Pancreatic Phase Contrast Cell Segmentation (U-Net)

[utterances-bot]

Pancreatic Phase Contrast Cell Segmentation (U-Net)

Bioimage.io -- an AI model repository for deep learning.

https://bioimage.io/?tags=pancreatic&id=10.5281%2Fzenodo.5914248&type=model

[carlosuc3m]

the link for the h5 weights is broken (https://zenodo.org/api/files/2d92e820-1b25-40f5-a2af-3219df97d7f7/unet_pancreatic_cell_segmentation.h5)

[FynnBe]

the file name is wrong. there is a keras_model.h5 file in the record. (keras weights are not validated (yet), so we didn't notice this). @iarganda could you please update the model accordingly?

[esgomezm]

Please point to the maintainers! I have corrected the specifications. Now it should work. Also, why does the model download say ZeroCostDL4Mic if the model is not compatible with ZeroCostDL4Mic?

[esgomezm]

@carlosuc3m can you check whether it works?

[carlosuc3m]

I will check it now with the BioEngine. however the yaml still points to a broken link: https://zenodo.org/api/files/2d92e820-1b25-40f5-a2af-3219df97d7f7/unet_pancreatic_cell_segmentation.h5 @esgomezm

[carlosuc3m]

I just checked the model and it does not work on the BioEngine. I guess it is because of the incorrect link in the yaml file, the source should be pointing to the correct file @esgomezm @oeway

[esgomezm]

@carlosuc3m it should work now! I have just updated the model manually in zenodo because the updater does not update the rdf.yaml file correctly in the zenodo repository. @oeway I remember this was already a problem a while ago and seems that it's still not working properly. Any idea?

[carlosuc3m]

it still does not work. The Bioimage.io collections rdf.yaml files keep pointing towards the incorrect keras weight source link. This model runs on keras on the BioEngine, so the keras link should not be broken and should point to a correct Keras model @esgomezm

[esgomezm]

Hi I cannot help with this one. The RDF file in the zenodo repository is correct and points to the keras model. There's something when updating the model that seems to be broken as it does not update correctly the model specifications. @oeway is probably not able to fix at the moment. @FynnBe do you know how to solve this?

[esgomezm]

Hi there! @oeway I'm trying to load this model using the bioimageio.core and still have the same problem: the system does not update the link to the keras weights. It still points to https://zenodo.org/api/files/2d92e820-1b25-40f5-a2af-3219df97d7f7/unet_pancreatic_cell_segmentation.h5

Any idea about how to solve this one?

[oeway]

Hi there! @oeway I'm trying to load this model using the bioimageio.core and still have the same problem: the system does not update the link to the keras weights. It still points to https://zenodo.org/api/files/2d92e820-1b25-40f5-a2af-3219df97d7f7/unet_pancreatic_cell_segmentation.h5

Any idea about how to solve this one?

I just checked, it appears that the latest version is not generated which make sense, since we decided to block it. Here, we said that @esgomezm will update with a newer version.

Here is the resource.yaml: https://github.com/bioimage-io/collection-bioimage-io/blob/main/collection/10.5281/zenodo.5914248/resource.yaml

And here are the available versions, note that the latest two versions in the resource.yaml are blocked. https://github.com/bioimage-io/collection-bioimage-io/tree/gh-pages/rdfs/10.5281/zenodo.5914248

Therefore, @esgomezm you should perhaps upload with a newer version (although I don't remember what needed to be changed for this one ;)

[carlosuc3m]

This model is still pointing to invalid keras weights @esgomezm @lmoyasans

[carlosuc3m]

Still broken

[carlosuc3m]

still invalid keras weights