Tile segmentation and fluorescence quantification of big 2D images.

Segmentation relies on Stardist (https://github.com/stardist/stardist). Examples of the three main ussages of the software can be found on the examples folder:

• compute_tile_overlap.py gives you an estimation of the tile overlap that should be used.
• remove_debris.ipynb gives you an estimation of the size on the debris in your data so that it can be thresholded out.
• fluo_quantification_and_thresholding.ipynb is an example of quantification of the fluorescence inside the segmented nuclei using the overlap and thresholding obtained with the other two scripts.

Installation

$ python -m pip install 'tilesegment @ git+https://github.com/dsb-lab/tilesegment'

Usage

For a ready to use example check examples/fluo_quantification_and_thresholding.ipynb