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).

Seven-channel iFISH microscopy of human hTERT RPE-1 nuclei from IDR study idr0123 (Mota et al.), complete Dataset 5: 50 fields, each a maximum-intensity projection of the original 61-slice stacks with one page per channel (DAPI plus six DNA FISH probes AF488, AT542, AF594, AT647N, AF700, AF790 marking 23 loci along chromosome 1), 1024x1024, 16-bit, 0.13 um/px. Includes 18,754 published spot coordinates as 9x9 px bounding boxes in six fluorophore classes. Every channel 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/ Please cite: Mota A, Schweitzer M, Wernersson E, Crosetto N, Bienko M. Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH. Scientific Data 9, 47 (2022).

Cell Painting compound-profiling images of human U2OS cells from the Broad Bioimage Benchmark Collection (BBBC022v1). One complete 384-well plate (plate 20585) of the 20-plate pilot: 3,456 fields of view (384 wells x 9 sites), each a five-channel OME-TIFF (Hoechst 33342, concanavalin A, SYTO 14, WGA/phalloidin, MitoTracker Deep Red) at 696x520, 16-bit, 20x, 0.656 um/px, packaged losslessly from the five original single-channel TIFFs. 320 wells treated with 320 distinct bioactive compounds plus 64 mock (vehicle control) wells; compound identity, concentration, SMILES and well role travel with each file as metadata. License: CC0 1.0 (public domain). Source: https://bbbc.broadinstitute.org/BBBC022. Please cite: Gustafsdottir, S.M. et al., Multiplex cytological profiling assay to measure diverse cellular states. PLOS ONE 8(12): e80999 (2013).

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.

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].

Live cell extraction

40_22.png 38 20_37.png: 19 40_21.png: 38 30_27.png: 29 35_32.png: 34 45_19.png: 44 15_6.png: 13 20_43.png: 19 45_20.png: 44 30_25.png: 29 45_14.png: 44 50_15.png: 49 25_10.png: 24 30_28.png: 29 20_35.png: 19 50_16.png: 49 50_14.png: 49