13. Draw Raster ROIs

Region of interest (ROI) is a binary layer, or mask, in which each voxel takes values 1 or 0. ROI voxels that have the value of 1 have attributes of foreground color and transparency (alpha value). Voxels that have the value of 0 are always completely transparent, regardless of the transparency value of the entire ROI layer. In FireVoxel, ROI layers are treated as 3D or 4D raster images.

Raster ROIs may be created manually or as a result of various commands.

13.1. Creating and editing ROIs with Paintbrush tool

Raster ROIs can be drawn manually using the paintbrush tool. Drawing is done on the active ROI layer. If there are no visible ROI layers (i.e., the document has ROI layers, but they are unmarked), a new ROI layer is created by default and the ROI is drawn on that layer. The ROI layer has the same matrix dimensions and voxel size as the underlying base image.

Paintbrush in Action

Fig. 13.1 Paintbrush tool for drawing and editing raster ROIs.

To draw an ROI, press and hold down Ctrl key and click and hold down the left mouse button. The cursor turns into a green ring filled with the ROI color (at 20% transparency), the paintbrush. Move the mouse to paint voxels that need to be included in the ROI. Any voxels touched by the green circle will be painted the ROI color (assigned the values of 1). Release the mouse button and Ctrl key to finish (Fig. 13.1).

To erase voxels from an ROI, hold down Ctrl key and click and hold down the right mouse button. The cursor turns into a red ring (without color inside), the eraser brush. Move the cursor to erase voxels. Any voxels touched by the eraser will be returned to zero state and become transparent. Release the mouse button (and Ctrl key) to finish.

Manually drawn ROIs do not need to be contiguous and consist of areas drawn on several different slices.

13.1.1. Adjust paintbrush size

While holding down Ctrl key, scroll the mouse wheel forward and backward to increase or decrease the diameter of the paintbrush/eraser.

13.1.2. Raster Paintbrush tool panel

The paintbrush properties panel (Fig. 13.2) can be accessed by clicking paintbrush icon on the main toolbar. The panel must be closed before the paintbrush can be used. The paintbrush settings are retained for one session. Closing and reopening FireVoxel restores the default settings.

Paintbrush Properties Panel

Fig. 13.2 Paintbrush properties panel.

The top portion marked Paint/Erase controls the grayscale value of the brush/eraser (and size). This option can be used for drawing on integer layers (images). It does not affect the paintbrush on ROI layers.

By default, the brush grayscale value is set to white (Signal = 255 and the eraser to black (Signal = 0)). Changing these values allows painting and erasing voxels with other grayscale values. The grayscale value can be entered into the text box labeled Signal or by clicking to the left or right of the circle in increments of 1. Clicking the square field above and below the central circle increases and decreases the brush radius by 0.25 mm.

Paintbrush allowed on Integer Volumes/ROIs/Real Volumes checkboxes control the types of layers the paintbrush is allowed to change. By default, the paintbrush is allowed only on ROI layers. If Integer Volumes box is checked, the brush can on paint image layers and may alter the base images, which is often undesirable. Users should exercise care when using this option.

Radius (mm) box sets the size of the paintbrush to a specified value (2 mm by default). This allows the user to control the paintbrush/eraser size more precisely than adjusting it by scrolling the mouse wheel. Entering the radius of 0 sets the brush size equal to 1 voxel.

Constrain by lower ROI layerADD DETAILS.

Use 3D checkbox when checked makes the paintbrush a sphere of the set radius. By default, this box is unchecked, and the ROIs are drawn on one slice at a time.

Modify all timepoints checkbox extends the ROI to all frames in a dynamic experiment. This results in a 4D ROI. The box is unchecked by default.

SmartZoom checkbox – The box is unchecked by default. ADD DETAILS.