Viewer for st_exp_protobuf data

Quick start: Click the button Open some example data files and layouts to view some examples. You can now create your own layout by filling out gene names in the add gene input field that is auto-completed. The added genes are visible as a new-line-separated list of names in the gene list. After clicking "Create layout from gene list", an OpenSeadragon window appears where each of the genes have had its gene expression values painted as circles on top of the cell tissue microscope photos.

Example files from a new gene expression meassurement technology: Some st_exp_protobuf files were created by the shell script download_and_convert_example_data.sh out of data sets from www.spatialtranscriptomicsresearch.org. The datasets are gene expression meassurements done with the technology described in the scientific paper Visualization and analysis of gene expression in tissue sections by spatial transcriptomics published in Science June 2016. The generated example files (e.g. example file (34 Mb), example file (17 Mb) can be opened in the viewer either as remote URL:s or as local files after downloading them.

Hosting st_exp_protobuf files: When using a URL for accessing the st_exp_protobuf file, the web server neeeds to support the HTTP request header RANGE (see Wikipedia article about Byte serving). You could for instance use Apache, nginx, http-server (from Node.js) or Amazon S3.

More in-depth information: The st_exp_protobuf file format stores pyramid image tiles of high-resolution microscope photos that can be displayed by a slightly modified OpenSeadragon. The file format also contains gene expression values stored indexed by gene. A small header in the beginning of the file contains indexes to the rest of the file. With this design, opening and displaying the gene expression will be very fast because only a fraction of the whole st_exp_protobuf file needs to be downloaded (or read). The relevant parts of the data will be retrieved as byte ranges.
The source code for this software project is located in the osd-spot-viewer github project under this directory and it is licensed under the MIT license.

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