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Contents:

  • Introduction
  • Testimonials
  • Installation
    • Install AxonDeepSeg
    • Testing the installation
      • Quick test
      • Comprehensive test
    • 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 a specific image from multiple folders
        • Morphometrics of all the images present in folder(s)
      • Axon Shape: Circle vs Ellipse
        • Circle
        • Ellipse
      • Morphometrics file
      • Colorization
      • Implementation details
        • Diameter estimation
        • Eccentricity estimation
    • Jupyter notebooks
  • Manual correction of segmentation masks
    • Napari plugin
      • Open image and mask
      • Modify the mask
      • Modify the mask
    • GIMP software
  • Training Models
  • Help
  • Citation
  • Changelog
    • 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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