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Documentation for napari (other than API docs)
BSD 3-Clause "New" or "Revised" License
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Create a migration guide for folks familiar with ImageJ/Fiji #134

Open psobolewskiPhD opened 1 year ago

psobolewskiPhD commented 1 year ago

🧰 Task

ImageJ/Fiji has a long track record as a GUI plus scripting image analysis tool. Many folks are likely to have at least basic familiarity with the tools and menu options that are available (e.g. contrast, crop, set scale, scale bars, thresholds, measurements, analyze particles, etc.) (Note: I list those because those are the ones I teach in my ImageJ/Fiji lab 🤣 )

The idea is to make a guide/tutorial that helps someone familiar with image analysis, but coming from the ImageJ/Fiji ecosystem, use napari for the same basic tasks. So the focus would be on how to accomplish a set of (basic) tasks in ImageJ/Fiji using napari and the plugin ecosystem (vanilla napari is likely too limited).

In my mind, this would leave out napari installation—just link to the existing install stuff—but would mention plugins or python packages (scikit-image in particular) that can be used to accomplish tasks using either GUI (plugins) or napari-console. Note: ImageJ is scriptable, so the idea of typing commands/scripts isn't totally foreign.

Also, I'm not sure about the best structure and placement of such a guide/tutorial, but I think it could be high-impact so maybe it should have some prominence? Also maybe the best structure would be a dedicated Usage subsection, with the idea that additional content could be added freely? There needs to be some critical mass to be useful, but additional content could be good first docs PR.

Note: the existing How-to guide on napari+imageJ (https://napari.org/stable/howtos/napari_imageJ.html) is 🤯 and not at all what I envision here. I think it's explaining how to interconnect the two tools? But honestly, I still have very little understanding of what it is really explaining or why. It has pretty good SEO, at least on google, but I really think for any casual ImageJ user, seeing such a how-to guide as a menu item would get their hopes up, while reading it would probably make them never consider napari again. In my case, I didn't come back to looking at napari until 7 months later? 🤷‍♂️

CC: @kandarpksk @dgmccart @Nadalyn-CZI @melissawm

jni commented 1 year ago

Linking to still-relevant discussion: napari/napari#3231

I wouldn't mind a "segment blobs, measure properties, and plot those properties (e.g. with a histogram)" type guide like this scikit-image one, ideally with a scientific question focus, and have that guide work in parallel with napari + plugins and fiji. Having said that, the multicolumn discussion we've had a few times (in the context of Python vs UI) might come back here...

psobolewskiPhD commented 11 months ago

Came up recently: Pete Bankhead's excellent intro to bioimage analysis book has side-by-side python and imageJ https://bioimagebook.github.io/index.html It doesn't use napari, but we could cherry pick a few examples? Either way it may be worth linking this somewhere on napari.org in a "New to python?" or something section.