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:
- Segmented images, allowing continuous or repeated sampling. In this mode analysis does not require previous tracing of the arbor
- Traced data (SWC, eSWC or SNT traces files)
- 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
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.
In Fiji, subscribe to the NeuroAnatomy update site:
- Run the Fiji Updater (Help › Update..., the penultimate entry in the Help › menu)
- Click Manage update sites
- Select the Neuroanatomy checkbox
- 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.
- Want to contribute?
- Thanks! Please, please do! Head over to morphonets/SNT
- 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
- Report it on the ImageJ forum
- See the plugin's FAQs, ImageJ's FAQs and Bug reporting best practices. Then, you can either:
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.