XuvTools is developed in a cooperative effort from:
  • Chair of Pattern Recognition and Image Processing [www]
  • Friedrich Miescher Institute for Biomedical Research [www]
  • Center for Biological Systems Analysis [www]

XuvTools - the "eXtend yoUr View" Toolkit

About: XuvTools (pronounced “ex-you-vee-tools”) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). XuvTools is free and open source software (see Licensing), so you can start using it immediately. Go to Downloads and give it a try.

The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (“stitching”) and a higher dynamic range (“HDR” recombination), or better resolution (multi view reconstruction), and to make these tools publicly available.

The technical details are described in our paper which can be found at Documentation.

<note warning> Note, while this is free software, if you use XuvTools in your research and/or find it useful, you have to cite us. Look at the xuvtools-bibtex example on how to do that. </note>

Where to start

Please read the following workshop presentation, and/or watch a video tutorial:

Features and Limitations of XuvTools

<note important> Limitations of XuvTools: (current limitations, we are working on it!)

  • No 2D Stitching: stacks need 4 Z-slices or more
  • No memory management: You need lots of RAM
  • No rotational alignment
  • The only supported output formats are: Imaris, HDF5 (No TIFF output support)

What XuvTools can do:

  • Full 3D Stitching
  • Scaling, if the voxel sizes are known from image data
  • Fully automatic stitching modes
  • Manual pre-alignment modes
  • Arbitrary large datasets
  • Reads stage coordinates if available
  • free, no hidden costs
  • Reads many many input formats via LOCI Bio-Formats and Dmitry Fedorov's BioImage.


Latest Version

<note important> Latest stable version is XuvTools 1.8.0, get it from the Download Section. XuvTools-1.8.0 brings many new features including a Windows installer (MSI, EXE) bundle, an improved dialog for Advanced Parameters, rewritten file readers based on Bio-Formats and BioImage, support for many more stage coordinates (Andor, Zeiss LSM), Zeiss stitching macro support, and fixed several issues including a major bug in the beta series. </note>

Roadmap for next Version

Roadmap: The next release will be XuvTools-1.8.1, that fixes some smaller issues. XuvTools-1.8.1 is now in beta-testing. See the Milestones and Roadmap for the upcoming release schedule.

50% completed

Registration and Mailing List

To register for the newsletter, get notification of new releases, to ask questions and to search the archives, continue to


  • Contact: Contact, or read about, the team behind XuvTools

More News And Updates

Also see the Changelog.

  • 10.05.2011: Development on an improved user interface started
  • 02.05.2011: XuvTools-1.8.1-beta3 released!
  • 19.01.2011: XuvTools-1.8.1-beta2 released!
  • 04.12.2010: XuvTools-1.8.0 final released!
  • 10.10.2010: XuvTools-1.8.0-beta7 released!
  • 01.08.2010: Bio-Formats based file reader finished
  • 18.02.2010: XuvTools-1.7.0 released!
start.txt · Last modified: 2011/05/09 09:16 by mario
Contact: admin(a)xuvtools.org