Usage

The Image Cropper Plugin allows you to crop subvolumes out of your orginial image volume by defining a cubic bounding box.

This box can be placed at an arbitrary position in the volume and can be easily adjusted by using the handles on each of the faces. Touching the handles changes the size of the box whereas touching the box itself changes its position.

As soon as the bounding box is placed at the desired position, pressing the button 'Crop' creates a new image assigned to the orginal image as child node containing only the selected subvolume. The size of the subvolume equals the size of the bounding box. Pressing the "Mask" button keeps the original image size but masks out the area not contained within the bounding box bounds. In case of 3D+t images the whole timeseries is cropped by default.

Bounding Box.

Basic Settings.

Advanced settings

In the advanced settings view you find additional features to manipulate the bounding box.

Advanced Settings.

Bounding Shape Color

By pressing the two color buttons you may change the color for the selected and unselected state of the box.

Overwrite original image

By enabling this checkbox the image is replaced by the cropped subvolume. Be careful to use this option since there is now Redo action available.

Crop current timestep only

If this checkbox is enabled the xD + t image is reduced to a xD image (3D+t –> 3D) with the timestep visible in the widget. This is useful if you want to extract a single image or its corresponding subvolume of the timeseries. The whole timeseries is cropped by default using the timeGeometry of the timestep visible in the widget.

Current issues

Due to the latest changes in MITK slicegeometry is it currently not supported to crop 2D images unless the are 3D images containing only a single slice. The user will be notified by a warning and and the input is handled as a single lable image.

Right now changing the shape or rotation of the bounding box is not supported but might be integrated in the future.