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

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Deep LearninggACSON
Overview

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

DOI

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.

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Comments
  • TODO list:

    TODO list:

    • stretch the Z-dimension in XY/XZ/YZ views
    • read the voxel sizes from Amira mesh files
    • machine-learning part - change the size of the labels or delete/modify the ones that were already placed
    • zooming kept when changing slides
    • When there are several datasets open, the slider may disappear, while the 3view plane view stays: image
    opened by AndreaBehan 0
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Andrea Behanova
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