ASA

Sholl Analysis

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:

• Ferreira T, Blackman A, Oyrer J, Jayabal A, Chung A, Watt A, Sjöström J, van Meyel D. Neuronal morphometry directly from bitmap images, Nature Methods 11(10): 982–984, 2014

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.

Resources

• Documentation page
• Release Notes
• API (Javadocs)

Installation

If you use Fiji, you already have Sholl Analysis installed and can start using it right away. Binaries are available from the documentation page or from the ImageJ Maven repository.

Help?

• Want to contribute?
  • Thanks! Please, please do! See here and here for details on how to fork ASA or here on how to initiate a pull request
  • Documentation updates are also welcome, so go ahead and improve the Sholl Analysis documentation page
• Having problems? Found a bug? Need to ask a question?
  • See the plugin’s FAQs, ImageJ’s FAQs and Bug reporting best practices. Then, you can either:
    • Open an issue on this repository
    • Report it on the ImageJ forum

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.

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