AxonDeepSeg
Contents:
Introduction
Quick Start
Help
Training Models
Testimonials
Installation
Which installation method should I use?
Install Options
Graphical User Interface (GUI)
Software Development with AxonDeepSeg
Existing models
Using AxonDeepSeg
Example dataset
Segmentation
Syntax
Segment a single image
Segment multiple images of the same resolution
Segment images from multiple folders
Morphometrics
Syntax
Morphometrics of a single image
Morphometrics of specific images from multiple folders
Morphometrics of all the images present in folder(s)
Morphometrics for Nerve Sections
Diameter Overlay
Axon Shape: Circle vs Ellipse
Circle
Ellipse
Morphometrics file
Colorization & Instance Segmentation
Implementation details
Diameter estimation
Eccentricity estimation
Postprocessing
Morphometrics aggregation
Quality Assessment (QA) Report
Generating QA Reports
Through Napari Plugin
Report Features
Summary Section
Histograms Section
Single Axon Viewer
Keyboard Shortcuts
Export Features
Technical Details
Manual correction of segmentation masks
Napari plugin
Open image and mask
Modify the mask
Axon removal toggle
Show axon metrics
Save the mask
GIMP software
Running the testing suite
Citation
Changelog
v5.5.0 (2026-03-31)
v5.4.0 (2026-02-11)
v5.3.0 (2025-10-10)
v5.2.0 (2025-09-04)
v5.1.1 (2025-07-02)
v5.1.0 (2025-06-27)
v5.0.1 (2025-02-07)
v5.0.0 (2025-01-23)
v4.1.0 (2022-10-07)
Version 4.0.0 - 2022-02-03
Version 3.3.0 - 2022-01-14
Version 3.2.0 - 2020-10-16
Version [3.0] - 2020-03-13
Version [2.1] - 2018-09-25
Version [2.0] - 2018-09-11
Version [1.1] - 2018-08-02
Version [1.0] - 2018-08-02
Version [0.6] - 2018-08-01
Version [0.4.1] - 2018-05-16
Version [0.3] - 2018-02-22
Licensing
Contributors
AxonDeepSeg
Index
Edit on GitHub
Index