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ankilab / DeepD3

Apache License 2.0
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several problems #8

Closed Pascal-bucketbreaker closed 1 month ago

Pascal-bucketbreaker commented 4 months ago
  1. Your tutorial does not mention the version of dependencies, so the latest version will be installed. This causes some problems:
    • astype(np.int64) is deprecated and will raise error
    • skimage.feature.peak_local_max() does not have parameter "indices" and will also raise error.
  2. When input is a 3-D tif image or a stack of 2-D tif image, the output can't be read by tifffile.

By the way, can I use the code as a program or 'import deepd3' then deepd3.inference(image)?

anki-xyz commented 3 months ago

Thank you Pascal, we look into this! You can indeed do import deepd3, but you would use from deepd3.core.analysis import Stack, use Stack as an object and use the method predictWholeImage to get a plane-by-plane inference.

Pascal-bucketbreaker commented 2 months ago

The method above running successfully. However, the GPU memory does not clean up after running. After prediction, the 16GB memory is all stucked.