Create course materials

[adamltyson]

• [ ] Interactive workflows in Python (Rob):

• [x] Basic image analysis techniques:

  • [x] Loading data
  • [x] Filtering
  • [x] Thresholding
  • [x] Post-processing (morphological filters etc)
  • [x] Measurements (e.g. regionprops)
  • [x] Visualisation - napari

• [ ] Processing large datasets effectively:

  • [x] Introduction to Dask
  • [x] Demonstration using BrainSaw data
  • [ ] Zarr?

• [ ] Tools for processing histology data:

  • [ ] 3D registration using brainglobe
  • [x] 3D cell detection with cellfinder
  • [ ] Segmentation of arbitrary structures with brainreg-segment (maybe with another plugin)
  • [x] ABBA/elastix for 2D sections

[adamltyson]

Started in #3

Also added a CNN notebook that we may or may not have time for.

[adamltyson]

Probably not going to use ABBA, it's a bit of a complex install for a short course. Maybe could use itk-elastix?