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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
- Description: Image to extract substack from.
- Type: InputImageP
- Output image
- Description: Substack image to be added to the current workspace.
- Type: OutputImageP
- Best-focus calculation
- Description: Method for determining the best-focus slice. "Largest standard deviation" calculates the standard deviation of each slice.
- Type: ChoiceP
- Default value: Largest standard deviation
- Choices:
- Manual
- Smallest mean intensity
- Largest mean intensity
- Smallest standard deviation
- Largest standard deviation
- Relative start slice
- Description: Index of start slice relative to determined best-focus slice (i.e. -5 is 5 slices below the best-focus).
- Type: IntegerP
- Default value: 0
- Relative end slice
- Description: Index of end slice relative to determined best-focus slice (i.e. 5 is 5 slices above the best-focus).
- Type: IntegerP
- Default value: 0
- Smooth timeseries
- Description: Apply median filter to best focus slice index over time. This should smooth the transitions over time (prevent large jumps between frames).
- Type: BooleanP
- Default value: false
- Smoothing range (odd numbers)
- Description: Number of frames over which to calculate the median. If the specified number is even it will be increased by 1.
- Type: IntegerP
- Default value: 5
- Reference image
- Calculation source
- Type: ChoiceP
- Default value: Internal
- Choices:
- External source
- Channel mode
- Description: 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.
- Type: ChoiceP
- Default value: Use single channel
- Choices:
- Use all channels
- Use single channel
- Channel
- Description: Channel to base the best-focus calculation on.
- Type: IntegerP
- Default value: 1