Sample Data

Name Description Dimensions of the data Size (MB) Scale Thumbnail
Clustered cell nuclei

One of the principal challenges in counting or segmenting cells or cell nuclei is dealing with clustered objects. To help assess algorithms' performance in this regard, synthetic 3D image sets of HL60 cell line are provided consisting of four subsets with increasing degree of clustering. Each subset is also provided in two diferent levels of quality: high SNR and low SNR.Ground truth is available as well. The datasets are part of Masaryk University Cell Image Collection (MUCIC) as well Broad Bioimage Benchmark Collection (BBBC) - entry BBBC024.

X:807 Y:565 Z:30 11 200 Many cells
Human colon tissue

One of the principal challenges in counting or segmenting cells or cell nuclei is dealing with clustered objects such as in tissues. To help assess algorithms' performance in this regard, synthetic 3D image sets of human colon tissue are provided in two diferent levels of quality: high SNR and low SNR. Ground truth is available as well. The datasets are part of Masaryk University Cell Image Collection (MUCIC) as well Broad Bioimage Benchmark Collection (BBBC) - entry BBBC027.

X:900 Y:800 Z:80 8 500 Tissue
Annotated two-photon images of dendritic spines

A fully annotated dataset of Two-Photon Laser Scanning Microscopy (2PLSM) images of three types of dendritic spines. We make a standard dendritic analysis dataset publicly available including raw data, manual annotations, and manual labels. Manual labels and annotation (segmentations) are provided by a neuroscience expert. The dataset has been used in [1] to perform dendritic spine analysis.

References

X:250 Y:250 10 Organella
BBBC003v1 MOUSE EMBRYOS

Fluorescence microscopy cannot be used to image human embryos to determine embryo viability for in vitro fertilization because the introduction of exogenous fluorescent dyes is considered a toxic procedure. As a result, embryo viability has been measured primarily using differential interference contrast (DIC). A human can readily segment the embryo (and, to some extent, individual cells) in a DIC image, but automatic segmentation remains a challenge due to the cosine-dependent shading inherent in DIC images.

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.

X:640 Y:480 C:1 3 Many cells
BBBC002v1

Five different samples of Drosophila melanogaster Kc167 cells were stained with Hoechst 33342, a DNA stain. The last sample (labeled nodsRNA) is of wild-type cells. Each of the other four samples (labeled 48, 340, Anillin, and mad2) has a different gene knocked down by RNAi. The sample preparation is described in more detail by Carpenter et al. (Genome Biology, 2006)

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.

X:512 Y:512 C:1 4 Many cells
HeLa Cells in Phase Contrast and Nucleus Marker with manually labelled outlines

Two-channel images (brightfield and fluorescent DNA stain) of HeLa cells in culture.

Cell and nucleus outlines are manually labelled. Very suitable for cell segmentation benchmark tests.

Published here: Van Valen, David A., et al. "Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments." PLoS Comput Biol 12.11 (2016): e1005177.

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005177

X:1280 Y:1280 Z:1 C:2 10
Tomato

Tomato confocal slice

X:810 Y:610 T:1 C:1 Z:1 1 Tissue
alkaline comet assay image

L6 cell undergoing electrophoresis, imaged under Zeiss Axioplan fluorescent microscope. from [1]


References

X:251 Y:77 C:1 0 Single cell
Fluorescent beads in solution

This time stack was acquired on a confocal microscope and shows free beads in water (then diffusing, but also some flow).

X:348 Y:260 T:100 C:1 Z:1 20 Single molecule
3D dataset of astrocytes in mouse cortex, two time frames

CPP labeled astrocytes in mouse cortex.

The astrozytes were imaged two times with a delay of 27 minutes. The animal was removed from the microscope during the waiting phase. Thus, there is some shift between the two frames.

Voxel size:
x: 500 nm
y: 500 nm
z: 2000 nm

X;505 Y:505 Z:101 T:2 C:1 105 Many cells

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