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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:

image

And here is an example of the viewer application:

image

Along with the :py~nanslice module that can be used in your Python scripts, there are several utitlity functions for use in :py~nanslice.jupyter notebooks, including a three-plane viewer. There are also three command line tools that will installed to your $PATH:

  • :py~nanslice.nanslicer Produces different kind of slice-plots including color bars
  • :py~nanslice.nanviewer A three-plane viewer. Requires PyQt.
  • :py~nanslice.nanvideo Converts time-series images to a movie file for easy viewing.

Why does :py~nanslice exist when there are plenty of other great MR viewing tools, e.g. FSLEyes or MRIcroGL? There are three reasons:

  • 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).

doc/modules

Indices and tables

  • genindex
  • modindex
  • search

Legal

Copyright 2018 tobias.wood@kcl.ac.uk

This Source Code Form is subject to the terms of the Mozilla Public License, v. 2.0. If a copy of the MPL was not distributed with this file, You can obtain one at http://mozilla.org/MPL/2.0/.