Imaging software episode

[K-Meech]

For https://github.com/HealthBioscienceIDEAS/microscopy-novice/issues/16

This adds a first draft of the imaging software episode. This aims to introduce different types of imaging software + provide an introduction to the main features of the Napari user interface. It has a few short exercises, but there will be more in later episodes once we get into the main content.

Any feedback is very welcome on the content of this lesson + also its general layout / structure / tone (I'll start planning the rest of the episodes in a similar style, so do let me know if anything should be changed here)

It's probably best to build this branch locally so you can see all the images + text together with the proper formatting.

[github-actions[bot]]

Thank you!

Thank you for your pull request :smiley:

:robot: This automated message can help you check the rendered files in your submission for clarity. If you have any questions, please feel free to open an issue in {sandpaper}.

If you have files that automatically render output (e.g. R Markdown), then you should check for the following:

• :dart: correct output
• :framed_picture: correct figures
• :question: new warnings
• :bangbang: new errors

Rendered Changes

:mag: Inspect the changes: https://github.com/HealthBioscienceIDEAS/microscopy-novice/compare/md-outputs..md-outputs-PR-21

The following changes were observed in the rendered markdown documents:

 fig/blank-napari-ui.png (new)     | Bin 0 -> 30428 bytes
 fig/cells-3d-napari.png (new)     | Bin 0 -> 470996 bytes
 fig/cells-napari.png (new)        | Bin 0 -> 239735 bytes
 fig/dim-slider-closeup.png (new)  | Bin 0 -> 52286 bytes
 fig/dim-slider.png (new)          | Bin 0 -> 430500 bytes
 fig/images-mosaic.png (new)       | Bin 0 -> 1308604 bytes
 fig/layer-controls-task.png (new) | Bin 0 -> 163515 bytes
 fig/layer-list.png (new)          | Bin 0 -> 6793 bytes
 fig/layer-reordering.png (new)    | Bin 0 -> 129444 bytes
 fig/points-task.png (new)         | Bin 0 -> 185678 bytes
 fig/roll-dims.png (new)           | Bin 0 -> 209885 bytes
 fig/transpose-dim.png (new)       | Bin 0 -> 318848 bytes
 fig/ui-sections-napari.png (new)  | Bin 0 -> 361446 bytes
 imaging-software.md (new)         | 561 ++++++++++++++++++++++++++++++++++++++
 md5sum.txt                        |  23 +-
 15 files changed, 573 insertions(+), 11 deletions(-)

What does this mean?

If you have source files that require output and figures to be generated (e.g. R Markdown), then it is important to make sure the generated figures and output are reproducible. This output provides a way for you to inspect the output in a diff-friendly manner so that it's easy to see the changes that occur due to new software versions or randomisation.

:stopwatch: Updated at 2023-12-01 13:44:00 +0000

[K-Meech]

Thanks for the comments @dpshelio ! I've made the formatting changes you suggested e.g. restricting line length / linking directly to napari icons. I'll save the rest of your suggestions until Dave has had a chance to review too. Then I can make all the changes in one go next week.

[davecash75]

When I do the build I get the following warning:

There are missing timings from 1 episode. • imaging-software.md ℹ The default value of 5 minutes will be used for teaching and exercises.

We should put a reasonable estimate down and then edit it when we test drive it with some users.

[davecash75]

More of a sandpaper layout question to @milanmlft and @K-Meech, should the episode list on the left come out so much when it is expanded? It really seems to eat into the main lesson page and make the questions look funny.

[milanmlft]

@davecash75, interesting, this doesn't seem to happen for me when I build locally Could you try reinstalling sandpaper to ensure you have the latest version?

This layout is what the Carpentries uses by default. You can always collapse the side bar to get more space.

[davecash75]

Hi @milanmlft I re-installed sandpaper from a fresh new R install maybe five minutes before I sent that screenshot. Even with a full screen view on my desktop, I am still getting the Questions element wrapping. It must be something unique to my Mac laptop though, as I also get it when looking at https://healthbioscienceideas.github.io/microscopy-novice/introduction.html

[K-Meech]

Thanks for the comments @davecash75 ! I'll make a new version this week incorporating all the suggestions so far and then send it around again.

[K-Meech]

@davecash75 @dpshelio I've made a new version incorporating your suggestions - could you take a look and let me know if anything else needs changing? Thanks!