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Moved from a psychology degree to a PhD in neuroscience - an electrophysiological investigation of the sources of sensory input to dopamine releasing neurons. From there I moved back to psychology with an experimental postdoc looking at perception with sensory substitution devices. I am looking to move back into neuroscience with my next postdoc, but in the meantime I'm blogging on a mixture of psychology and neuroscience.

Automatic and reliable plotting of histology/recording sites

I feel a little bit guilty for coming back to use the blog for my own gain when I’ve not posted anything for a while, but I needed someone more permenant than twitter to ask for advice.

I’m trying to create a way of reliably plotting anatomical data like recording sites onto diagrams of brain structures, rather than exporting pages of a pdf atlas as images then copying and pasting symbols in Illustrator and moving them around until they look like they’re in the right place.

What I had in mind was some bit of code that would take stereotaxic coordinates of points (e.g. recording sites) and an image from a brain atlas and combine the two. The end result will be a bit like this.

I’m learning Matlab at the moment, so I’d planned to stick with that, but it doesn’t seem to deal with importing vector images very easily. My options now seem to be:

  1. try to plot the recording sites in Matlab at the appropriate scale without the images from the atlas, export the recording sites as a vector image, then combine the two in illustrator
  2. move back to R, which seems to handle vectors more readily (pdf guide)

Does anyone have any suggestions? Advice?



4 comments to Automatic and reliable plotting of histology/recording sites

  • Have you looked at ImageJ, its origins are in biomedical imaging so potentially someone has already addressed the problem.

    I assume by “vector images” you mean they are in a format such as pdf or svg. You could have a look on the Mathworks file exchange site.

  • Darren Hoyland

    Yeah, move over to python and have the best of both worlds…

  • @Ian I hadn’t heard of ImageJ. I’ve just had a quick look and it seems to be mostly about manipulating bitmap images? And yes, vector images as in pdf. I’ve got a diagrammatic brain atlas in pdf that I open a page at a time in Illustrator, then paste markers in appropriate places based on the paper diagrams I made from looking at slides.

    @Darren Looking at a new language had crossed my mind, but this might be enough of a time sink as it is…

    Mat suggested plotting the points, along with major landmarks – probably origin/axes in the stereotaxic coordinates – then exporting that from Matlab as an eps. Illustrator can then import eps files apparently.

  • Yes, not much handles PDF as vector images – the other (free) option is Inks cape. Personally I would probably do a bulk conversion of the vector images to some sort of bitmap.

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