Semi-automated

The method to use for thresholding. Currently only OTSU is available.

This package implements the interscale orthonormal wavelet thresholding algorithm based on the SURE-LET principle. A multichannel extension is also available. Java Applets are available too.

Anisotropic filters are a class of filter that reduces noise in an image while trying to preserve sharp edges

There are two implementations of Tschumperle/ R. Deriche filter ("anisotropic diffusion") for ImageJ Plugin

1. in the "imaging book" codes: see the javadoc here.

2. in Xlib

The Sholl technique is used to describe neuronal arbors. This plugin can perform Sholl directly on 2D and 3D grayscale images of isolated neurons. Its internal algorithm to collect data is based upon how Sholl analysis is done by hand — it creates a series of concentric shells (circles or spheres) around the focus of a neuronal arbor, and counts how many times connected voxels defining the arbor intersect the sampling shells. The major advantages of this plugin over other implementations are:

• When analyzing images directly, it does not require previous tracing of the arbor (although it can also analyze traced arbors)
• It combines curve fitting with several methods to automatically retrieve quantitative descriptors from sampled data, which allows direct statistical comparisons between arbors
• It allows continuous and repeated sampling around user-defined foci
• It allows batch processing