Sholl Analysis: Neuronal morphometry directly from bitmap images

[JohnTigue]

Neuronal morphometry directly from bitmap images

• Published: 29 September 2014
• Tiago A Ferreira, Arne V Blackman, Julia Oyrer, Sriram Jayabal, Andrew J Chung, Alanna J Watt, P Jesper Sjöström & Donald J van Meyel
• Nature Methods volume 11, pages 982–984(2014)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5271921/:

In 1953, Donald Sholl published his well-known technique for quantitative analysis of the complex arbors of dendrites and axons1, but conventional methods still require their reconstruction via time-consuming manual or semi-automated tracing from microscopy images. To bypass this reconstruction step and perform the Sholl technique directly on images instead, we developed Sholl Analysis, an open-source program for ImageJ/Fiji2 (Supplementary Fig. 1). The plug-in employs an improved algorithm to retrieve data from two- or three-dimensional (2D or 3D) bitmap images in any format supported by the Bio-Formats library (Supplementary Methods). It pairs this data retrieval with curve-fitting, regression analysis and statistical inference so that users can automatically extract a collection of Sholl-based metrics of arborization

In our experience, the software required only 10–15 min of processing for each of the analyzed PV interneurons, whereas manual reconstructions of such cells typically take 3–4 h4, and longer yet for Purkinje cells. Because it bypasses reconstruction entirely, morphometry directly from bitmap images is an efficient method for quantification of neuronal arbors and classification of cells.

Code:

• https://imagej.net/Sholl_Analysis
• GPLv3

[JohnTigue]

This just has to be done! Very high info return on compute.

[JohnTigue]

The Sholl Analysis software can be applied universally to grayscale images of neurons of different shapes or sizes provided that they can be distinguished spatially or spectrally. It can be used in synergy with additional tools that sample bitmap images directly, such as skeletonization algorithms (http://fiji.sc/Strahler) to automate the hierarchical ordering of branches within arbors5.

See #218