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#Stack on how to
#Stack on movie

The intermediate images are progressively scaled so that the last frame is 100%. The first slice image is the whole of the original image, scaled so that it fits into the framesize of the ROI.

#Stack on movie

The Zoomify plugin will generate a movie sequence such that the first frame includes the whole image and the last is the user defined ROI at 100%. 111-126.Īn alternative method for cropping a stack is found with Plugins › Stacks › Crop (3D) After selecting ‘OK’, you will be presented with panels of the ZY and XZ planes, as well as the original stack, where you can use the mouse to crop the stack in any of the three directions. Viergever, Quantitative Evaluation of Convolution-Based Methods for Medical Image Interpolation, Medical Image Analysis, vol. More details about each TransformJ plugin can be found on this website.Į. Images and stacks can be resized and rotated with native functions or with the more sophisticated TransformJ set of plugins from Erik Meijering.

Control the position of individual slices or groups of slices.

Stack Sorter: Image › Stacks › Tools › Stack Sorter.

No automatic resizing, so the smaller stack should not be used as the destination.

Superimpose the source by specifying the X and Y coordinates for the location of the upper left hand corner.

Used with two stacks, one is the source and the other the destination.

Stack Inserter: Image › Stacks › Tools › Insert

Interleave is the reverse process and may be applied to two stacks at a time.

Deinterleave will distribute slices between new stacks as indicated by the specified number of channels.

(De)Interleave: Image › Stacks › Tools › DeInterleave and Interleave

If the two stacks contain a different number of slices, the shorter will have blank slices appended to the end so they are the same length.

Stack Combine: Image › Stacks › Tools › Combine For example, concatenating two 25-slice stacks would result in a 25-slice stack with two different time points at each slice.

“Open as a 4D Image” option interprets separate stacks as belonging to a single 4D dataset.

Stacks must be the same dimension and image type.

Reversing stack: Image › Stacks › Tools › ReverseĬoncatenate: Image › Stacks › Tools › Concatenate

Can do reverse operation with Image › Stack › Tools › Montage to Stack, but will need to specify the number of rows and columns to ensure the correct number of slices.

Ideal for generating a montage of a stack for a lab book.

When using “Images to Stack”, the original images will close once the stack is formed.

If different sized images are used, you will be presented with options to make the size uniform.

“ Images to Stack” requires images to be the same size.

Stack to images/Images to stack: Image › Stacks › Stack to images (Images to Stack…). Option to delete the slices from the original stack.Indicate a range or list of slices to include in new substack increments are possible.

Select the slices to remove: Image › Stacks › Tools › Make substack Indicate the first and last slices in the range to remove, as well as the increment of slices to remove between the first and last slices.Deletes the currently displayed slice in a stack.ĭeleting a number of slices: Image › Stacks › Tools › Slice remover.Some of these functions are described below.ĭeleting a single slice: Image › Stacks › Delete Slice The slices in a stack can be manipulated in many ways.

#Stack on how to

If you’d like to help, check out the how to help guide! Slice shuffling/removing/Adding The content of this page has not been vetted since shifting away from MediaWiki.