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Bioinformatics. 2013 Jun 15;29(12):1580-2. doi: 10.1093/bioinformatics/btt175. Epub 2013 Apr 16.

CellH5: a format for data exchange in high-content screening.

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Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030 Vienna, Austria.


High-throughput microscopy data require a diversity of analytical approaches. However, the construction of workflows that use algorithms from different software packages is difficult owing to a lack of interoperability. To overcome this limitation, we present CellH5, an HDF5 data format for cell-based assays in high-throughput microscopy, which stores high-dimensional image data along with inter-object relations in graphs. CellH5Browser, an interactive gallery image browser, demonstrates the versatility and performance of the file format on live imaging data of dividing human cells. CellH5 provides new opportunities for integrated data analysis by multiple software platforms.


Source code is freely available at under the GPL license and at under the Artistic-2.0 license. Demo datasets and the CellH5Browser are available at A Fiji importer for cellh5 will be released soon.

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