Image analysis scripts developed under the QIM project at Lund University. Members of the QIM project can import the code on LUNARC with

sys.path.insert(0, '/lunarc/nobackup/projects/qim')

The documentation on how to use the LUNARC clusters can be found here

Script for merging a stack of tif files to a single file

Convert .vol files (from ID19 (?)) to .tif

Python script to read and plot data from txm files.

Script for converting txm files to tif

Jupyter notebook producing a quick overview of some data

Jupyter notebook illustrating segmentation and basic quantification of 3D data.

Jupyter notebook illustrating how to use the registration module to segment based on a dual histogram

Tools for reading and converting between data formats

Module for registering two volumes and doing segmentation based on the dual histogram.

Various small helper functions.

.yml files for setting up python environments on Aurora. Not very useful any longer.