For a spectrum image (SI) acquisition, it is necessary to allocate a region on the survey image to use for acquisition. A green region of interest (ROI) marker identifies these regions. The type of the SI marker depends on the SI mode and can be either point, line, or rectangle ROIs. You can position, resize, and remove the survey ROI like any other ROI marker.

  1. Add a survey ROI by selecting a SI mode.

If the SI palette is in mode selection state, selecting any mode automatically adds the appropriate survey ROI to the survey image, which is also automatically assigned by this action. The position and size are the same as the one used for the last SI acquisition of that type.

  1. Add a survey ROI by using the floating menu.

When you right-click a recent image on the View workspace, the SI ROI tool in the floating menu appears. This dropdown menu allows you to select the SI type. With this tool, you can create the survey ROI directly on the image. Then, the image is automatically assigned as a survey image while the spectrum imaging mode is adjusted. Other, now obsolete survey ROIs are automatically removed.

Note: For Multi-Point, keep the Shift key pressed while adding a point to keep the tool active and allow the selection of multiple points in a series of clicks.

  1. Remove a survey ROI.

Use the mouse to click the ROI marker while you press the Delete key on the keyboard. If you remove all survey ROIs of the current SI mode, the STEM-SI palette automatically reverts to mode selection state.

Survey ROI types

2D Array

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

Resizing the survey ROI keeps the total number of pixels and hence total acquisition time approximately constant. The SI size in pixels, as well as the sampling resolution, change automatically when you resize the ROI.

The survey ROI snaps to positions of the appropriate size and aspect ratio. The smaller the total number of pixels in the SI, the rougher those snaps may appear.

Line Scan

A one-dimensional (1D) SI consists of an array of equally spaced points along a line. It is represented as a single, line ROI in the survey image. A yellow cross indicates the start position of the scan. If the averaging option is enabled, the cross is replaced by a yellow line that indicates the averaging direction and width.

Resizing the green survey ROI adjusts the sampling resolution, but keeps the number of sampled points constant. Changing the dimensions of the yellow survey ROI adjusts the averaging width, but keeps the number of sampling points along that direction constant. You can adjust the averaging direction angle by pressing the Ctrl key down while you drag the green handle of the yellow survey ROI. Deleting the yellow survey ROI will switch the averaging option off.


A set of point spectra acquired with identical parameters from individual spatial positions collected in a 1D SI data container. Each point is represented by a single, numbered point ROI in the survey image. This number specifies the spectrum position within the SI data container.

It is most convenient to add points using the SI ROI tool from the floating menu. Keeping the Shift key pressed allows you to add multiple points in a series of mouse clicks. You can remove individual points by selecting them and pressing the Delete key. Once deleted, this automatically renumbers the remaining points.

Click the Arrange points buttons to arrange the selected set of points or if none are selected, all points. If a rectangular ROI is selected, it arranges points within this area. Otherwise, it arranges them over the entire survey image.

Auto arrange points
Selection of points and destination area (left). Randomize positions in the area where each point is given an arbitrary position within the area (right).

Auto arrange points
Arranged points along a regular grid (left). Arrange point along a regular grid, but randomize around this position (right).

Time Series

A set of spectra sequentially acquired with identical parameters from the identical sample area collected in a 1D SI data container. The sample position is either represented by a point ROI for stationary acquisition or by a rectangular ROI if the 2D Scan option is enabled.

Resizing the 2D Scan area is restricted by the number of sampling points of the scan, which in turn is limited by the SI Pixel Time. Slower scans allow a higher sampling. To access a larger scan area, it can, therefore, be necessary to either reduce sampling with the spin controls for the 2D Scan fields and/or to increase the Pixel Time.