Consider moving to ImageJ-MATLAB instead of Miji

bahanonu / ciatah

CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).

https://git.io/ciatah_docs

MIT License

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Consider moving to ImageJ-MATLAB instead of Miji #80

Open imagejan opened 3 years ago

imagejan commented 3 years ago

As mentioned on https://imagej.net/plugins/miji, this legacy project is mostly replaced by the functionality in ImageJ-MATLAB:

https://imagej.net/scripting/matlab#running-imagej2-within-matlab

I don't know the usage of Miji in ciatah in detail, and I don't know how involved a transition would be, but it might simplify it for users to just enable the ImageJ-MATLAB update site in Fiji (especially since the Miji website seems to be offline at the moment).

I know that @kouichi-c-nakamura worked quite a bit with the ImageJ-MATLAB integration, he might be able to give helpful advice.

bahanonu commented 3 years ago

Thanks for reaching out and the heads up about the Miji site (ciatah's been updated with a mij.jar backup URL).

CIAtah uses Miji mainly to display movies and allow certain movie modification operations as an alt to ciatah Matlab GUIs. e.g. https://bahanonu.github.io/ciatah/pipeline_detailed_modify_movies/.

I'd previously considered switching to ImageJ-MATLAB, but continue to use Miji + ij.jar as it still works across Matlab versions, is seamless on the user end for ciatah to download and setup (e.g. no user Fiji/Imagej GUI interactions needed), and avoids Fiji/Bio-Formats conflicts (on to-do list).

I'll reach out to you or @kouichi-c-nakamura once I upgrade to ImageJ-MATLAB if any questions/issues arise.

kouichi-c-nakamura commented 3 years ago

Thanks. I have to say, I no longer do extensive image analyses using ImageJ these days. And I don't know much about CIAtah.

Here are my thoughts:

(Miji) still works across MATLAB versions
- ImageJ-MATLAB worked on R2018b, which is 3 years ago. This will become less relevant eventually, I guess?
seamless on the user end for CIAtah to download and setup (e.g. no user Fiji/Imagej GUI interactions needed)
- We need to compare the steps required to use Miji and ImageJ-MATLAB. If ImageJ-MATLAB still has disadvantages, they are better to be fixed. I edited the documentation a lot and clarified the steps, but people may still find it tedious.
avoids Fiji/Bio-Formats conflicts (on to-do list).
- I don't know about this.