Example scenarios are available from Main Window Toolbar->Help->Examples. This opens a File Selection dialog in the directory where example scenarios should be installed. In RPM installation this is /usr/share/prostack/examples. There is a number of subdirectories each for one example scenario. The subdirectory contains a scenario in AP format in the file with extension .ap and input images. The user can open, run and modify these examples. In RPM installation this directory is not writable for the ordinary user and the attempt to save the modified scenario will fail with the error message on the screen.
A whole-embryo mask is used to bring the averaged images obtained in each microscope channel to standard orientation. The mask is a binary image, where the values of pixels belonging to the embryo are set to one and those outside the embryo to zero. It is constructed by consequent thresholding and median filtering of the pixel maximum image followed by several cycles of erosion and dilation. To determine the rotation angle the invariant moments of the mask are calculated. Both the whole-embryo mask and the averaged channel images are rotated by this angle and the non-informative image areas outside the embryo boundaries are cropped.
As structural elements applied to smooth the mask depend on the image orientation, the procedure of embryo rotation may somewhat corrupt the embryo contour. Therefore the whole-embryo mask is to be remade to exactly cover each of the averaged channel images. The averaged images are thus cropped to the exact size of the corrected whole-embryo mask. A nuclear mask is the binary image with nonzero pixels corresponding exclusively to within-nucleus pixels. The contrast of images is enhanced by the local histogram equalization method followed by Crimmins algorithm to remove the speckle noise. After that a watershed image is created. In this image the lines of single pixel width define the watershed domains, which enclose regions occupied by nuclei. The nucleus boundaries are found by the Shen-Castan edge detection method. The quality of nuclear mask is inspected visually by superimposing it on the histone or pixel maximum image.
This scenario allows to automatically identify and count objects in images of the Drosophila Kc167 cells.
This scenario illustrates the process of identification of objects in a stack.