Select and Survey ROI

Survey region of interest

For a spectrum image (SI) acquisition, you must define a survey region of interest (ROI) on the survey image. Survey ROIs are displayed in green and indicate the area or locations where data will be acquired.

The type of survey ROI depends on the selected SI mode and can be one of the following:

• Point
• Line
• Rectangle

You can position, resize, and remove the survey ROI like any other ROI marker.

Add a Survey ROI

You can add a survey ROI using either the STEM SI palette or the floating menu.

Add a Survey ROI using the STEM SI palette

When the STEM SI palette is in mode selection state, selecting any SI mode automatically adds the appropriate survey ROI to the image. The system assigns:

• The same position and size used for the most recent SI acquisition of that mode.

The tool creates the survey ROI directly on the image. The image is automatically assigned as the survey image, and the spectrum imaging mode is adjusted accordingly. Any obsolete survey ROIs are removed automatically.

Note: For Multi‑Point mode, hold down the Shift key while adding points to keep the tool active and allow multiple points to be added in succession.

Remove a Survey ROI

To remove a survey ROI:

1. Select the ROI marker.
2. Press the Delete key.

If you remove all survey ROIs for the current SI mode, the STEM SI palette automatically returns to mode selection state.

Survey ROI types

2D Array

A 2D SI consists of an array of equally spaced points in X and Y directions. It is represented as a single, rectangular ROI in the survey image.

• Resizing the ROI keeps the total number of pixels and total acquisition time constant.
• The SI pixel dimensions and sampling resolution adjust automatically.
• The ROI snaps to valid sizes and aspect ratios. With fewer SI pixels, snapping may appear coarser.

Line Scan

A 1D SI consists of equally spaced points along a line and is represented by a single‑line ROI.

• A yellow cross marks the start position of the scan.
• When averaging is enabled, the cross is replaced by a yellow line indicating the averaging direction and width.

Behavior:

• Resizing the green line ROI changes the sampling resolution while keeping the number of points constant.
• Adjusting the yellow ROI changes the averaging width while keeping the number of sampling points constant.
• To change the averaging direction, hold Ctrl while dragging the green handle of the yellow ROI.
• Deleting the yellow ROI disables averaging.

Multi-Point

Multi‑Point SI acquires point spectra with identical parameters from multiple spatial locations and stores them in a 1D SI data container.

• Each point is represented by a numbered point ROI.
• The number indicates the spectrum position within the data container.

Usage:

• Add points using the SI ROI tool in the floating menu.
• Hold Shift to add multiple points consecutively.
• Remove individual points by selecting them and pressing Delete.
• Remaining points are automatically renumbered.

Arrange Points

• Use the Arrange Points buttons to arrange selected points, or all points if none are selected.
• If a rectangular ROI is selected, points are arranged within that area.
• Otherwise, points are arranged across the entire survey image.

Arrangement options include:

• Random distribution within the selected area.
• Regular grid arrangement.
• Grid arrangement with randomized offsets.

Time Series

A Time Series SI acquires spectra sequentially from the same sample area using identical parameters and stores them in a 1D SI data container.

• A point ROI represents stationary acquisition.
• A rectangular ROI represents acquisition with the 2D Scan option enabled.

Resizing the 2D Scan area is limited by:

• The number of sampling points, which is constrained by the SI Pixel Time.

To enable larger scan areas:

• Reduce sampling using the 2D Scan spin controls, and/or
• Increase the Pixel Time.

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