This is a really simple code to make the interface available at http://wiki.ljp.upmc.fr/zebrain/. It contains a collection of scripts used to produce the base svg files and the JavaScript that makes it interactive in browser.
Use the slider to scroll between layers. Hover your mouse over a contour to display it's area. In the text area, enter a list of space-separated integers corresponding to regions. Also allows keywords like "all", "none" and "vestibular" to display a pre-defined set of regions. Every feature is presented on this annotated screenshot. The interface is designed to be light and readable even on a small screen.
If you want to produce yourself the base svg files (for example to make an overlay for some figures), here is the way to go:
You will need:
- bash
- MATLAB
- ImageJ
- potrace (
sudo apt install potrace) - python3
- a web browser (tested with Firefox and Chromium)
Clone the repo and run the scripts inside it as follows.
- download.sh download
MaskDatabase.mat(120Mo) andRef20131120pt14pl2.nrrd(230Mo) from Z-Brain Atlas - export_zebrain.m with matlab export masks as PNG and correspondence table
- export.ijm with imagej export layers as JPEG
- vectorize.sh with potrace (inkscape) vectorize to svg
- extract.py with python combine and tag svgs
- combine.py with python combine all svgs in one file
- region-names.py with python convert region names to json
- serve.sh with python serve the files and open the browser
Please file an issue to report a bug or request a feature.