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Hello,
I'm trying to implement the SwinUNETR tutorial in order to segment Light-Sheet Scans of ZebraFish embryos.
All the process goes well, until I try to visualize my output, which is empty. Also, my training loss and Dice Metric seem odd...
I'm not really sure what the next steps are to have better results...
Here are my transforms, training and validation processes, and what I get with a trained model.
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Hello,
![transforms](https://private-user-images.githubusercontent.com/168013196/327379875-7b18e724-fe2a-4abb-82ae-d59c733ef6c5.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MTg4NTg2MDYsIm5iZiI6MTcxODg1ODMwNiwicGF0aCI6Ii8xNjgwMTMxOTYvMzI3Mzc5ODc1LTdiMThlNzI0LWZlMmEtNGFiYi04MmFlLWQ1OWM3MzNlZjZjNS5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNjIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDYyMFQwNDM4MjZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT00NjJjZWUwOWM2NjY1Nzg0NmI3ZDdjMTJjNGI4MTUwYTYyNWNkYjQ2MDIyMGM1MmE0OWNkY2VkNDJjYTMyNDAzJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.WFGgovIWVp6Bm_Tb7djQgU1pzD2uONATvABwMD0kt1M)
![datavisualisation](https://private-user-images.githubusercontent.com/168013196/327379856-dadeebd8-9cc9-4953-b053-1677207dd60e.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MTg4NTg2MDYsIm5iZiI6MTcxODg1ODMwNiwicGF0aCI6Ii8xNjgwMTMxOTYvMzI3Mzc5ODU2LWRhZGVlYmQ4LTljYzktNDk1My1iMDUzLTE2NzcyMDdkZDYwZS5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNjIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDYyMFQwNDM4MjZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1kNjAwMTYwZWFhMTFjMjEzYmZjOTRkM2U0YjQ5MmRiNmFhNTNjNGUwZTM3MGNkMjI4MzJkNjc2MTk3YzcxNWNhJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.QjOHyvDkHywAZ2YK5gqWho3k6KDghtriTONEm7z8Dxg)
![training and validation](https://private-user-images.githubusercontent.com/168013196/327380249-143b5018-c8cf-4768-b7f5-d28dc9aee795.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MTg4NTg2MDYsIm5iZiI6MTcxODg1ODMwNiwicGF0aCI6Ii8xNjgwMTMxOTYvMzI3MzgwMjQ5LTE0M2I1MDE4LWM4Y2YtNDc2OC1iN2Y1LWQyOGRjOWFlZTc5NS5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNjIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDYyMFQwNDM4MjZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1jZDdmZDZiNDkzYjdmMzllNGYxYTA2NzVkNWNmNjUzMmI1ODVkNmZiZTljNTE2Y2FkMzVhZmE3NGNmYzQxYTdjJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.Qw0OyHxhs5rQ4p4iiICZiq6fgxfxh9aYoE2nNaau1gs)
![Dice_Metric1](https://private-user-images.githubusercontent.com/168013196/327379865-d538f89f-d834-40bb-816f-5db439305dce.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MTg4NTg2MDYsIm5iZiI6MTcxODg1ODMwNiwicGF0aCI6Ii8xNjgwMTMxOTYvMzI3Mzc5ODY1LWQ1MzhmODlmLWQ4MzQtNDBiYi04MTZmLTVkYjQzOTMwNWRjZS5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNjIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDYyMFQwNDM4MjZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT00ZmU3ZDVkYTgzNTY2MDUxMzIzYTM4MTk4MzhmMmEzNDBhOWM3MDg0N2YxNTM2MTMzOTY5ZGVjM2MwZmM2MDQ4JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9._isPYCnlMZt2jCQnBwx_46FMTkTO0k7cr0IV8Rguzns)
![output_1](https://private-user-images.githubusercontent.com/168013196/327379868-e9acedcd-0f72-4aa0-9dc4-a7949503ec70.PNG?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MTg4NTg2MDYsIm5iZiI6MTcxODg1ODMwNiwicGF0aCI6Ii8xNjgwMTMxOTYvMzI3Mzc5ODY4LWU5YWNlZGNkLTBmNzItNGFhMC05ZGM0LWE3OTQ5NTAzZWM3MC5QTkc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNjIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDYyMFQwNDM4MjZaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1lNTM1YzQyZTMxZDBjNzM3OGQ2MjMzNjM5MzhiYTk3M2I2NDc1ODM0MzMxZjY1MGJiMjNlMjk1OTBlZjhlNjA1JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.L3R95xiCLunL0dKsJOnVwurIzf4V5elYe7B2hZImWso)
I'm trying to implement the SwinUNETR tutorial in order to segment Light-Sheet Scans of ZebraFish embryos.
All the process goes well, until I try to visualize my output, which is empty. Also, my training loss and Dice Metric seem odd...
I'm not really sure what the next steps are to have better results...
Here are my transforms, training and validation processes, and what I get with a trained model.
Thank you in advance for your help.
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