ROI from Grayscale Segmentation

The ROI from Grayscale Segmentation dialog box is displayed when selecting Segmentation ... from the Process menu.

The Segmentation dialog window enables dynamic modification of the pixel thresholding values as well as other relevant ROI related options. The red bar indicates the pixel level which is currently segmented (note the segmentation color is always red). The threshold can be adjusted interactively by right-clicking on of the edges of the bar and dragging it to the left/right to expand/reduce the length of the bar. The length of the color bar then reflects the range of segmented pixels which is also reflected in the editable number boxes in either end of the threshold bar. The upper/lower segmentation values can be edited manually by entering the appropriate values in the boxes. The numbers above the boxes indicate the maximum and minimum pixel values in the current image. It is also possible to generate a segmented version of the input data according to the segmentation settings and further so copy the segmented pixels to the ROI buffer.

Update segmentation range on image scroll: The max values is updated according to the maximum pixel value in the current slice. If not checked, the max value will remain fixed on image scroll

Image pixel masking:

Enable pixel masking: when selected, the input data will be modified upon exiting the segmentation tool to reflect the segmentation settings.

Create binary mask: when selected, foreground pixels (that is red pixels) are set to a fixed value as specified in the <mask pxl value> field

Keep pixel mask pos fixed for multiple images: as default, the mask is update for each slice according to the max pixel values in that slice. When this option is checked, the mask is kept the same for all slices in the input series and in accordance with the segmentation status at exit.

Save segmented ROI->Buffer scope:

Current slice: The segmentation setting will only be applied to the current slice.
All slices: All slices in the series will sequentially be scrolled through and the segmentation will be applied to all slices in turn and saved to the ROI Buffer. This is an efficient way of applying the same segmentation setting to many slices and save the resulting segmented pixels to the ROI Buffer.

Save ROI to buffer: Save the segmented pixels as a scatter ROI to a ROI buffer.

Save segment

The segmented pixels are save as a single ROI file (with extension .seg). The ROI can then be reloaded as a scatter ROI on any dataset. This is a very useful function for e.g. creating ROI s from pixel segmentation which is subsequently applied in e.g. dynamic ROI analysis. Once the segmentation is reloaded as a scatter ROI, all ROI functions can be accessed like for any other ROI. Image size and zoom/pan settings applied when the segment is saved will be recorded in the .seg file and the same settings will be applied upon loading the .seg file.

Reset

Resets the segmentation range to default values.