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Zebrain contour

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.

Interface usage

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.

screenshot

Script usage

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.

  1. download.sh download MaskDatabase.mat (120Mo) and Ref20131120pt14pl2.nrrd (230Mo) from Z-Brain Atlas
  2. export_zebrain.m with matlab export masks as PNG and correspondence table
  3. export.ijm with imagej export layers as JPEG
  4. vectorize.sh with potrace (inkscape) vectorize to svg
  5. extract.py with python combine and tag svgs
  6. combine.py with python combine all svgs in one file
  7. region-names.py with python convert region names to json
  8. serve.sh with python serve the files and open the browser

Bug or feature request

Please file an issue to report a bug or request a feature.