Mouse Embryos

Accession number BBBC003 · Version 1

Example images

DIC.         Ground Truth






     DIC Image                                    Foreground


Biological application

Fluorescence microscopy cannot be used to image human embryos to determine embryo viability for in vitro fertilization because the introduction of exogenous fluorescent dyes is considered a toxic procedure. As a result, embryo viability has been measured primarily using differential interference contrast (DIC). A human can readily segment the embryo (and, to some extent, individual cells) in a DIC image, but automatic segmentation remains a challenge due to the cosine-dependent shading inherent in DIC images.


There are 15 images. The images were acquired using a Nikon Eclipse TE200 microscope with a 20x, 0.45 NA objective lens and a 0.52 NA condenser lens, and are provided courtesy of the W.M. Keck 3D Fusion Microscope Facility at Northeastern University. Each image contains 640 x 480 pixels with an approximate size of 0.42 x 0.42 μm. (2.5 MB)

Ground truth  Counts button C Foreground background button F

For the purpose of collecting ground truth, the samples were Hoechst-stained and imaged by confocal microscopy, and the cells were counted by a simple human. A tab-delimited text file contains cell counts in each of the 15 images.

 BBBC003_v1_counts.txt (279 bytes)

The pixels belonging to the mouse embryo were manually identified as foreground. (23 kB)

Published results using this image set

button_f.png Foreground background button F    Citation
1.25% Warger et al., J. Biomed. Opt., 2008
0.83% Newmark et al., Microsc. Microanal., 2007


The images were acquired by Bill Warger and Judy Newmark. Judy Newmark counted the cells, and Tom Morgan identified the foreground.

Recommended citation

"We used image set BBBC003v1 from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."


Creative Commons LicenseThe Synthetic 1 images are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License by Pekka Ruusuvuori.