Accession number BBBC050 · Version 2
Example images
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Biological application
Cell dynamics during the early mouse embryogenesis change spatiotemporally. For understanding the mechanism of this developmental process, imaging cell dynamics by live-cell imaging of fluorescently labeled nuclei and performing nuclei segmentation of these images by image processing are essential. This dataset contains the fluorescence images and Ground Truth used when performing nuclei segmentation using deep learning. Fluorescence images are time-series images from fertilization to blastocyst formation. Ground Truth is supervised data of the cell nuclear region.
Images
[train]
Time-series 3D images of early mouse embryos with nuclei fluorescently labeled with mRFP1 fused to the chromatin marker histone H2B, imaged with IX71 microscope equipped with a 20x oil lens.
- Spatial Resolution: (x, y, z) = (0.8, 0.8, 1.75) μm/pixel
- Temporal Resolution: 10 min
- Embryo number: 11
[test]
Time-series 3D images of early mouse embryos with nuclei fluorescently labeled with mCherry fused to the chromatin marker histone H2B, imaged with CV1000 microscope equipped with a 20x oil lens.
- Spatial Resolution: (x, y, z) = (0.8, 0.8, 2.0) μm/pixel
- Temporal Resolution: 10 min
- Embryo number: 4
Ground truth 
Ground Truth was manually annotated to the region and central region of cell nuclei of the time-series 3D image. There are three types of Ground Truth as follows: GroundTruth_NSN: All regions of cell nuclei are annotated with the same label GroundTruth_NDN: All central regions of cell nuclei are annotated with the same label GroundTruth_QCANet: All regions of cell nuclei are annotated with different labels.
Published results using this image set
Tokuoka, Yuta, et al. “3D convolutional neural networks-based segmentation to acquire quantitative criteria of the nucleus during mouse embryogenesis.” npj Syst Biol Appl 6, 32 (2020). https://doi.org/10.1038/s41540-020-00152-8
For more information
The image set was generated by the Funahashi Laboratory at Keio University, Kanagawa, Japan. Please contact Akira Funahashi regarding this dataset.
Recommended citation
"We used image set BBBC050 [Tokuoka, Yuta, et al. npj Syst Biol Appl 6, 32 (2020)], available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."
Copyright
The images and ground truth are licensed under a Creative Commons Attribution 3.0 Unported License (Commercial use allowed) by Akira Funahashi.