This is a pure Python module for taking slices through MR Images and displaying them in beautiful ways. It is friendly to both clinical and pre-clinical data, and includes dual-coding overlays.
Here is a Jupyter Notebook demonstrating the functionality.
This is an example of an image you can make with it:
And here is an example of the viewer application:
Along with the
nanslice module that can be used in your Python scripts, there are
several utitlity functions for use in
jupyter notebooks, including a three-plane
viewer. There are also three command line tools that will installed to your $PATH:
nanslicerProduces different kind of slice-plots including color bars
nanviewerA three-plane viewer. Requires PyQt.
nanvideoConverts time-series images to a movie file for easy viewing.
- Compatibility with pre-clinical data. Small animals (rodents) are scanned in a different orientation to humans, and hence have different definitions of superior-inferior and posterior-anterior. This makes using such images with clinically focussed tools tedious.
- Support for dual-coding overlays
- Inner-Platform Effect. Seen as you have to learn scripting languages if you want to have repeatable plots in other tools, you might as well build your plots with a common language straight away.
(Note: I love both MRIcroGL and FSLEyes, I use them all the time)
Okay, there’s a fourth reason. I am fussy about plots. I spend a lot of time on then. Having
immediate access to all of
matplotlib is a brilliant way to make beautiful plots (and also
to waste hours obessessing about your choice of fonts. Avenir Next is a hell of a drug).