Mouse embryo blastocyst cells

Accession number BBBC032 · 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 not only in XY plane but also in XZ and YZ planes. Manually annotated ground truth provides a reference for image analysis software testing purposes. These images of mouse embryo blastocyst cells also have changing nuclei intensity in Z plane which makes finding the right threshold for successful segmentation a difficult task. This image set also contains GAPDH transcripts that can be quantified in each cell.


Images acquired by using PerkinElmer Ultraview VoX spinning disk microscope combined with a Leica SP8 with a 63x immersion objective (Distance between Z-slices = 0.5 um) (1.14 GB)

Ground truth  Foreground background button F

Ground truth 3D image contains manually annotated and segmented nuclei

BBBC032_v1_DatasetGroundTruth.tif (473.5 MB)

For more information

These images were generated by the Laboratory for Modeling Development and Regeneration at Hubrecht Institute, The Netherlands. Please contact Nicolas Rivron and/or Javier Frias Aldeguer 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 BBBC032v1 Rivron et al. 2018, available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."


CC0To the extent possible under law, Nicolas Rivron has waived all copyright and related or neighboring rights to BBBC032v1.

  • 647 channel (BMP4blastocystC0): BMP4 transcripts
  • 568 channel (BMP4blastocystC1): GAPDH transcripts
  • 488 channel (BMP4blastocystC2): WGA
  • 405 channel (BMP4blastocystC3): Hoechst
  • Width = 103.424 microns (1024)
  • Height = 135.744 microns (1344)
  • Depth = 86 microns (172)