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Regions of Interest/Stimulus Editor Panel

 

Overview


The REGIONS OF INTEREST or STIMULUS EDITOR window is used to configure a regions of interest group (ROI group) for imaging or stimulus groups for photostimulation. The same interface is used to edit imaging ROI groups and stimulus groups. Clicking Edit ROIs from the MAIN CONTROLS GUI opens the REGIONS OF INTEREST editor to edit imaging ROIs. Clicking Edit from the PHOTOSTIMULATION CONTROLS GUI with a stimulus group selected will open the STIMULUS EDITOR to edit the selected stimulus group.

ROI groups consist of one or more 3D ROIs, which are defined by 2D scanfields.  You can find a complete description of multiple region of interest imaging in the following concepts guide articles:

Stimulus groups are special cases of ROI groups where scanfields are parametric 2D stimulation paths instead of fields to raster scan. More details about photostimulation and stimulus groups can be found in the following articles:

ROI Display


The ROI display graphic allows you to visualize and modify scanfields on the selected Z plane. The ROI display graphic contains several elements:

  • Scanner Fields of View (FOVs): The ROI display view is in the reference coordinate system which extends from 0 to 1 in the X and Y directions. Within the view, the field of view of each scanner within the reference space is represented by the thin dotted lines. The field of view of the current scanner (the currently selected imaging scanner when editing imaging ROIs or the photostim scanner when editing stimulation patterns) is shown in green. All other scanner FOVs are shown in yellow.
  • Context Image: A context image can be loaded to use as a reference for drawing scanfields and stimulation patters. The context image is shown with a blue outline.
  • Scanfields: Scanfields for each ROI at the selected Z plane are displayed with a thick outline. The scanfield of the selected ROI is in green while other ROIs are in red. A scanfield defined at the current Z plane is shown with a solid outline. A scanfield that has been interpolated is shown with a dotted outline.

With the ROI display in focus, the mouse wheel can be used to zoom in and out. Holding down shift while using the mouse wheel while traverse Z levels.

Copies the current image buffer into the ROI display as a context image. Checking Use TIFF allows copying from a saved TIFF file instead of from the current image buffer.
Moves the ROI display through z planes. Snaps to Z planes in the current stack to be imaged.
Moves the ROI display through z planes. Snaps to Z planes where scanfields have been defined.
Current Z plane of the ROI display. Use this field to go directly to a desired Z plane.

ROI Table/ROI Controls


Load or save the current ROI group to a file.

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The current ROI group is saved in the cfg file. This allows saving and loading the ROI group alone.

Name of the ROI group.
Indicates which ROI is selected.
Displays time required to scan each scanfield.
Displays type of scanfield or stimulation pattern.
Enables or disables scanning of the ROI.
Enables or disables displaying the ROI during image acquisition
Indicated number of control points (defined scanfields) that exist for the ROI
Indicates the maximum and minimum Z plane where a scanfield has been defined for the ROI. The ROI only exists between these planes
Add a new ROI to the ROI group.
Delete the selected ROI.
Move the selected ROI up or to the top of the scanning order.
Move the selected ROI down or to the bottom of the scanning order.
Setting indicates that the selected ROI only exists at the Z planes where a scanfield is defined. The scanfields will not be interpolated and the ROI will not be imaged at Z planes without a defined scanfield.

Default Scanfield Controls


These settings apply to the next scanfield that will be drawn. They do not change the currently selected or any existing scanfields.

When drawing the next scanfield or modifying an already drawn scanfield, constrain the X or Y dimension to the settings below. When the fix box is check, the settings for the currently selected scanfield are copied automatically.

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When resonant scanning, all ROIs must have the same size and pixel count in the X direction. It is therefore useful to fix the X dimension after drawing the first scanfield.

Specifies the default scanfield size. If the fix constraint is on for X or Y, this is the size that the new scanfield will be constrained to.
Specifies the default pixel ratio for the next scanfield that will be drawn.

Selected Scanfield Controls


These settings change properties of the currently selected scanfield.

If the current ROI does not have a scanfield at the current Z plane, this will add a new one. A ROI can only have a single scanfield on a given Z plane. If the current ROI already has a scanfield at the current Z plane, this will re-define the scanfield. After clicking this button, click and drag in the ROI display to draw the scanfield
If the selected ROI has a scanfield defined at the current Z plane, this will remove it.

Pixel resolution of the selected scanfield.

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For resonant scanning, all scanfields in the ROI group must have the same pixel resolution. Changing one will change all.

Rotation angle of the current scanfield.

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Rotation is only supported for galvo-galvo scanners.

Size of the selected scanfield in reference coordinates.
Ratio of pixels to size in reference coordinates.

Ratio of pixels to size in microns.

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This field uses the angular resolution setting under the ROI display to calculate this value.


Default Stimulus Controls (Stimulus Editor)


These settings configure the next stimulus that will be drawn. They do not change the currently selected or any existing stimulus functions.

Specifies the kind of stimulus pattern to draw.

Specifies custom parameters of the stimulus function.

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Each stimulus function may have parameters that can be specified here. See Built-in and Custom Stimulus Functions for more details.

Specifies duration of the next stimulus pattern drawn.
Specifies number of times to repeat the next pattern drawn.

Specifies default size of the next stimulus pattern drawn.

 

Specifies the rotation angle of the next stimulus pattern drawn.
Specifies the beam power for the next stimulus function drawn. This should be a vector with an element for each beam or a scalar if the same power is desired for all beams.

Selected Stimulus Controls (Stimulus Editor)


These settings change properties of the currently selected scanfield.

For stimulus groups, each ROI can have only one stimulus function. If the current ROI does not have a stimulus function defined, this will add a new one. If the current ROI already has a stimulus function this will re-define it. After clicking this button, click and drag in the ROI display to draw the stimulus.
Removes the defined stimulus function from the ROI.
Specifies the parametric function for the selected stimulus.

Specifies custom parameters of the selected stimulus function.

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Each stimulus function may have parameters that can be specified here. See Built-in and Custom Stimulus Functions for more details.
Specifies duration of selected stimulus.
Specifies number of times to repeat stimulus function.
Specifies position of center of selected stimulus function in reference coordinate system.
Specifies size of selected stimulus function.
Specifies rotation angle of selected stimulus function.
Specifies the beam power for the selected stimulus function. This should be a vector with an element for each beam or a scalar if the same power is desired for all beams.
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