Creates a nice "exploded" visualization of segmented cells in a tissue.
| Original image | Original with cell labels | Exploded visualization |
|---|---|---|
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Can be used with 2D and 3D (+channels) image data
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Works by shifting the centroids of segmented objects apart by a given amount and then reconstructing the segmented objects around their shifted centroids
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Keep in mind that output images may be substantially larger than input images, especially for
scale_factor > 2 -
See
nbs/examples.ipynbfor some basic usage examples (requires jupyter, matplotlib) -
Requires python 3, numpy, scikit-image
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Installation:
- Clone this repo
- Open CLI and navigate to repo folder
- Activate your environment of choice
- Run
pip install -e .