Visualize gene expression on top of cell tissues by use of OpenSeadragon
Quick start: First select a local st_exp_protobuf file or open a remote URL
to a st_exp_protobuf file. After that the "add gene" input field will provide auto-completion functionality when typing gene names. Add some genes
so that they appear as a new-line-separated list of genes in the gene list. Now click "Create layout from gene list". An OpenSeadragon window will
now appear where each of the genes have had its gene expression values painted as circles on top of the cell tissue microscope photos.
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.