For questions please contact: tischitischer@gmail.com
This repository conatins a Fiji script to run elastix registration algorithms; Fiji handles the data and runs elastix via system calls.
- install fiji: https://fiji.sc/
- Windows
- install elastix: http://elastix.isi.uu.nl/download.php
- install corresponding Visual C++: http://www.microsoft.com/en-us/download/details.aspx?id=30679
- see also here: http://elastix.isi.uu.nl/FAQ.php
- download and extract this repository: https://github.com/tischi/fiji-registration/archive/master.zip
- move AutoMic_JavaTools-1.1.0-SNAPSHOT-19072016.jar to Fiji's plugin folder
- drag fiji--elastix--interactive.py onto Fiji and [Run]
- select a file in the .../examples/2d-affine folder
- it should work with default settings
- the results will appear in an automatically created output folder named .../examples/2d-affine--fiji
- elastix manual: http://elastix.isi.uu.nl/download/elastix_manual_v4.8.pdf
- the output folder must be created outside the input folder, otherwise the software gets confused.
- the reference_image_index is used to determine the reference file (counting from 0 using the python sort() command on the image filenames)
- using a Mask file is usually improving the results; one good way to make one is to blur and threshold the reference image; the values in the mask image need to be 0 and 1(not 255!)
- elastix seems to use signed-integers; thus one needs to use float for real 16bit images