crop3D

Crops a given sub-stack out of a given image stack.

Note: If the destination image pre-exists already, it will be overwritten and keep it’s dimensions.

Parameters

source : Image The image where a part will be cropped out. destination : Image The cropped image will be stored in this variable. start_x : Number The horizontal position of the region to crop in the source image. start_y : Number The vertical position of the region to crop in the source image. start_z : Number The slice position of the region to crop in the source image. Slices are counted 0-based; the first slice is z=0. width : Number The width of the region to crop in the source image. height : Number The height of the region to crop in the source image. depth : Number The depth of the region to crop in the source image.

Category: Transformations

Availability: Available in Fiji by activating the update sites clij and clij2. This function is part of clij2_-2.5.0.1.jar.

crop3D often follows after

copySlice (1)

crop3D is often followed by

minimum3DSphere (1)

Usage in ImageJ macro

Ext.CLIJ2_crop3D(Image source, Image destination, Number start_x, Number start_y, Number start_z, Number width, Number height, Number depth);

Example notebooks

crop_and_paste_images.ipynb
voronoi_otsu_labeling.ipynb
affine_transforms.ipynb

Example scripts

allocateBigImages.ijm
oddEven.ijm

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