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BBBC specifications


Unique identifier OMICS_27488
Alternative name Broad Bioimage Benchmark Collection
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline Anne E. Carpenter
  • person_outline Vebjorn Ljosa
  • person_outline BBBC Team

Publication for Broad Bioimage Benchmark Collection

BBBC citations


Assessing microscope image focus quality with deep learning

BMC Bioinformatics
PMCID: 5853029
PMID: 29540156
DOI: 10.1186/s12859-018-2087-4

[…] rogramming Language: Python.Operating system(s): Platform independentOther requirements: TensorFlow 1.0 or higherLicense: Apache 2.0The datasets analysed during the current study are available in the Broad Bioimage Benchmark Collection repository, [, ]. […]


Systematic and general method for quantifying localization in microscopy images

PMCID: 5200903
PMID: 27979831
DOI: 10.1242/bio.019893

[…] Images of Drosophila melanogaster Kc167 cells [BBBC007_v1 (A9)] and whole organism Caenorhabditis elegans (BBBC012v1) were obtained from the Broad Bioimage Benchmark Collection (). Hand drawn boundaries of D. melanogaster cells were downloaded fro […]


Segmentation of Image Data from Complex Organotypic 3D Models of Cancer Tissues with Markov Random Fields

PLoS One
PMCID: 4668034
PMID: 26630674
DOI: 10.1371/journal.pone.0143798

[…] rast microscopy and with a ground truth segmentation of the entire embryo structure. We additionally consider segmentation performance with the 2D phase contrast ‘Melanoma’ and ‘Tscratch’ image data (BBBC019), also from the Broad Bioimage Benchmark Collection. The Melanoma image data consist of 20 images each with dimension 1024 × 1280 pixels while the Tscratch image data consist of 24 images each […]


Joint modeling of cell and nuclear shape variation

Mol Biol Cell
PMCID: 4710235
PMID: 26354424
DOI: 10.1091/mbc.E15-06-0370

[…] accuracy of constructing cell shape spaces for large image collections without computing all pairwise distances, using standard approaches for estimating full distance matrices.Using images from the Broad Bioimage Benchmark Collection and the Kahn Dynamic Proteomics Database, we demonstrated that drug treatment or protein tagging not only can change cell shape, but can also disrupt the relationsh […]


A Benchmark Data Set to Evaluate the Illumination Robustness of Image Processing Algorithms for Object Segmentation and Classification

PLoS One
PMCID: 4508044
PMID: 26191792
DOI: 10.1371/journal.pone.0131098

[…] a street scene with pedestrians, a lion sitting on grass, visual event recognition in videos etc. also exist. In other cases, there are sets with incomplete ground truth such as images containing cells with only the total number of cells as ground truth without any information of the type and shape of the objects to be segmented.Major problems in image processin […]


Pattern Recognition Software and Techniques for Biological Image Analysis

PLoS Comput Biol
PMCID: 2991255
PMID: 21124870
DOI: 10.1371/journal.pcbi.1000974

[…] ations, etc. Some useful publicly available image datasets include the PSLID datasets (, the IICBU benchmark suite (, and the Broad Bioimage Benchmark Collection […]


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BBBC institution(s)
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
BBBC funding source(s)
Supported by NIH R01 GM089652.

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