Can I get numeric data from a color map?
Maybe You can try some workaround (first manually then programatically):


Convert to grey-scale
Make density map (digital)
Trace=vectorise image with any Inkscape / Illustrator / etc...
Map vector parts with density map values.


You can write js script for Adobe Illustrator (Gimp /  probably also) to automate some things. I'm not suggesting to spend money, just play around with demo until you wiil find Ideal Solution.

Also probably You can try any online API from Big4 or new emergers:


tensorflow
https://cloud.google.com/vision/
https://aws.amazon.com/rekognition/
https://www.ibm.com/watson/services/visual-recognition/
http://opentracing.io/


Also there are some commercial with free options 
i.e. imagga - "Sign up for Free: Tag up to 2000 images per month"

You can try DEMO Vector Magic's Desktop edition $295.00 / license One-time charge allows Group shapes by color (unfortunately do not offer special pricing for Academic Institutions or Non-profits)

Also have you tried FreeMat COLORMAP - Image Colormap Function?