Three Pane Crop

PlugIn for ImageJ


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)"


Starting the PlugIn

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:

  1. Dragging the blue and magenta boxes in the corners of any of the panes inwards. (You will probably want to check that this is right by stepping through the slices in each pane with the scroll bars or by holding down "Shift" while moving your mouse in one of the panes.)
  2. If you are using an 8 bit or 32 bit float greyscale image, and have, for instance, a mostly empty image, you might want to specify a value in the "Set crop above value" field and hit the button. This will set the crop boundaries to the minimal stack that encloses all of the values in the image above that value. (For RGB images, this value is tested against the average of the red, green and blue components, which probably isn't very helpful.)
  3. Alternatively, you can specify the crop boundaries manually by entering values for the maxima and minima in the dialog and hitting the "Set from fields above" button.

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.

Cropping Multiple Images

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.

Known Bugs


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.