XuvTools - the "eXtend yoUr View" Toolkit

About: XuvTools 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.

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.

The technical details are described in the following paper:

M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt. XuvTools: free, fast and reliable stitching of large 3D datasets. Journal of Microscopy, 233(1):42–60, 2009
- PDF on Publisher site (free access)
- doi:10.1111/j.1365-2818.2008.03094.x

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.

Features and Limitations of XuvTools

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 (but you have to cite us)
Read many input formats: BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III, JPEG, PNG, BMP, IBW, OME, RAW

Latest Version

Latest stable version is XuvTools 1.7.0, get it from the Download Section. XuvTools-1.7.0 brings better project file support, including saving of thumbnails and fixes some bugs from 1.6.0.

Roadmap for next Version

Roadmap: The next release after XuvTools-1.7.0 will be XuvTools-1.8.0, that fixes many more issues, and has an improved dialog for Advanced Parameters. XuvTools-1.8.0 will be in alpha-testing soon. The release after XuvTools-1.8.0 should feature 2D stitching support, and should fix the long-standing bug that “stacks are too flat”.

70% completed

Registration and Mailing List

We have new releases frequently, typically once per month. If you want to be notified of new stable releases, beta releases or want to subscribe to our news feed, please register at

http://special.xuvtools.org/register.php

Links

Download: Download XuvTools
Documentation: Readme
Download: download Test-Datasets to get started

Developers Pages: Development
Developers Time Schedule: Current ToDo List
Developers History: Latest Changelog

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

More News And Updates

Also see the Changelog.

18.02.2010: Version 1.7.0 released!
18.01.2010: Release Candidate 1 for XuvTools 1.7.0 available for download.
11.12.2009: Fixed several bugs concerning usability and GUI-consistency.
28.11.2009: Many bugs and issues have been fixed (total 15 bugs, see Changelog)
26.11.2009: Support for reading/writing thumbnails from project files
18.11.2009: Improved writing of Imaris 5.5 MultiResolution files, including some bugfixes.
10.11.2009: XuvTools 1.6.0 successfully tested on Windows 7 x64 and x86.

			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] www.XuvTools.org Table of Contents XuvTools - the "eXtend yoUr View" Toolkit Features and Limitations of XuvTools Latest Version Roadmap for next Version Registration and Mailing List Links More News And Updates XuvTools - the "eXtend yoUr View" Toolkit About: XuvTools 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. 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. The technical details are described in the following paper: M. Emmenlauer, O. Ronneberger, A. Ponti, P. Schwarb, A. Griffa, A. Filippi, R. Nitschke, W. Driever, and H. Burkhardt. XuvTools: free, fast and reliable stitching of large 3D datasets. Journal of Microscopy, 233(1):42–60, 2009 PDF on Publisher site (free access) doi:10.1111/j.1365-2818.2008.03094.x 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. Features and Limitations of XuvTools 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 (but you have to cite us) Read many input formats: BioRad PIC, TIFF, Metamorph STK (uncompressed and LZW compressed), Fluoview TIFF, Carl Zeiss LSM 5, PSIA TIFF, Nanoscope II/III, JPEG, PNG, BMP, IBW, OME, RAW Latest Version Latest stable version is XuvTools 1.7.0, get it from the Download Section. XuvTools-1.7.0 brings better project file support, including saving of thumbnails and fixes some bugs from 1.6.0. Roadmap for next Version Roadmap: The next release after XuvTools-1.7.0 will be XuvTools-1.8.0, that fixes many more issues, and has an improved dialog for Advanced Parameters. XuvTools-1.8.0 will be in alpha-testing soon. The release after XuvTools-1.8.0 should feature 2D stitching support, and should fix the long-standing bug that “stacks are too flat”. 70% completed Registration and Mailing List We have new releases frequently, typically once per month. If you want to be notified of new stable releases, beta releases or want to subscribe to our news feed, please register at http://special.xuvtools.org/register.php Links Download: Download XuvTools Documentation: Readme Download: download Test-Datasets to get started Developers Pages: Development Developers Time Schedule: Current ToDo List Developers History: Latest Changelog Contact: Contact, or read about, the team behind XuvTools More News And Updates Also see the Changelog. 18.02.2010: Version 1.7.0 released! 18.01.2010: Release Candidate 1 for XuvTools 1.7.0 available for download. 11.12.2009: Fixed several bugs concerning usability and GUI-consistency. 28.11.2009: Many bugs and issues have been fixed (total 15 bugs, see Changelog) 26.11.2009: Support for reading/writing thumbnails from project files 18.11.2009: Improved writing of Imaris 5.5 MultiResolution files, including some bugfixes. 10.11.2009: XuvTools 1.6.0 successfully tested on Windows 7 x64 and x86.
			start.txt · Last modified: 2010/03/09 13:01 by mario Contact: mario(a)xuvtools.org