Artifact Removal Filters

The Artifact Removal filters can be used to remove stripes and ring artifacts from image data.

The destriping filters work by adding a pattern that interferes with the image to remove stripes, as shown in the example below for vertical destriping.

Original data (left) and preview after destriping (right)

Artifact removal filters and settings

	What it does	Settings
Arbitrary Angle Destriping	Removes stripes that appear at an arbitrary angle, using the Fourier-Wavelet based method.	Angle Sigma foreground Sigma background Levels Wavelet
Horizontal Destriping*	Removes horizontal stripes, using the Fourier-Wavelet based method.	Sigma foreground Sigma background Levels Wavelet
Ring Artifact Removal**	Removes ring artifacts. As shown below, the ring artifact removal filter requires a circular region. This region can be created automatically at the image center or manually with the three-point circle tool (see Using the Region Tools). Original data (left) and preview after removing ring artifacts(right)	Minimum angle in degrees Maximum width in pixels Circular region
Vertical Destriping*	Removes vertical stripes, using the Fourier-Wavelet based method.	Sigma foreground Sigma background Levels Wavelet

* Implemented with two different destriping algorithms from Pystripe (https://github.com/chunglabmit/pystripe). The first uses wavelets to deconvolve along the striping direction. The second, which is adapted from https://github.com/ChristophKirst/ClearMap2, uses a combination of background estimation from a linear patch in the striping direction and a square background patch. You should also refer to:
Kirst, et al. "Mapping the Fine-Scale Organization and Plasticity of the Brain Vasculature." Cell 180.4 (2020): 780-795 (https://doi.org/10.1016/j.cell.2020.01.028).
Renier et al. "Mapping of brain activity by automated volume analysis of immediate early genes." Cell 165.7 (2016): 1789-1802 (https://doi.org/10.1016/j.cell.2016.05.007).

** Implemented from TomoPy's module for data correction and masking functions (https://tomopy.readthedocs.io/en/stable/api/tomopy.misc.corr.html#tomopy.misc.corr.remove_ring).