tissue_exploder

Creates a nice "exploded" visualization of segmented cells in a tissue.

Original image	Original with cell labels	Exploded visualization

Notes

• Can be used with 2D and 3D (+channels) image data

• Works by shifting the centroids of segmented objects apart by a given amount and then reconstructing the segmented objects around their shifted centroids

• Keep in mind that output images may be substantially larger than input images, especially for scale_factor > 2

• See nbs/examples.ipynb for some basic usage examples (requires jupyter, matplotlib)

• Requires python 3, numpy, scikit-image

• Installation:

  • Clone this repo
  • Open CLI and navigate to repo folder
  • Activate your environment of choice
  • Run pip install -e .