To crop a 3D image for stitching:

1. Collect 3D panel images.

2. Deconvolve the .r3d file that you collected.

3. Open the deconvolved file in an Image window (this file has a .d3d file extension). Then choose Edit | Copy Region on the main softWorRx menu. Drag the .d3d file into the Input field and click Details.

4. Under the Output Options section, enter values in the X/Y/Width/Height, Z (Start, End, Inc), and Time (Start/End/Inc) fields. (The Dimensions (XYZT) field displays the dimensions of the panel.) Use the following equation to determine the Width and Height Output Options:

   Width = x-2n
   Height = y-2n

   Where “x” and “y” are dimensions X and Y respectively and “n” is the number of border rolloff voxels.   

5. Click Close to close the Region Details window. Then click Do It in the Copy Region window. (The cropped panel stack is displayed in a new Image window.)  

6. Choose File | Save on the Image window menu to save the new cropped panel stack.

7. Stitch the cropped deconvolved file.