Extracting randomly rotated patches from the WSI. about pathology-whole-slide-data HOT 4 CLOSED

Hi Mart,

Great, there is options already! I'll try those. I think I should manage with the information provided. Good to hear that you're working on documentation. I'll let you know if I have any further issues or questions.

Thanks,

Michel

from pathology-whole-slide-data.

Dear Michel,

In the batch iterator, you can use any albumentations augmentation. This augmentation callback was implemented by @thijsgelton via batch callbacks. Here is an example config file that includes the configuration and shows how you can use callbacks and in specific the albumentations callback: https://github.com/DIAGNijmegen/pathology-whole-slide-data/blob/main/tests/test_files/user_config.yml

You can also create a Batch or Sample callback and use custom data augmentations. For example, you can subclass SampleCallback and use your own subclass. All patches and labels will be passed through if you add your callback in your config file.

You can use random angle rotation in a custom SampleCallback and crop via the FitOutput sample callback. Please note that this is a sample callback, so the rotation should also be a sample callback and should be specified before the cropping callback. There is no batch cropping callback, but I will implement that soon.

For training HookNet, we used spatial, color, noise, and stain augmentations. Due to low-resolution and high-resolution patches, you will have to be careful in applying distortive augmentations because the effect will be more severe in the low-resolution patch and, therefore can misalign the patches.

I am working on documentation, but this is not done yet, so please let me know if anything is unclear.

Best wishes,
Mart

from pathology-whole-slide-data.

Dear Michel,

In the batch iterator, you can use any albumentations augmentation. This augmentation callback was implemented by @thijsgelton via batch callbacks. Here is an example config file that includes the configuration and shows how you can use callbacks and in specific the albumentations callback: https://github.com/DIAGNijmegen/pathology-whole-slide-data/blob/main/tests/test_files/user_config.yml

You can also create a Batch or Sample callback and use custom data augmentations. For example, you can subclass SampleCallback and use your own subclass. All patches and labels will be passed through if you add your callback in your config file.

You can use random angle rotation in a custom SampleCallback and crop via the FitOutput sample callback. Please note that this is a sample callback, so the rotation should also be a sample callback and should be specified before the cropping callback. There is no batch cropping callback, but I will implement that soon.

For training HookNet, we used spatial, color, noise, and stain augmentations. Due to low-resolution and high-resolution patches, you will have to be careful in applying distortive augmentations because the effect will be more severe in the low-resolution patch and, therefore can misalign the patches.

I am working on documentation, but this is not done yet, so please let me know if anything is unclear.

Best wishes, Mart

Hi Mart,
I'm also in the process of applying augmentation technique. The usr_config you shared in this reply can not be found anymore. Would it be possible that you could share a new one? Thanks!

from pathology-whole-slide-data.

Dear @yuling-luo

You can add something like this to your user config:

batch_callbacks:
      - "*object": wholeslidedata.interoperability.albumentations.callbacks.AlbumentationsSegmentationBatchCallback
        augmentations:
          - RandomRotate90:
              p: 0.5
          - Flip:
              p: 0.5
          - RandomSizedCrop:
              p: 1
              min_max_height: [ 100, 200 ]
              height: 284
              width: 284
          - ElasticTransform:
              p: 0.5
              alpha: 45
              sigma: 6
              alpha_affine: 4
          - HueSaturationValue:
              hue_shift_limit: 0.2
              sat_shift_limit: 0.3
              val_shift_limit: 0.2
              p: 0.5
          - GridDistortion:
              p: 1.0
          - RandomBrightnessContrast:
              p: 0.4

Please note that you will need albumentations==1.2.1, newer version of albumentations wont work (will have to update the callback to make it compatible with newer versions.)

Let me know if you have any trouble

from pathology-whole-slide-data.