Filter image

Apply intensity filters to an image (or image stack) in the workspace.

Description

Apply intensity filters to an image (or image stack) in the workspace. Filters are applied to each Z-stack independently (i.e. channels and timepoints do not interact with each other).

Parameters

Parameter	Description
Input image	Image to apply filter to.
Apply to input image	Select if the filter should be applied directly to the input image, or if it should be applied to a duplicate, then stored as a different image in the workspace.
Output image	Name of the output image created during the filtering process. This image will be added to the workspace.
Filter mode	Filter to be applied to the image. "DoG 2D" Difference of Gaussian filter in 2D. "Gaussian 2D" "Gaussian 3D" "Gradient 2D" "LoG 2D (approximation)" Approximation of a Laplacian of Gaussian filter in 2D. This is used to enhance spot-like features of sizes similar to the setting for "Filter radius". "Maximum 2D" "Maximum 3D" "Mean 2D" "Mean 3D" "Median 2D" "Median 3D" "Minimum 2D" "Minimum 3D" "Ridge enhancement 2D" Uses initial image processing steps from "Ridge Detection" plugin to enhance ridge-like structures. "Rolling frame" Filters the image at each frame based on frames before and/after. The frame window over which the statistics are calculated is user-controllable "Variance 2D" "Variance 3D"
Filter radius	Range the filter is calculated over. Often also referred to as "sigma". Value specified in pixel units, unless "calibrated units" is enabled.
Filter radius 2
Calibrated units	Choose if filter radius is specified in pixel (set to "false") or calibrated (set to "true") units. What units are used are controlled from "Input control".
Rolling filter method	Statistic to apply for rolling frame filtering.
Window indices	When "Filter mode" is set to "Rolling frame", the rolling frame statistic will be calculated for each frame using these relative frames (i.e. with indices set to "-1,1" the statistic would be calculated based on the frames immediately before and after).
Contour contrast	When "Filter mode" is set to "Ridge enhancement 2D", this parameter controls whether the ridges to be enhanced are bright (brighter than the background) or dark (darker than the background).