Working with ROIs

Create regions of interest (ROIs) for cortical areas or other structures and compare their signals. Open image data first; a project binding is not required.

1. Draw an ROI

1. Open the ROIs tab.
2. Choose Rectangle , Ellipse , or Polygon .
3. Drag a rectangle or ellipse. For a polygon, click each vertex and double-click the last vertex.
4. Move or resize the shape while its handles are visible.
5. Double-click inside the ROI, or press Enter, to confirm. Press Escape to cancel.

The current ROI tab includes drawing, threshold, Allen Atlas, file, import, and export tools.

The handles remain visible while drawing. Double-click inside the ROI or press Enter to confirm it.

2. Edit and organize ROIs

1. Use Select in the ROI table to enter edit mode.
2. Drag the ROI or its handles. Double-click inside it, or press Enter, to confirm the edit.
3. Click the Name cell to rename it and the Color cell to choose a new overlay and trace color.
4. Select several rows to move or resize them together, or right-click the group for Boolean operations.

3. Create ROIs by threshold

Choose Threshold to preview connected image regions above or below a chosen intensity. Adjust the threshold, minimum size, hole removal, and border smoothing, then choose Create ROIs. See Threshold-based ROIs for details.

The dialog compares the threshold overlay with the connected candidate regions before they are added.

4. Place Allen Atlas areas

Choose Allen Atlas to select cortical areas from the Allen Mouse Brain Atlas and place their two-dimensional outlines over the current image. Estimated Bregma and Lambda positions appear as a red and green dot, respectively, for placement aid only. This is not automatic anatomical registration. See Allen Atlas selection and placement.

5. Save or load ROIs

Choose Save to write a .roi file. Choose Load to replace the current list or append another ROI set.

What is saved?
Drawing, editing, thresholding, Boolean operations, and atlas placement remain in memory until Save. A .roi file stores the ROI shapes and their descriptive information; it does not alter the imaging data.

See the full ROI management reference.