ScanImage 2018 : Motion Correction Windows

Created by Georg Jaindl, last modified by Daniel Park on Dec 10, 2018
Channel Window Context MenuMotion Correction Display WindowMotion Correction Window

 

 

 

Channel Window Context Menu

Set motion correction reference

Uses the currently displayed image as the motion correction reference image.

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In mROI mode, the ROI under the mouse cursor when opening the context menu is used as the reference geometry for the motion correction

Enable motion correction

Enable motion correction.

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A reference image has to be selected prior to enabling motion correction.

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If Photostim Motion Correction is configured, enabling motion correction will start tracking the sample with the photostimulation galvos.

If ROI Integration Windows is used, enabling motion correction will track the selected regions of interest.

Show motion

Shows the Motion Correction Display Window.

Stabilize Display

Stabilize the Channel Display.

Correct Motion with Stage

Move the stage to correct for sample motion.

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To use this feature, the motor coordinate system must be aligned to the scanner coordinate system. See Motor Alignment Window for more information.

Main display

If motion correction is enabled, shows the detected motion offset. If motion correction is disabled, shows an overlay of the reference image and the currently acquired image.

The display can be navigated using the mouse:

ControlAction
Mouse wheelZooms the image
Click + dragPan the image
Ctrl + mouse wheelChanges the image transparency

Motion Correction Display Window

Enable

Enable Motion Correction

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A reference image has to be selected prior to enabling motion correction.

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If Photostim Motion Correction is configured, enabling motion correction will start tracking the sample with the photostimulation galvos.

If ROI Integration Windows is used, enabling motion correction will track the selected regions of interest.

ConfigureShows the Motion Correction Window
Load Image

Load a reference image for motion correction from a Tiff file.

Motion Correction Window

Enable Motion Correction

Enable Motion Correction

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A reference image has to be selected prior to enabling motion correction.

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If Photostim Motion Correction is configured, enabling motion correction will start tracking the sample with the photostimulation galvos.

If ROI Integration Windows is used, enabling motion correction will track the selected regions of interest.

Show Motion DisplayOpens the Motion Correction Display Window
GPU Acceleration

Configure ScanImate to use the built-in GPU accelerated Preprocess and Motion detection functions.

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This option can only be selected if the Matlab Parallel Computing Toolbox is installed and a CUDA enabled GPU is available.

Load Reference ImageLoad a reference image for motion correction from a Tiff file.
Preprocess Function SelectSelect a reference image pre-process function.
Motion detection function SelectSelect a motion detection function.

Attachments:

Motion Correction Display.PNG (image/png)
Motion Correction Display Configure.png (image/png)
Motion Correction Display Enable.png (image/png)
Motion Correction Display Load Image.png (image/png)
Motion Correction Configuration Enable.png (image/png)
Motion Correction Configuration GPU Acceleration.png (image/png)
Motion Correction Configuration Load Reference Image.png (image/png)
Motion Correction Configuration Select Motion Detection Fcn.png (image/png)
Motion Correction Configuration Show Motion Display.png (image/png)
Motion Correction Configuration.PNG (image/png)
Channel Display Context Menu.png (image/png)