Yolo_predict_tutorial_deepsea

[mjoudy]

Hi all,

This is a tutorial for yolo prediction tool based on deepsea seanoe dataset. Please kindly give your feedback.

[kostrykin]

Thanks! Some comments inside.

[yvanlebras]

Hi Mohammad. I added previously added content from the older PR (sorry, I was not seeing there was 2 identicial PR...) proposing a format more linked with GTN material with hands-on, comment tip and warning. I also propose to be co-author and to propose this tutorial in both Imaging and Ecology GTN sections (if this seems ok for you @shiltemann @bebatut @hexylena ).

Plaese, don't hesitate to modify / comment / revert !

[anuprulez]

@yvanlebras I agree. We can have this tutorial for both - Ecology and BioImaging. Actually, i was talking to @sunyi000 two days back and he suggested the same. He plans to work on a new tutorial for Yolo training tool. @mjoudy can you use images from BioImage model zoo (https://bioimage.io/#/models) to make prediction using Yolo models? Some sample images you can find in this tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/process-image-bioimageio/tutorial.html

[anuprulez]

@yvanlebras @kostrykin thank you very much for your work on this. @mjoudy please address the issues mentioned

[yvanlebras]

For SEANOE data part, I can also add some steps further to take all txt files to produce a summary of number of each species detected if relevant / of interest.

[mjoudy]

Hi Mohammad. I added previously added content from the older PR (sorry, I was not seeing there was 2 identicial PR...) proposing a format more linked with GTN material with hands-on, comment tip and warning. I also propose to be co-author and to propose this tutorial in both Imaging and Ecology GTN sections (if this seems ok for you @shiltemann @bebatut @hexylena ).

Plaese, don't hesitate to modify / comment / revert !

Thanks Yvan. sorry I had made a mistake and opened two PR. after a while I closed one of them.
Thank you for your suggestions and help.

[mjoudy]

@yvanlebras I agree. We can have this tutorial for both - Ecology and BioImaging. Actually, i was talking to @sunyi000 two days back and he suggested the same. He plans to work on a new tutorial for Yolo training tool. @mjoudy can you use images from BioImage model zoo (https://bioimage.io/#/models) to make prediction using Yolo models? Some sample images you can find in this tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/process-image-bioimageio/tutorial.html

Thank you Anup for suggestions. Actually, as far as I know, images and models in the BioImage zoo are not yolo-based. Please let me know if there are any. Currently, I am looking for some bio-inspired yolo pre-trained models to make a better example for the segmentation part.

[kostrykin]

I have gathered a list of open issues:

• https://github.com/galaxyproject/training-material/pull/6258/files#r2230652505
• https://github.com/galaxyproject/training-material/pull/6258/files#r2230658220
• https://github.com/galaxyproject/training-material/pull/6258/files#r2270065822
• https://github.com/galaxyproject/training-material/pull/6258/files#r2244759562
  I was actually going to work on this one, but I got blocked by the one below:
• https://github.com/galaxyproject/training-material/pull/6258/files#r2270096781

[yvanlebras]

Hi everyone. Really sorry to come back just now on this PR! I created a new history to try on "just" 2 input images https://usegalaxy.eu/u/ylebras/h/yolo-training-on-just-2-images so we can put these files in Zenodo for a more easier to follow and use tutorial! Will try to create the GTN Zenodo repo, and / or Arthur will continue and finish this tutorial!
When I was tested, I saw that the last version of the tool, v4, is not workinf properly apparently (see error datasert on previously mentionned history)...

[shiltemann]

Thanks @mjoudy! I just pushed some changes to address the linting errors.

Thanks @yvanlebras and @kostrykin for reviewing testing and improving this

[kostrykin]

Hi everyone. Really sorry to come back just now on this PR! I created a new history to try on "just" 2 input images https://usegalaxy.eu/u/ylebras/h/yolo-training-on-just-2-images so we can put these files in Zenodo for a more easier to follow and use tutorial! Will try to create the GTN Zenodo repo, and / or Arthur will continue and finish this tutorial! When I was tested, I saw that the last version of the tool, v4, is not workinf properly apparently (see error datasert on previously mentionned history)...

The error is with the toolshed.g2.bx.psu.edu/repos/bgruening/yolo_predict/yolo_predict/8.3.0+galaxy4 tool, @sunyi000 can you maybe help with this?

[sunyi000]

Hi everyone. Really sorry to come back just now on this PR! I created a new history to try on "just" 2 input images https://usegalaxy.eu/u/ylebras/h/yolo-training-on-just-2-images so we can put these files in Zenodo for a more easier to follow and use tutorial! Will try to create the GTN Zenodo repo, and / or Arthur will continue and finish this tutorial! When I was tested, I saw that the last version of the tool, v4, is not workinf properly apparently (see error datasert on previously mentionned history)...

The error is with the toolshed.g2.bx.psu.edu/repos/bgruening/yolo_predict/yolo_predict/8.3.0+galaxy4 tool, @sunyi000 can you maybe help with this?

from the output in history, looks like a detection model is used for segmentation tasks, so the masks are None?

[yvanlebras]

Hi everyone, hope all is ok for each of you. It seems to me the tuto is in a standby process. If ok for you all, I can propose to modify it removing the last part "Segmentation with an Ultralytics example" just malking prediction on underwater species? Also, I wanted to push this tuto on Ecology topic. Can we put this tuto on both Imaging and Ecology topics ?

[bgruening]

Please feel free to take it over @yvanlebras. Thanks.

[shiltemann]

Thanks @yvanlebras 👍

For adding a tutorial to two topics, I recently implemented this, have a look at the subtopics section of this tutorial https://galaxyproject.github.io/training-material/topics/contributing/tutorials/create-new-topic/tutorial.html#subtopics

and also this PR: #6531

basically you can define crosstopic_tutorials in a subtopic to include tutorials from different topics in the tutorial list

[yvanlebras]

Thank you Saskia, Amazing !!!!

[yvanlebras]

So, if ok for you, I will propose a yolo oriented tuto reusing what we were doing here in the Ecology topic, and then we can close this PR if relevant for you all

[shiltemann]

closing this in favour of #6757