locpix#

locpix is a Python library for analysing point cloud data from SMLM. This includes the following functionality:

  1. Preprocess : Initialises project and converts .csv files representing SMLM data (point cloud) into .parquet files, necessary for this software

  2. Annotate : Generating histograms from the SMLM data and manually annotating these histograms to extract relevant localisations and adding markers to the images as seeds for the watershed algorithm.

  3. Segmentation:

    1. Classic segmentation : Use classic method to segment histograms to extract relevant localisations

    2. Cellpose segmentation : Use Cellpose method to segment histograms to extract relevant localisations

    3. Ilastik segmentation : Use Ilastik method to segment histograms to extract relevant localisations

    4. UNET segmentation : Use UNET to segment histograms to extract relevant localisations

  4. Membrane performance : Performance metrics calculation based on the localisations (not the histograms!)

Note

This project is under active development.

For GitHub please see GitHub <”https://github.com/oubino/locpix”> For the bug tracker please see Bug Tracker <”https://github.com/oubino/locpix/issues”>