Motion Tab

Feature: Motion Correction

Motion Estimator Panel

Motion Detection Settings

Element	Description
Enable Motion Detection checkbox	Enables/Disables motion detection.
History Length	Sets the number of motion estimate points to be used and stored in memory.
Select Estimator	Opens a file dialog in the +scanimage/+components/+motionEstimators package. Selecting one of the functions in the immediate dialog changes the motion estimator that is to be used. For more information regarding specific motion estimators, see Motion Estimators.

Motion Estimators

Element	Description
Select Slice	On click, enables a slice selection tool to select a reference slice to detect motion with. When the tool is enabled, the button will turn green. Hitting esc will cancel the selection.
Select Volume	On click, enables a volume selection tool to select a reference volume to detect motion with. When the tool is enabled, the button will turn green. Hitting esc will cancel the selection.
Load	Loads a motion estimation reference from a previously saved file.
Save	Saves the selected motion estimator to a file.
Save All	Saves all motion estimators to a file.
Reprocess Estimators / Corrector	Recreates and reloads all estimators and correctors. Useful when debugging and modifying custom estimator/corrector classes.
Enable All	Enables all ROI estimators.
Disable All	Disables all ROI estimators.
Clear	Clears all estimators.
Delete	Deletes the currently selected estimator.

Table Column	Description
Sel(ect)	Selects/deselects the estimator regions of interest.
Enable	Enables/disables the estimator region of interest.
ROI Name	Name of the region of interest.
#z	Number of z slices in the region.

Motion Corrector Panel

Element	Description
Select Corrector	Opens a file dialog into the +scanimage/+components/+motionCorrectors package through which a motion corrector class may be selected.
Reset at end of Acquisition checkbox	If enabled, the correction values will reset after each acquisition. This is the equivalent of clicking on the Reset button after an acquisition ends.
Reset	Resets all motion correction values to zero.
Manual/Auto XY | Z	For each axis button, forces a motion correction event on that axis set (XY or Z). If the paired checkbox is checked, the axes will be corrected at a particular interval as defined by the motion corrector.
Bounds	Sets the correction limits of each axis set. The XY axes bounds units are in optical degrees while the Z bounds unit is in microns. Increasing or decreasing these values will increase or decrease the maximum distance of correction whenever a correction event occurs.
Device	Selects the hardware device that will be used for correction.

Simple Motion Corrector Settings

Element	Description
Running Average Length	The averaging window size in seconds used to smooth the motion correction value.
Correction Interval	The interval in seconds to wait after each motion correction event. Increasing this value will slow the rate of correction events regardless of sample movement. This field may be tweaked for performance in case the correction calculation is taking too long and throttling MATLAB or other processes.
Correction Threshold	Threshold for motion correction in the array format: [X degrees, Y degrees, Z microns]
Threshold Exceed Time	The time window interval in seconds used to determine if a correction is needed when checked. Increasing this value decreases the sensitivity of the corrector as all history values must exceed the designated threshold.
Plot Confidence	When set to true, opens a live graph window plotting the confidence interval over time.

Marius Motion Corrector Settings

Element	Description
Running Average Length	The averaging window size in seconds used to smooth the motion correction value.
Correction Interval	The interval in seconds to wait after each motion correction event. Increasing this value will slow the rate of correction events regardless of sample movement. This field may be tweaked for performance in case the correction calculation is taking too long and throttling MATLAB or other processes.
Correction Threshold	Threshold for motion correction in the array format: [X degrees, Y degrees, Z microns]
Threshold Exceed Time	The time window interval in seconds used to determine if a correction is needed when checked. Increasing this value decreases the sensitivity of the corrector as all history values must exceed the designated threshold.
pC	Time smoothing factor for the z-correlation.
zUpSampling	Upsampling factor for z-correlation.
separateZs	If set to true, separates Zs will be used for motion correction.
showPlots	If set to true, the correlation, confidence and deltaZ graphs will be displayed.