Nuclei segmentation dataset from the 2018 Data Science Bowl (BBBC038v1, Broad Bioimage Benchmark Collection). 670 microscopy images with 29,442 individually segmented nuclei as polygon annotations, converted from the official per-nucleus masks. Spans fluorescence and brightfield/histology imagery across multiple organisms and staining protocols. License: CC0 1.0 (public domain). Source: https://bbbc.broadinstitute.org/BBBC038. Please cite: Caicedo et al., Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods 16, 1247-1253 (2019).

Two-channel cell segmentation dataset of Drosophila melanogaster Kc167 cells (BBBC007v1, Broad Bioimage Benchmark Collection). 16 fields of view, each as a DNA image and an actin image (32 grayscale 8-bit images, 400 to 512 px), with 1,264 hand-outlined nuclei and 1,221 hand-outlined cells converted from the official outline rasters to polygon annotations. The benchmark task is finding the boundaries between touching cells, using the nuclei as seeds. License: CC0 1.0 (public domain). Source: https://bbbc.broadinstitute.org/BBBC007. Please cite: Jones, Carpenter & Golland, Voronoi-based segmentation of cells on image manifolds, Proc. ICCV Workshop on Computer Vision for Biomedical Image Applications (CVBIA), 2005; and Ljosa, Sokolnicki & Carpenter, Annotated high-throughput microscopy image sets for validation, Nature Methods 9, 637 (2012).

Astrocyte detection dataset from rat brain tissue (BBBC042, Broad Bioimage Benchmark Collection). 1,117 annotated brightfield microscopy images (990x708) with roughly 15,000 astrocytes labeled as bounding boxes, from the deep-learning astrocyte detection study by Suleymanova et al. License: CC0 1.0 (public domain). Source: https://bbbc.broadinstitute.org/BBBC042. Please cite: Suleymanova I. et al., A deep convolutional neural network approach for astrocyte detection. Scientific Reports 8:12878 (2018), doi 10.1038/s41598-018-31284-x.

Seven-channel iFISH microscopy of human cell nuclei from IDR study idr0123 (Mota et al.): DAPI plus six spectrally distinct DNA FISH probes (AF488, AT542, AF594, AT647N, AF700, AF790) marking loci along chromosome 1, imaged at 1024x1024, 16-bit, 0.13 um/px. Each file is one field with one page per channel (maximum-intensity Z projection of the original 61-slice stack), so every fluorophore can be shown, hidden, and window-leveled independently in the browser. License: CC BY 4.0. Source and original Z-stacks: https://idr.openmicroscopy.org/study/idr0123/

Nucleus segmentation dataset of U2OS cells from a chemical screen (BBBC039v1, Broad Bioimage Benchmark Collection). 200 fluorescence microscopy fields (520x696, 16-bit TIFF, Hoechst-stained nuclei) spanning 200 bioactive-compound treatments, with 19,379 individually segmented nucleus instances decoded from the official per-pixel class masks (interior/boundary) and converted to polygon annotations (3 fields have no annotated nuclei). Includes the official train (100) / validation (50) / test (50) split. License: CC0 1.0 (public domain). Source: https://bbbc.broadinstitute.org/BBBC039. Please cite: Caicedo et al. 2018, image set BBBC039v1, available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012].

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