qim

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')

Contents

docs

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

scripts

mergeTiffs

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

readVol.py

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

txmViewer.py

Python script to read and plot data from txm files.

txm2tiff

Script for converting txm files to tif

notebooks

data_summary.ipynb

Jupyter notebook producing a quick overview of some data

foam_ex.ipynb

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

segmentation_v2.ipynb

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

Modules

inout

Tools for reading and converting between data formats

registration

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

tools

Various small helper functions.

envs

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