Nc2cccc(c2)C(F)(F)F A01 20585 NIFLUMIC ACID Biomol International Inc. 3 1267540690627 20585/ 20585/ 20585/ 20585/ 20585/

Nucleus segmentation annotations

Part of this dataset has been used for nucleus segmentation research, and a subset of 200 images have been selected for manual annotation of nucleus shapes. These annotations and more details about the segmentation problem can be found in the BBBC039 dataset.

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

CC0To 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.