Image registration

2D registration (sections in a stack)

Wang CW, Ka SM and Chen A. 2014. Robust image registration of biological microscopic images. Sci Rep 4:6050. http://www.nature.com/srep/2014/140813/srep06050/full/srep06050.html

http://www-o.ntust.edu.tw/~cweiwang/ImageRegistration/

Wang CW, Budiman Gosno E and Li YS. 2015. Fully automatic and robust 3D registration of serial-section microscopic images. Sci Rep 5:15051.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4598826/

http://www-o.ntust.edu.tw/%7ecweiwang/3Dregistration/

Reading .vsi whole-slide images from Olympus scanner:

http://biop.epfl.ch/TOOL_VSI_Reader.html

http://imagej.net/OlympusImageJPlugin

TrakEM:

http://imagej.net/TrakEM2

Possum:

uses a reference volume for alignment

https://github.com/pmajka/poSSum

Majka P and Wojcik DK. 2015. Possum-A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections. Neuroinformatics. http://www.ncbi.nlm.nih.gov/pubmed/26687079

Voloom (commercial):
https://micro-dimensions.com/voloom

3D registration (volume images)

elastix:

http://elastix.isi.uu.nl/index.php

http://elastix.isi.uu.nl/download/elastix_manual_v4.8.pdf

Atlas Toolkit: (ImageJ plugins)

http://imagej.net/Atlas_Toolkit

https://www.youtube.com/watch?v=2JwRZm5dst8

ImageJ Action Bar Plugin:

Extends ImageJ's graphical user interface to provide one or many easy to use button bar(s).

http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start

http://imagej.net/BUnwarpJ

3D image visualization

3D Slicer

DICOM, 3D printing, image registration, visualization

Fedorov A, et al. 2012. 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magn Reson Imaging 30:1323-41. http://www.ncbi.nlm.nih.gov/pubmed/22770690

https://www.slicer.org/