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Project-MONAI / MONAILabel

MONAI Label is an intelligent open source image labeling and learning tool.
https://docs.monai.io/projects/label
Apache License 2.0
626 stars 196 forks source link

Cellprofiler app + plugin #1724

Closed binliunls closed 3 months ago

tangy5 commented 4 months ago

looking forward to this!

tangy5 commented 3 months ago

Will look at it soon, thanks, this is great

tangy5 commented 3 months ago

Hi @binliunls , the app generally looks good, but why is the vista developed as an app instead of a model? I assume it will be the only model if we consider it as a new app. Can we do the vista2d model as a model in pathology app?

binliunls commented 3 months ago

Hi @binliunls , the app generally looks good, but why is the vista developed as an app instead of a model? I assume it will be the only model if we consider it as a new app. Can we do the vista2d model as a model in pathology app?

Hi @tangy5 , actually this should be a monai bundle app since the vista2d is a typical monai bundle from the inference aspect. However, the writter of this vista2d is difference from regular bundles which use SaveImage. So I created this app. The other way to solve this is to add the writter logic to the parent class monai bundle app directly. However this will lose the flexibility of adapting other vista2d workflows like train/activate learning to MONAI label. Because the vista2d training and active learning may not comply the MONAI bundle standard.

I would suggest that we keep this app here until all the vista2d workflows (training, validation, inference and active learning) can be adapted to the MONAI bundle app. Then I can make another PR to delete this app and add some explanation of how to start vista2d with MONAI bundle app.

Thanks Bin

tangy5 commented 3 months ago

Hi @binliunls , the app generally looks good, but why is the vista developed as an app instead of a model? I assume it will be the only model if we consider it as a new app. Can we do the vista2d model as a model in pathology app?

Hi @tangy5 , actually this should be a monai bundle app since the vista2d is a typical monai bundle from the inference aspect. However, the writter of this vista2d is difference from regular bundles which use SaveImage. So I created this app. The other way to solve this is to add the writter logic to the parent class monai bundle app directly. However this will lose the flexibility of adapting other vista2d workflows like train/activate learning to MONAI label. Because the vista2d training and active learning may not comply the MONAI bundle standard.

I would suggest that we keep this app here until all the vista2d workflows (training, validation, inference and active learning) can be adapted to the MONAI bundle app. Then I can make another PR to delete this app and add some explanation of how to start vista2d with MONAI bundle app.

Thanks Bin

Good, I think the app design is good. Refactoring to a model and customization will be too much, it isn't worth the effort.

tangy5 commented 3 months ago

@binliunls , before merge, please make sure all workflow are working normally about Ceelprofiler. Let's talk about about moving the vista2d mode to monaibundle app later. And please keep consistent on the name "VISTA2d" over "vista" as Sachi mentioned. Thank you

binliunls commented 3 months ago

Created a PR in the cellprofiler plugin repo for the cellprofiler CI test.

Nic-Ma commented 3 months ago

Hi @binliunls ,

Could you please help also develop a tutorial and submit to: https://github.com/Project-MONAI/tutorials/tree/main/monailabel?

Thanks in advance.

binliunls commented 3 months ago

Hi @binliunls ,

Could you please help also develop a tutorial and submit to: https://github.com/Project-MONAI/tutorials/tree/main/monailabel?

Thanks in advance.

Merged https://github.com/Project-MONAI/tutorials/pull/1803