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Image processing in python
This page contains links to python tools primarly for image processing available at Empa's gitlab.
ROBert's PYthon LIBrary (robpylib)
A collection of often used routines. Useful for image IO.
Requires git and pre-installation of python modules via conda recommended. Can be installed by:
pip install git+https://gitlab.empa.ch/firo/robpylib.git
TOMCAT processing
Methods (mostly python) employed to process and post-process large time-resolved X-ray tomographic microscopy datasets on wicking in yarns. Contains for example, parallelized image registration, machine-learning segmentation or surface mesh extraction. Requires robpylib and Fiji/ImageJ with the xlib and Trainable Weka segmentation plugins.
git clone https://gitlab.empa.ch/firo/tomcat-processing.git
I will attempt to improve the description and documentation in the future.
ICON processing
Methods (mostly python) employed to process and post-process neutron radiography on uptake in textiles. The code is pretty messy and inefficient. Recommended to take interesting methods, but re-develop if necessary.
git clone https://gitlab.empa.ch/firo/icon-processing.git
VIS processing
Methods to process and post-process time series of backlight photography taken with Nikon D90 on wicking in thin electro-spun membranes.
git clone https://gitlab.empa.ch/firo/espun-membrane-processing.git
Volume visualization in Blender with python
This is a repository to automatically render beautifully 4D-image data. In development, keep posted!
git clone https://gitlab.empa.ch/firo/tomcat_blender.git
Videos
Convert ImageJ-avi to mkv as recommended by the ETH research collection for long time storage.
ffmpeg -i input.avi output.mkv -acodec libfaac -vcodec ffv1
currently best working method to get videos suitable for ppt-presentations:
ffmpeg -i input-video.mkv -vf "crop=trunc(iw/2)*2:trunc(ih/2)*2" -q:a 2 -q:v 4 -vcodec wmv2 -acodec wmav2 output-video.avi