Clustered cell nuclei

Description

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)](http://cbia.fi.muni.cz/datasets/) as well [Broad Bioimage Benchmark Collection (BBBC)](https://data.broadinstitute.org/bbbc/) - entry BBBC024.

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Human colon tissue

Description
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)](http://cbia.fi.muni.cz/datasets/) as well [Broad Bioimage Benchmark Collection (BBBC)](https://data.broadinstitute.org/bbbc/) - entry BBBC027.
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Annotated two-photon images of dendritic spines

Description
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 Ghani2016 to perform dendritic spine analysis.
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Digital Reconstructions of Neuronal Morphology: Three Decades of Research Trends

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BBBC003v1 MOUSE EMBRYOS

Description
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 ?m.
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Dendritic Spine Classification using Shape and Appearance Features based on Two-Photon Microscopy

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BBBC002v1

Description
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)](http://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-10-r1…) 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. This image set belongs to the Broad Bioimage Benchmark Collection (BBBC). The BBBC resource is described in the following publication: Ljosa V, Sokolnicki KL, Carpenter AE (2012). Anno tated high-throughput microscopy image sets for validation. Nature Methods 9(7):637 / doi. PMID: 22743765 PMCID: PMC3627348. Available at [http://dx.doi.org/10.1038/nmeth.2083](http://www.nature.com/nmeth/journal/v9/n7/full/nmeth.2083.html)
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Muscle stem cells contribute to myofibres in sedentary adult mice

Description
In terms of image analysis, this article includes an analysis of 2D myofibre labeled with a dye to identify myofibre borders. Keefe, A.C. et al. Muscle stem cells contribute to myofibres in sedentary adult mice. Nat. Commun. 6:7087 doi: 10.1038/ncomms8087 (2015). An open source version based on python is available at: https://github.com/stevendflygare/muscleQNT
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HeLa Cells in Phase Contrast and Nucleus Marker with manually labelled outlines

Description
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.1…
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