A plugin for ImageJ/Fiji, the de facto standard in scientific image processing, that uses automated Sholl to perform neuronal morphometry directly from bitmap images.
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 does not require previous tracing of the arbor (although analysis can be applied to previously traced arbors)
- It combines curve fitting with several methods to automatically retrieve quantitative descriptors from sampled data
- It allows continuous and repeated sampling around user-defined foci
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
- Complementary routines provided by IJ BAR and its
update site:
- Routines for Bitmap Morphometry
- Routines for Data Analysis
##Installation If you use Fiji, you already have Sholl Analysis installed and can start using it right away. If you are not using Fiji, download the latest stable binary from fiji.sc or from jenkins.imagej.net and drop it into the main ImageJ window (see the documentation page for further details). For information on development builds see Release Notes.
- 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, Fiji FAQs
and Bug reporting best practices. Then, you can either:
- Open an issue on this repository
- Report it on the ImageJ mailing list
- Use Fiji's Report a Bug command
- See the plugin's FAQs, Fiji FAQs
and Bug reporting best practices. Then, you can either:
##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.