Induced pluripotent human stem cells

Accession number BBBC034 · Version 1

Example images

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Description of the biological application

Segmenting nuclei in 3D images can be challenging especially when nuclei are clustered and have different intensity. This image set contains a clustered monolayer of nuclei that can be difficult to segment and is provided along with manually annotated ground truth that can be used for image analysis software testing purposes.

Edge and center regions of the same cell colony can have different morphology and intensity. Analysis of 3D images can provide a complete picture of such differences. Two of the image sets contain clustered monolayer of cells at the edge and center of the hiPSC colony.


Images were obtained by using Zeiss AxioObserver microscope with C-Apochromat 100x/1.25 water immersion objective and Hamamatsu ORCA-Flash 4.0 camera.

  • Channel1 (AICS-12_134_C=0): CellMask Deep Red plasma membrane
  • Channel2 (AICS-12_134_C=1): GFP edited channel
  • Channel3 (AICS-12_134_C=2): DNA channel
  • Channel4 (AICS-12_134_C=3): Brightfield
  • Width = 66.56 microns (1024)
  • Height = 66.56 microns (1024)
  • Depth = 15.08 microns (52)

Center and edge colony images

  • Channel1 (C=1): CellMask Deep Red plasma membrane
  • Channel3 (C=3): EGFP beta-actin
  • Channel5 (C=5): Hoechst DNA (572.2 MB)

Ground truth  Biological labels button B

Ground truth 3D image contains manually annotated and segmented nuclei. There are no ground truth images for the center or edge colony images.

 BBBC034DatasetGroundTruth.csv (872 KB)

For more information

These images were generated by the AICS Microscopy & Image Analysis Team at the Allen Institute for Cell Science in Seattle, Washington. Please contact Derek Thirstrup for more information.

Published results using this image set

The proposed data set will be evaluated in a publication to be submitted.

Recommended citation

"We used image set BBBC034v1 Thirstrup et al. 2018, available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."


Creative Commons LicenseThe images and ground truth are licensed under a Creative Commons Attribution 4.0 International license by the Allen Institute for Cell Science. Contact for more information about the copyright.