Need a place for users to share scripts/tools that employ ilastik

[k-dominik]

#142 nudged me to open this issue: ilastik users code around ilastik all the time. May it be shell/python/imagej scripts/macros for batch processing, or data preparation (e.g. conversion to h5) and probably even more stuff I cannot even think about. We should have a place to share those. I can see the following possibilities:

• we could have a contrib section here in our documentation repo where users can open PRs, adding their scripts along some docs
• we could open a new repo for user contributions of this kind

what do you guys think?

[emilmelnikov]

I would just manually put them right into the repo if the volume is low. Otherwise, a separate repo (that's the Fiji way, I think they even have multiple such repos).

[nkicg6]

I think it is a good idea, and I like the idea of keeping it central, with PR's for some standardized docs/info along with links to the scripts (hosted here or elsewhere). I really think it would be best if the docs for the scripts should be central, even if code isn't.

[imagesc-bot]

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

https://forum.image.sc/t/running-headless-ilastik-from-windows/43952/4

[ofrag]

For me both options suggested by Dominik look good and useful. The key is to help me find them easily by some visible and descriptive link to the repo in Ilastik documentation.

[ofrag]

In case people find it useful, we regularly use 2 utility ImageJ macros in prep for ilastik training (and other things):
one extract images from big proprietary microscopy files (lif, nd2, czi) and save them as tif or hdf5
the other let you scale and crop multiple EM images (to remove the info part of the image) and save them as tiff or hdf5. It allows using scale-bar and crop region from previous image to make the processing faster.
you can find them in our Github repo

[emilmelnikov]

We can also use github's repo tags/topics for this. So, we ask people who have their own ilastik-related code/scripts to put them in a repo, tag that repo with ilastik-contrib, ilastik-scripts, or whatever, and write a short repo description. On our side, we add a link to the topic to our docs.

Some people already have tags on their repos: https://github.com/topics/ilastik, but I think it makes more sense to reserve ilastik tag for big-ish projects.

cc @k-dominik

[k-dominik]

Hey @emilmelnikov, I think using those tags makes a lot of sense! We should maybe add a few examples (so come up with useful stuff) and then add something here. I also think we should encourage users to open a PR with this repo in order to place a link directly to their specific repo along with some description.

[emilmelnikov]

We should maybe add a few examples (so come up with useful stuff) and then add something here.

Maybe we can adapt some existing code from our group?

I also think we should encourage users to open a PR with this repo in order to place a link directly to their specific repo along with some description.

Github has REST API for that, so we can use it to query by topic, and dynamically show these repos.

[k-dominik]

Github has REST API for that, so we can use it to query by topic, and dynamically show these repos.

I would want to avoid doing anything dynamic there and rather have a guarantee on what is on our site, as anyone can add any tag to their repos.

[emilmelnikov]

I would want to avoid doing anything dynamic there and rather have a guarantee on what is on our site, as anyone can add any tag to their repos.

Fair point...

Where do you want to display this? Documentation, download, or community page?