AxonDeepSeg Logo

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
  • Search

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