3D HL60 Cell line (synthetic data)

Accession number BBBC024 · Version 1

Example images

In focus Out of focus
3D image 3D foreground

Biological application

One of the principal challenges in counting or segmenting nuclei is dealing with clustered nuclei. To help assess algorithms' performance in this regard, this synthetic image set consists of four subsets with increasing degree of clustering. Each subset is also provided in two diferent levels of quality: high SNR and low SNR.


Four subsets (each in high and low SNR variant) of 30 images each are provided. Each image contains 20 HL60 cell nuclei, but the nuclei cluster with different probabilities (0%, 25%, 50%, and 75%) in the four subsets. The dataset was generated using the virtual microscope imitating the microscope Zeiss S100 (objective Zeiss 63x/1.40 Oil DIC) attached to confocal unit Atto CARV and CCD camera Micromax 1300-YHS.

clustering probability SNR download images (ICS) (TIFF)
0% low BBBC024_v1_c00_lowSNR_images.zip BBBC024_v1_c00_lowSNR_images_TIFF.zip
0% high BBBC024_v1_c00_highSNR_images.zip BBBC024_v1_c00_highSNR_images_TIFF.zip
25% low BBBC024_v1_c25_lowSNR_images.zip BBBC024_v1_c25_lowSNR_images_TIFF.zip
25% high BBBC024_v1_c25_highSNR_images.zip BBBC024_v1_c25_highSNR_images_TIFF.zip
50% low BBBC024_v1_c50_lowSNR_images.zip BBBC024_v1_c50_lowSNR_images_TIFF.zip
50% high BBBC024_v1_c50_highSNR_images.zip BBBC024_v1_c50_highSNR_images_TIFF.zip
75% low BBBC024_v1_c75_lowSNR_images.zip BBBC024_v1_c75_lowSNR_images_TIFF.zip
75% high BBBC024_v1_c75_highSNR_images.zip BBBC024_v1_c75_highSNR_images_TIFF.zip

Ground truth 

Each image contains exactly 20 masks; this is the ground truth for counting. Ground truth for foreground/background segmentation are available as labeled 16bit grayscale images:

clustering probability SNR download foreground
0% low BBBC024_v1_c00_lowSNR_foreground.zip
0% high BBBC024_v1_c00_highSNR_foreground.zip
25% low BBBC024_v1_c25_lowSNR_foreground.zip
25% high BBBC024_v1_c25_highSNR_foreground.zip
50% low BBBC024_v1_c50_lowSNR_foreground.zip
50% high BBBC024_v1_c50_highSNR_foreground.zip
75% low BBBC024_v1_c75_lowSNR_foreground.zip
75% high BBBC024_v1_c75_highSNR_foreground.zip

Recommended citation

"We used image set BBBC024vl [Svoboda David, Kozubkek Michal, Stejskal Stanislav. Generation of Digital Phantoms of Cell Nuclei and Simulation of Image Formation in 3D Image Cytometry. Cytometry Part A, John Wiley & Sons, Inc., 75A, 6, pp. 494-509, 16 pages. ISSN 1552-4922. 2009.] from the Broad Bioimage Benchmark Collection."


Creative Commons LicenseThe images and ground truth are licensed under a Creative Commons Attribution 3.0 Unported License by David Svoboda.