Annotated high-throughput microscopy image sets for validation
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TissueMNIST is a 2D dataset based on BBBC051, containing 236,386 human kidney cortex cells organized into 8 categories.
“We use the BBBC05128, available from the Broad Bioimage Benchmark Collection29. The dataset contains 236,386 human kidney cortex cells, segmented from 3 reference tissue specimens and organized into 8 categories.”
From MedMNIST v2 - A large-scale lightweight benchmark for 2D and 3D biomedical image classification (2023) · cites this paper as [29]
The BBBC021 dataset contains 13,200 3-channel fluorescent microscopy images of MCF7 cells acquired across 10 experimental batches.
“The one most comparable to RxRx1-wilds is the BBBC021 dataset (Ljosa et al., 2012), which contains 13,200 3-channel fluorescent microscopy images of MCF7 cells acquired across 10 experimental batches.”
From WILDS: A Benchmark of in-the-Wild Distribution Shifts (2020) · cites this paper as Ljosa et al., 2012
The main text (page not available) describes the BBBC as a collection of microscopy image sets, but does not identify BBBC021 or give its specifications. Searches for BBBC021, MCF7 cells, image count, channels, and experimental batches found no passage verifying the claimed details. (LLM, conf=0.75)
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Research works printed but not linked: 2
- [1]Carpenter AE Genome Biol 2006 7 R100 17076895 PMC1794559
- [2]Kamentsky L Bioinformatics 2011 27 1179 80 21349861 PMC3072555
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Steinmetz, P., Frouin, F., Morard, V., & Buvat, I. (2026) · doi:10.64898/2026.05.04.26350496
- Authors
- Ljosa, V., Sokolnicki, K. L., & Carpenter, A. E.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Ljosa, Vebjorn
- Carpenter, Anne E
- ORCID
- Carpenter, Anne E
- Venue
- Nature Methods
- Published
- 2012-06-28
- Volume
- 9
- Issue
- 7
- Pages
- 637-637
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC3627348
- OpenAlex
- W2019062120
- Cited by
- 601
- References
- 0
- Citations by year
- 2026: 48 · 2025: 51 · 2024: 70 · 2023: 71 · 2022: 71 · 2021: 80 · 2020: 62 · 2019: 41 · 2018: 28 · 2017: 20 · 2016: 25 · 2015: 13 · 2014: 10 · 2013: 8 · 2012: 2
- FWCI
- 4.83
- Type
- journal article
- Language
- en
- Update notices
- erratum (2013-04-29)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (GM089652)
- National Institute of General Medical Sciences (R01GM089652)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Cell Image Analysis Techniques
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Digital Imaging for Blood Diseases
- Physical Sciences › Engineering › Media Technology › Image Processing Techniques and Applications
- Keywords
- high-throughput imaging, ground truth, algorithm comparison, experimental artifacts, CellProfiler, ImageJ, performance indicators
- MeSH terms
- Algorithms, Image Processing, Computer-Assisted, Microscopy, Reproducibility of Results, Databases, Factual, High-Throughput Screening Assays
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