locpix#
locpix is a Python library for analysing point cloud data from SMLM. This includes the following functionality:
Preprocess : Initialises project and converts .csv files representing SMLM data (point cloud) into .parquet files, necessary for this software
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.
Segmentation:
Classic segmentation : Use classic method to segment histograms to extract relevant localisations
Cellpose segmentation : Use Cellpose method to segment histograms to extract relevant localisations
Ilastik segmentation : Use Ilastik method to segment histograms to extract relevant localisations
UNET segmentation : Use UNET to segment histograms to extract relevant localisations
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”>