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imagej / pyimagej

Use ImageJ from Python
https://pyimagej.readthedocs.io/
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Improve doc examples content and structure #93

Closed mmarras closed 2 years ago

mmarras commented 3 years ago

Dear all,

I'd like to see a more in-depth how-to-use pyimagej. I have followed the recommendation to raise use questions at image.sc. Please see here for my recent post to ask for more explanation on how-to-use run_marco(). The feedback rate is very low, i.e., none for pyimagej.

Maybe improvements can be twofold:

  1. An improved verbal description of what can be done with the pyimagej package (maybe in terms of use-cases), so the right expectations are set before people start to invest time.
  2. An improved notebook on how to use PyImageJ.
imagesc-bot commented 3 years ago

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/first-steps-with-pyimagej-after-installing-applying-run-macro-to-image/45199/2

ctrueden commented 3 years ago

As of 38a52b3381efc496c0391d12cc197ab6885900c9, the new doc folder goes into more technical details with better organization. Also, more notebooks are nearing completion; will reply again here about that soon. But it still won't reach the level of your request, @mmarras. The PyImageJ developers aren't bioimage analysts, we're research software engineers, and so we don't have in-depth real-world image analysis workflows. There have been a couple posted on forum.image.sc, but no one is curating them. It could be you, if you want to contribute.

mmarras commented 3 years ago

That would be worthwhile to pick up. You have a recommendation on where to start?

Any update? Otherwise?

imagejan commented 3 years ago

I'd also be interested in seeing a (curated) list of real-world use cases for pyimagej (maybe right in the README?).

One example is https://github.com/PMEAL/porespy that uses some ImageJ filters via pyimagej.

ctrueden commented 2 years ago

@mmarras @imagejan I have pushed some improvements to the READMEs. There is now a section collecting real-world examples; see doc/examples/README.md. It's pretty bare, but you are welcome to add more items to the list.

There is also a new doc/README.md that links to the numbered tutorial sequence, as well as reference documentation.

If you feel anything is missing, you can reply back here, or open a new issue.