Cellprofiler app + plugin

[binliunls]

No description provided.

[tangy5]

looking forward to this!

[tangy5]

Will look at it soon, thanks, this is great

[SachidanandAlle]

if it's vista2d then better to use sample-apps/vista2d. we have conflicting vista3d also

[binliunls]

Will do

[SachidanandAlle]

does this change break any existing checkpoints for other models? bundles? other apps?

[binliunls]

I don't think so. Because of this line model_state_dict = checkpoint.get(self.model_state_dict, checkpoint). If the checkpoint is the model_state_dict, then it will return the checkpoint directly. Otherwise it will return the model_state_dict. I think this is why this line exists here. And the old condition logic which uses the checkpoint looks like a bug to me. Please correct me if there are other cases.

Thanks
Bin

[tangy5]

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]

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]

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]

The trainer is empty now right?
And we only support inference.

[binliunls]

Yes, we currently only need inference for this APP. If there is a requirement for trainning, we can also add it.

[tangy5]

@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]

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

[Nic-Ma]

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]

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 Project-MONAI/tutorials#1803