Best focus stack

Description

Extract a Z-substack from an input stack based on either manually-selected slices, or an automatically-calculated best-focus slice. For automated methods, best focus is determined using the local 2D variance of pixels in each slice. It is possible to extract a fixed number of slices above and below the determined best-focus slice.

Parameters

Input image (default = "") Image to extract substack from.

Output image (default = "") Substack image to be added to the current workspace.

Best-focus calculation (default = "Largest standard deviation") Method for determining the best-focus slice. "Largest standard deviation" calculates the standard deviation of each slice.

Relative start slice (default = "0") Index of start slice relative to determined best-focus slice (i.e. -5 is 5 slices below the best-focus).

Relative end slice (default = "0") Index of end slice relative to determined best-focus slice (i.e. 5 is 5 slices above the best-focus).

Smooth timeseries (default = "false") Apply median filter to best focus slice index over time. This should smooth the transitions over time (prevent large jumps between frames).

Smoothing range (odd numbers) (default = "5") Number of frames over which to calculate the median. If the specified number is even it will be increased by 1.

Reference image (default = "")

Calculation source (default = "Internal")

External source (default = "")

Channel mode (default = "Use single channel") How many channels to use when calculating the best-focus slice. "Use all channels" will use all channels, whereas "Use single channel" will base the calculation on a single, user-defined channel.

Channel (default = "1") Channel to base the best-focus calculation on.