Overview

The ROI/Stimulus Group Editor is used for defining ROI's for imaging, photostimulation, and image analysis. The interface facilitates designing 3D regions and scan paths using collected images as a reference.

Imaging 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:

• Multiple Region of Interest (MROI) Imaging
• Scanfields, ROIs, ROI Groups

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:

• Photostimulation
• Creating Stimulus Groups

ROI Display

The main display contains a number of different elements identified by the legend at the bottom. The display can be switched between 2D and 3D viewing modes. In 2D mode the main display shows data at the current Z position with an accompanying side projection display at the right. The side projection can be switched between XZ and YZ modes with the controls below. The pointer between the main view and the projection view can be used to move the z plane which the main view is currently showing. The main view and side projection view both support mouse click and drag to pan and mouse wheel zoom. If you hold shift while using the mouse wheel (or if the mouse is hovering over the z control slider between the main and projection view) it will move the current Z position. The ROI display includes the following elements, all of which can be shown/hidden using the check boxes in the legend.

In addition to the legend, the bottom panel contains additional view controls:

ROI Group Table/ROI Group Controls

The right hand side of the interface displays information about the ROI group currently being edited. The controls at the top operate on the entire ROI group:

The ROI table displays information about all the ROIs in the ROI group and all the scanfields within each ROI. This table displays different information depending on whether you are currently editing an imaging ROI group, stimulation pattern, or analysis ROI group.

Imaging ROI Table
For each ROI in the group and each scanfield in each ROI, the following information is listed in the table

Stimulation Pattern Table
For each stimulus function in the pattern, the following information is listed in the table

Analysis ROI Table
For each ROI in the group and each scanfield in each ROI, the following information is listed in the table

ROI Table Controls
Below the ROI table, there are controls for adding, removing, and reordering ROIs

New ROI Panel

To access the new ROI panel, click the Add ROI button or use the hotkeys detailed in a later section. With the New ROI panel open there are multiple ways to create a new ROI. You can click and draw a ROI in the main view, create using position and size entered in the text fields, or use the cell picker.

Drawing ROIs in the Main View
To draw an ROI in the main view, select Top Left Rectangle or Center Point Rectangle depending on how you want to draw the ROI. Click and drag in the main view to draw the ROI in the desired location. If you click and release without dragging, an ROI will be created at the position you clicked using the default size entered in the new ROI panel. If the lock checkbox is selected for either width or height, the corresponding dimension will be constrained to the entered value while dragging. After drawing the ROI, if the Draw Multiple checkbox is off, the new ROI will be selected and the New ROI panel will close to be replaced by the Selected ROI panel showing propertied of the ROI that was just created. If the Draw Multiple checkbox is on, the New ROI panel will stay open allowing you to quickly draw multiple ROIs.

Create ROI Using the Entered Position
To create an ROI by entering the position, Top Left Rectangle or Center Point Rectangle must be selected. You can then manually enter values for center position, width, height, and rotation. After entering the desired position, click the Create Using Defaults button to create the ROI. After creating the ROI, if the Draw Multiple checkbox is off, the new ROI will be selected and the New ROI panel will close to be replaced by the Selected ROI panel showing propertied of the ROI that was just created. If the Draw Multiple checkbox is on, the New ROI panel will stay open allowing you to quickly add multiple ROIs.

Create ROI using the Cell Picker
Using the cell picker is detailed in a later section.

Additional Parameters
In addition to the position and size, additional parameters for the new ROI can be specified on the right hand side of the New ROI panel. The available parameters depend on what kind of ROI group is being edited.

Imaging ROI Parameters
For imaging ROIs, the pixel resolution can be specified. This can be done in terms of pixel count or pixel ratio. If pixel ratio is used, the pixel count will be set by the size of the new ROI.

Stimulus Function Parameters
For stimulus groups, the following parameters can be specified:

Analysis ROI Parameters
For analysis ROIs, the following parameters can be specified:

Selected ROI/Scanfield Properties Panel

If there is an item selected in the ROI table, the bottom right panel will show properties of the selected item. The following properties will be available for the indicated type of selected item:

Imaging ROI

Imaging Scanfield

 Stimulus Function

Analysis ROI

Stimulation Quick Add Panel

When editing stimulation patterns, it is important to put pauses between stimulation functions to allow the scanner time to transition from one ROI to another. The quick add panel provides the means to do so quickly.

Using the Cell Picker

The cell picker allows you to select ROIs from a context image using image segmentation to identify features in the image. The cell picker is available for creating imaging ROIs, stimulus patterns, and analysis ROIs. In order to use the cell picker, you must have a context image currently showing. You can obtain a context image by showing the live context image, taking a snapshot, or loading an image from a file. The cell picker can be accessed from the New ROI panel by selecting Cell Picker. Once in cell picker mode, You can choose a selection mode. The selection mode selects which segmentation routine is used to identify cells in the image. The built in modes are Disk, Annular, and Manual (manual mode does not use segmentation; it will just use a default cell size around where the mouse is clicked). You can also define your own custom segmentation routine. Once the desired selection mode is chosen, click anywhere within a context image in the main view to find a cell at the clicked point. If the segmentation routine finds a cell, it will be indicated with a green highlight. At this point, you can continue clicking to identify more cells. The currently selected cell can be increased in size using the Dilate button or shrunk using the Erode button. Once all the desired cells are selected, click the Add Selected Cells button to create the ROIs.

Depending on the type of ROI group currently being edited, additional options are available for how the ROIs are created:

Imaging ROI Cell Picker Options

Stimulation Function Cell Picker Options

Imaging ROI Cell Picker Options

Hotkeys

The following hotkeys are available in the ROI editor interfaace:

The following hotkeys are available when the New ROI panel is open

The following hotkeys are available when the New ROI panel is open in cell picker mode