From 2a81e5ff57fd0389f5f3b055c8abaa6f7a060d8a Mon Sep 17 00:00:00 2001
From: Fischer Robert <robert.fischer@psi.ch>
Date: Tue, 4 Oct 2022 14:02:30 +0200
Subject: [PATCH] backup von EMPAwiki image processing, to be included in
 readme

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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
+```
+