List of Data Sets
identifier | Preview | has imaging details | has biological terms | has format | has Ground truth | |
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Cell Tracking Challenge Dataset |
1667 | |
Microscopy settings for each dataset are available by clicking on the "More Details Button" |
cell motility, cell migration | tif | |
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. |
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Nuclei segmentation in histopathology images |
1602 | ![]() |
histopathology, nuclei | The dataset contains ground truth annotation for the segmentation of the nuclei. |
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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. |
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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 |
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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 |
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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. |
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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:
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neurite arbor | Manually traced digital neural reconstructions, |
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CREMI challenge |
1182 | ![]() |
Serial section Transmission Electron Microscopy (ssTEM). |
hdf5 |
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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.
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