aabdz/gacson

gACSON software for visualization, processing and analysis of three-dimensional electron microscopy images

gACSON

gACSON software is to visualize, segment, and analyze the morphology of neurons in three-dimensional electron microscopy images.

If you use any part of gACSON in your research, please cite the software as

The segmentation algorithm used in gACSON is based on ACSON pipeline described in Abdollahzadeh, A., Belevich, I., Jokitalo, E., Tohka, J. & Sierra, A. Automated 3D Axonal Morphometry of WhiteMatter.Sci. Reports9, 6084 (2019).

Graphical user interface (GUI) for the segmentation and quantification of EM images in grey matter in MATLAB, enabling user interactive segmentation, proofreading, and correcting errors of an automated segmentation.

This software uses BM4D Matlab software, which can be found in http://www.cs.tut.fi/~foi/GCF-BM3D/

This software uses Bio-Formats 5.9.2 package, which can be found in https://www.openmicroscopy.org/bio-formats/downloads/

In order to be able to use this software, please download these two packages. They are not included to gACSON.

The path to the Bioformats has to be adjusted in file gACSON.m on the line 156.

This version of the software has been implemented and tested in Matlab R2018b.