This post contains a quick description/recipe for making vector files of brain atlas images suitable for publication and presentations. This post is as much for communication as for personal records.
Step 1 - The atlas itself
Starting material should be as good quality as possible. I used .eps files from Paxinos Rat Brain Atlas for doing this. On the cheap side of life, a very nice online resource can be found here. Images could be imported to most image processing freeware and processed in a very similar way.
Step 2 - Load images into Inkscape
The process looks like this. Import files into Inkscape using the import dialog box.
Step 3 - Convert to Grayscale
The blue borders are not really my thing. I would rather have them in grayscale (or white, to overlay ). We’ll do grayscale for now. In Inkscape, do:
Extensions > Color > Grayscale
Step 4 - Get rid of the junk
Probably, all the letters are . We can do Ctr+F and find an a (or other letters). That helps us to get rid of the text fast and with little clicking.
Final Thoughts
From here on, just fixing it the way you want it. Here’s the final result, after cleaning all the stuff I didn’t like.
Afterward
At some point, I decided to create a package to do this in R. If you are familiar with R and ggplot2, but you can get vector images programatically from the Allen Brain Atlas. Check nobrainr here.
Reuse
Citation
@online{andina2018,
author = {Andina, Matias},
title = {Making Atlas Images},
date = {2018-05-19},
url = {https://matiasandina.com/posts/2018-05-18-making-atlas-images},
langid = {en}
}