Episode 4, Exercise 4 Visu with matplotlib

[sommerc]

Brief description

1. Give examples for basic imshow functionality
2. Introduce named/built-in matplotlib colormaps and vmin, vmax arguments and discuss their properties and requiremnts in terms:
   • contrast
   • relation to the input channels' wavelength
   • accessiblity and perceptual uniformity (color blindness)
   • mixing/blending with other colormaps (see Episode 4 - Visualization with Napari)
3. Basic subploting with matplotlib and most relevant Axes functions set_title, set_xlim, set_axes_off etc
4. Add colorbar to imshow plot + basic positioning

Learning objective(s)

covered

Volunteer(s)

@sommerc

[wangliyuan72]

To add on a comment on colourmaps: be aware and conscious of colour blind friendly palette when making a choice on the display and visuaulisation.

[marcodallavecchia]

We definitely don't want to convert this into a full data visualization section but we should by default take in consideration colour blindness in all our examples and perhaps even perceptually uniform colormaps (here and here)

[sommerc]

Good point! I added a more points to the introduction of colormaps