search

HealthBioscienceIDEAS / microscopy-novice

https://healthbioscienceideas.github.io/microscopy-novice/
Other
1 stars 0 forks source link

Choosing acquisition settings episode #42

Closed K-Meech closed 5 months ago

K-Meech commented 6 months ago

Closes https://github.com/HealthBioscienceIDEAS/microscopy-novice/issues/35

This adds a first draft of the 'choosing acquisition settings' episode. This aims to introduce key factors to consider when choosing acquisition settings on a light microscope. Like the last episode, it's quite theoretical, so it focuses on introducing general concepts with a few small examples and exercises.

There are a few scripts under episodes/files/ added here to generate some of the plots in this episode.

Again this one focuses on light microscopy concepts - so it would be great to get feedback from people with more light microscopy experience!

github-actions[bot] commented 6 months ago

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:

Rendered Changes

:mag: Inspect the changes: https://github.com/HealthBioscienceIDEAS/microscopy-novice/compare/md-outputs..md-outputs-PR-42

The following changes were observed in the rendered markdown documents:

 choosing-acquisition-settings.md (new)             | 670 +++++++++++++++++++++
 config.yaml                                        |   1 +
 fig/acquisition-tradeoffs.png (new)                | Bin 0 -> 40116 bytes
 fig/aliasing.png (new)                             | Bin 0 -> 18474 bytes
 fig/exercise-qc-histograms.png (new)               | Bin 0 -> 95451 bytes
 fig/image-with-noise.png (new)                     | Bin 0 -> 634267 bytes
 fig/nyquist-1.png (new)                            | Bin 0 -> 10987 bytes
 fig/nyquist-2.png (new)                            | Bin 0 -> 12206 bytes
 fig/nyquist-3.png (new)                            | Bin 0 -> 12772 bytes
 fig/pixel-size-magnification-exercise-1.png (new)  | Bin 0 -> 15816 bytes
 fig/pixel-size-magnification-exercise-2.png (new)  | Bin 0 -> 7561 bytes
 fig/snr-comparison-high.png (new)                  | Bin 0 -> 54177 bytes
 fig/snr-comparison-low.png (new)                   | Bin 0 -> 59270 bytes
 .../QC_histogram_exercise.py (new)                 |  44 ++
 .../image_with_noise.py (new)                      |  34 ++
 .../snr_comparison.py (new)                        |  44 ++
 md5sum.txt                                         |   3 +-
 17 files changed, 795 insertions(+), 1 deletion(-)
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 2024-02-07 13:36:18 +0000

K-Meech commented 6 months ago

@thompson318 @davecash75 - I made a new version of the 'choosing acquisition settings' episode incorporating your comments. Could you take another look and approve or request changes?

I made a separate issue - https://github.com/HealthBioscienceIDEAS/microscopy-novice/issues/47 - for improving the docstring/comments on all plot scripts after the episodes are complete.