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Transform Virtual Stack Slices

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on GitHub


Registration, Transform

{| |style=”vertical-align:top” | Transform Virtual Stack scheme - All images are transformed based on the XML files |}

This plugin takes a sequence of image slices stored in a folder, and delivers a list of transformed image slices (with enlarged canvas) applying a list of transforms stored as .XML files in another folder.

This is a complementary plugin of Register Virtual Stack Slices. It allows reproducing the results of Register Virtual Stack Slices by loading the corresponding transform files (saved by checking the option “Save transforms” in the main dialog).

User Manual


  • Source folder: You have a folder with an ordered list of image files in it that Fiji can open.
  • Each image represents a slice in a sequence.
  • Output folder: You have or create a folder to store the resulting virtual stack with the transformed images.
  • Transform folder: You have a folder with the transform files (from a Register Virtual Stack Slices execution).
  • Interpolate: Toggle the interpolation for the result images.

Step 1: launch the “Plugins - Transform - Transform Virtual Stack Slices” plugin. <div class="thumbnail" > Transform Virtual Stack main dialog </div> Step 2: choose the source, output and transform folders:

  • Select a source folder containing the slices, at one slice per image file.
  • Select the target folder where resulting transformed slices will be automatically stored as TIFF files.
  • Select the transform folder, where the .XML files from a Register Virtual Stack Slices are stored.

Results: on success, a virtual stack will open showing all the transformed images contained in the output folder. The virtual stack can be closed with no ill effect: images are saved in the output folder.

API documentation

The latest documentation of the package can be found here:


This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation (

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.