This is a simple plugin for ImageJ for cropping 3D image stacks in all three dimensions, from a three window view of the image stack. I find this more intuitive than the alternatives that I've used.
Please let me know of any problems you have with this plugin or any suggestions you have. I hope this is of some use to you.
This plugin is now bundled as part of Fiji (a distribution of ImageJ with many useful plugins), and no longer supported as a standalone ImageJ plugin. Please download and install Fiji and you will find the plugin in "Plugins > Stacks > Crop (3D)"
When starting the plugin from the Plugins -> Stacks -> Crop (3D) menu option, you should be presented with a dialog like this:
This tells you which image you are going to crop and gives you two options. If you don't have enough memory for the full three pane view then unselecting the first option will let you just use an overlay of a single pane of the normal xy slices. The second option indicates whether the origin in the calibration information of your image will be updated when you crop it. So, if the origin of your image is currently 0,0,0 (which you can check in the image info) then after cropping may be updated to something like -20,-20,-40. Unselect this option if you just want to keep the original values for the origin in the cropped file.
Once you click "OK", the plugin will generate the images for the XZ and ZY panes - this may take a little time - and you will see something like this:
You can now set the crop boundaries in one of three ways:
Once you're happy with those boundaries, clicking "Crop" will produce a new cropped image. Cancel will remove the extra panes and overlays and return you to the original image.
If you have any other images of exactly the same dimensions open in ImageJ when you launch the plugin then it will give the option to crop those extra images to the same boundaries:
The only key you need to know about is "Shift". If you hold down shift while you move your mouse over one of the panes then the other panes will be updated to show the corresponding slices.
This plugin is licensed under the GPL (the GNU General Public License version 3). The source code for the plugin is available from the Fiji git repository.