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README.md

Sholl Analysis

Maintenance DOI Travis GPL License Codacy Badge

⚠️ ⚠️This project is now part of SNT. The most up-to-date code for this plugin can now be found at morphonets/SNT ⚠️ ⚠️

A plugin for ImageJ, the de facto standard in scientific image processing, that uses automated Sholl to perform neuronal morphometry directly from bitmap images. It is part of Fiji.

Sholl analysis (Sholl, D.A., 1953) is a method used by neuroanatomists to describe neuronal arbors. The plugin takes the original technique beyond conventional approaches, offering major advantages over other implementations:

  • It can perform the analysis in either 2D or 3D from three distinct sources:
    1. Segmented images, allowing continuous or repeated sampling. In this mode analysis does not require previous tracing of the arbor
    2. Traced data (SWC, eSWC or SNT traces files)
    3. Tabular data (CSV and related files)
  • It combines curve fitting with several methods to automatically retrieve quantitative descriptors from sampled data (currently ~20 metrics)
  • Allows analysis of sub-compartments centered on user-defined foci
  • It is scriptable and capable of batch processing

Why ASA? Throughout 2012 the plugin was temporarily called Advanced Sholl Analysis, hence the acronym

Publication

This program is described in Nature methods. Please cite it if you use it in your own research:

The manuscript uses Sholl Analysis to describe and classify morphologically challenging cells and is accompanied by a Supplementary Note that presents the software in greater detail.

Installation

In Fiji, subscribe to the NeuroAnatomy update site:

  1. Run the Fiji Updater (Help › Update..., the penultimate entry in the Help › menu)
  2. Click Manage update sites
  3. Select the Neuroanatomy checkbox
  4. Click Apply changes and Restart Fiji. Sholl-related commands will be registered under Plugins>Neuroanatomy> in the main menu and SNT scripts under Templates>Neuroanatomy> in Fiji's Script Editor. The plugin can also be accessed from SNT itself.

The documentation page contains usage details.

Help?

License

This program is free software: you can redistribute them and/or modify them under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.