The "MORPHO" menu allows you to specify some preliminary information relating to the entire image set before you begin image-by-image digitization. IT IS VERY IMPORTANT THAT YOU CORRECTLY SET "ZSPACING," "X IMAGE SIZE" AND "Y IMAGE SIZE" BEFORE PROCEEDING TO THE NEXT MENU: The values you provide here are used to correctly scale the reconstruction. While it is possible to rescale the reconstruction later in Skandha3, it is much better to get the values right in the first place.
The "Zspacing" value is the distance in centimeters between successive tiff files. Skandha Morpho will construct the Z coordinates for all the points you digitize simply by multiplying the frame number by the Zspacing. If you neglect to set this value properly at this point, your reconstruction will emerge squashed or stretched on the Z axis. Click on this value and type in the correct number. (Number format in Skandha4 is fairly flexible; with or without decimal point is fine. Exponentials can be entered as "1.4e-10" or such.)
The "X Image Size" is the actual size in centimeters of the full X (horizontal) field of view in your images, on the original specimen. (Skandha Morpho assumes that all images in a given set are at the same magnification.) Unless the value displayed happens to be correct, select this entry and type in the correct value.
The "Y Image Size" is the matching vertical size. Since we currently only handle square images, it should be set to the same value as "X Image Size".
If you have already measured a number of contours on this image set, and wish to add more contours to the same file, you may click "Read GRAPHIX file" at this point, and supply the name of the file to read. (It is also perfectly reasonable to make a new file for each measuring session.)
When you complete the above, select "Contour-Tracing Menu". This takes you to the menu in which you will spend the vast majority of your Skandha Morpho digitizing time.