/tissue_exploder

Create a nice exploded visualization of segmented cells in a tissue.

Primary LanguagePythonMIT LicenseMIT

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 .