Making atlas images


Massachusetts Institute of Technology


May 19, 2018

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.

Inkscape Import 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.


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.



BibTeX citation:
  author = {Andina, Matias},
  title = {Making Atlas Images},
  date = {2018-05-19},
  url = {},
  langid = {en}
For attribution, please cite this work as:
Andina, Matias. 2018. “Making Atlas Images.” May 19, 2018.

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