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Is it possible to crop a stack with the Huygens Pro?


Yes, there are basically three ways, in order of simplicity, depending on if you want to use the gui or scripting.

Using a GUI
You can directly crop an image using the crop tool, which can be found in the buttonbar, and under Edit -> Crop. Or with the shortcut Alt-B. At startup the Intelligent Cropper estimates the region you will need for deconvolution. Read more at Intelligent Cropper. In Essential the cropper is found under Tools -> Crop...

Using scripting - crop symmetrically
In case you want to crop using the Tcl Shell or within a script and if you can get away by removing a symmetrical border you can use the add/remove border command, border. There you specify the total sizes of the to be removed border, for instance '-100 -120 -40' to cut away 50 pixels in X on each side, 60 in Y and so on. Type <imagename> border ? to see how the command is used.

Using scripting - crop any part
In case you want an arbitrary part of an image you should first create a destination image which has the exact same size as that part. There are two methods to do this:
  1. One way is to use the repl command to create a copy and use add/remove border to trim it down to the desired size. In this way the microscopic and other parameters of the destination are sure to be correct.
  2. The other way is to create a new image with the desired size and then call for the adopt command to copy the microscopic parameters from the original to the cropped image.
After the new image is created, then use the cp command (see Operations windows under Arithmetic->Copy image part) on the original and specify source, destination and span as follows:
  • source: the coordinates of the origin of the region you want to take out.
  • destination: leave at 0 0 0 0 0(default)
  • span: set to a size as large or larger than the sizes of the destination image. For instance if the destination has size {100 100 40} span could be {100 100 100 1 1}. The last '1' (ones) are for the (not used) time and channel dimensions.
If you don't like the result you modify the source coordinates and press 'Run' again.

See also: cp and repl


Keywords: cropping remove border copy part of image
Categories: Faq Visualization, Huygens Faq, Imported Faqs
Platforms: Irix Linux
Related products: Hu Pro