gACSON is a freely available Matlab-based software, developed for visualization, segmentation, assessment, and morphology analysis of myelinated axons in 3D-EM volumes of brain tissue samples.
If you use gACSON in your research, please cite it 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).
This software uses several external packages as follows:
- Bio-Formats package: https://www.openmicroscopy.org/bio-formats/downloads/
- Block-matching and 4D filtering (BM4D) algorithm for image denoising: http://www.cs.tut.fi/~foi/GCF-BM3D/
- SLIC supervoxels https://github.com/fk128/SLICSupervoxels
- Accurate fast marching and skeletonization: https://www.mathworks.com/matlabcentral/fileexchange/24531-accurate-fast-marching?s_tid=prof_contriblnk
Please download the Bio-Formats and BM4D packages and place them into the gACSON directory. SLIC supervoxels and Accurate fast marching and skeletonization code is included in gACSON package, but they are distributed under a different open-source licence. Check the licence information in the respective directories.
This version of the software has been implemented and tested in Matlab R2020b.
A manual is available here - posted separately due to the file size. Please note that many of the slides contain videos - if they are not visible please download the file.
Displaying an EM image with its overlaid segmentation:
Machine learning-based semantic segmentation of myelin:
Evaluation panel: