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[FEA] Investigate using black

4

Previously we tried to use black for formatting Python, but ran into some issues. It would be good to revisit this at some point cc @grlee77 @quasiben

jakirkham

[gpuCI] Forward-merge branch-22.10 to branch-22.12 [skip gpuci]

1

Forward-merge triggered by push to `branch-22.10` that creates a PR to keep `branch-22.12` up-to-date. If this PR is unable to be immediately merged due to conflicts, it will remain open...

GPUtester

**Describe the bug** `cucim.skimage.util.img_as_float` returns `np.float32` while `skimage.util.img_as_float` returns `np.float64` if the input image is from dtype `np.uint16` **Steps/Code to reproduce bug** ```python import sys import skimage import cucim import...

monzelr

Adding scikit-image' Blob detection (second try)

8

Hi again, due to renaming my branch to `add-blob-detection`, the old PR #411 had been closed. This PR solves issue #398. Basically, I followed the suggestions by @grlee77 and here...

monzelr

Adding `extras_require`

2

We have a TODO flagged here for `install_requires`. Also `cupy` and other dependencies are not currently listed. It would be worthwhile to update these particularly for package formats relying on...

jakirkham

Please review/merge #406 before this one as those changes are also present here. This PR adds support for anisotropic pixel/voxel shape to `distance_transform_edt` via the `sampling` kwarg. The changes involve...

grlee77

This PR adds a demo for `distance_transform_edt`. One illustrates computing distances from a sparse set of background points while the other illustrates computing distances on a binary object. The output...

grlee77

This PR gives a further 2-4x speedup to the 2D and 3D distance transform functions by creating dedicated elementwise CUDA kernels for the pre- and post-processing steps. These include, for...

grlee77

## Description We can easily preserve float16 dtype for many `cucim.skimage.filters` and `cucim.skimage.transform` functions because the underlying CuPy-based kernels already support it. This may generally be desirable, but two potential...

grlee77

[FEA] Quick Hash of WSI

2

Often times MONAI users need to collate the patches extracted from the same WSI. Currently, we are relying on the file path to perform such operation but similar to OpenSlide...

drbeh