List of Data Sets

	identifier	has imaging details	has biological terms	has format	has Ground truth
Systems Science of Biological Dynamics database (SSBD:database)	1644	Diverse microscopes (mostly light microscopy, but some electronic microscopy as well). SSBD tries to store and curate 4D datasets, ie images that are 3D together with time element.			It also stores all the qualitative data (i.e. segmented data or ROIs) separately as numerical datasets. Quantitative data are represented by using a unified data format, the Biological Dynamics Markup Language.
Nuclei segmentation in histopathology images	1602		histopathology, nuclei		The dataset contains ground truth annotation for the segmentation of the nuclei.
MoNuSeg - Multi-organ nuclei segmentation challenge	1601		histopathology, nuclei
FAIRsharing Eurobioimaging collection	1579	Diverse			Some have ground Truth available, such as the BBBC Broad Bioimage Benchmark Collection.
muscle cross-sections	1577	Immunofluorescent sections were imaged on a Nikon AR1 confocal or Nikon Widefield CCD Microscope. Each confocal image is a composite of maximum projections, derived from stacks of optical sections.	Muscle Stem Cells, Muscle	tiff	NO. Data used to exemplify muscleQNT: Muscle fiber counting
Mouse embryos	1576	There are 15 images. The images were acquired using a Nikon Eclipse TE200 microscope with a 20x, 0.45 NA objective lens and a 0.52 NA condenser lens, and are provided courtesy of the W.M. Keck 3D Fusion Microscope Facility at Northeastern University. Each image contains 640 x 480 pixels with an approximate size of 0.42 x 0.42 μm.	embryo, cells	tiff	For the purpose of collecting ground truth, the samples were Hoechst-stained and imaged by confocal microscopy, and the cells were counted by a simple human. A tab-delimited text file contains cell counts in each of the 15 images.
two-photon images of dendritic spines	1575	Two-photon imaging was performed using a galvanometer-based scanning system (Prairie Technologies, acquired by Bruker Inc.) on an Olympus BX61WI equipped with 60X water immersion objective (0.9 NA), using a Ti:sapphire laser (Coherent Inc.) controlled by PrairieView software at 910 nm. Z-stacks (0.3 μm axial spacing) from secondary or tertiary dendrites from CA1 neurons were collected every 5 min for up to 4 h. The field of view was 19.8 × 19.8 μm at 1024 × 1024 pixels.	Dendritic Spine		Annotated data and mask labels provided
Human colon tissue	1574	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.	tissue, cells	tiff	Ground Truth is provided as binary masks.
Clustered Cell Nuclei Data	1573	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	nuclei, HL60 cells	tiff	Ground Truth is provided as segmentation mask.
CSIRO science image library	1571		plant, textiles, minerals
Breast Cancer Histopathological Database (BreakHis)	1569	histopathology images - 700X460 pixels,RGB 8-bit images stored as PNG	breast cancer, histopathology		Image patch classified as benign or malignant
Zebrafish larvae - Widefiled/Brightfield	1559		zebrafish	tif
Medaka embryo in 96 well plate - Widefield Brightfield	1558		medaka, embryo	jpg
ANHIR: Automatic Non-rigid Histological Image Registration	1472		pathology		The Ground truth is denoted using landmarks - key points that are marked consistently for each set of images with different stains.
BBBC002v1	1434	There are 10 fields of view of each sample, for a total of 50 fields of view. The images were acquired on a Zeiss Axiovert 200M microscope. The images provided here are a single channel, DNA. The image size is 512 x 512 pixels. The images are provided as 8-bit TIFF files.	Drosophila melanogaster, RNAi	tiff	A tab-delimited text file contains the number of cells in each image, as determined by two different human counters. To compare an algorithm's results to these, first compute for each sample the algorithm's mean cell count over the 10 images of the sample. Next, calculate the absolute difference between this mean and the average of the humans' counts for the sample, then divide by the latter to obtain the deviation from ground truth (in percent). The mean of these values over all 5 samples is the final result. Note: The two human observers vary by 16% for this image set.
Diadem challenge	1191	Imaging varies by neuron type and species, includes: Transmitted light brightfield Confocal in-vivo 2-photon laser scanning	neurite arbor		Manually traced digital neural reconstructions,
CREMI challenge	1182	Serial section Transmission Electron Microscopy (ssTEM).		hdf5	Neuron segmentation Synaptic cleft segmentation Synaptic partner annotation
Arabidopsis plants (low resolution)	1146		Arabidopsis thaliana	jpg
Arabidopsis plants (high resolution)	1145		Arabidopsis thaliana
leaves stained with gfp and rfp	1143		plant virurs, leaf infection
Artemia color images	1139		Artemia	tif
Microtubules 3D	1137		microtubules
Arabidopsis thaliana seedlings	1131		Arabidopsis thaliana seedlings	jpg
2D bright field yeast cell images with ground truth annotations	41	Bright field microscopy	yeast		yes. binary segmentation masks in-focus cells' center point coordinates text files