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TeraStitcher

A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images (BMC Bioinformatics 2012, 13:316)

TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently visualized (see TeraFly) and processed.

Images for this research were produced by the Biophisics lab of LENS. The software was developed by the Department of Engineering of University Campus Bio-Medico of Rome (Italy).

Main features

• designed for images exceeding the TeraByte size
• fast and reliable 3D stitching based on a multi-MIP approach
• typical memory requirement below 4 GB (8 at most)
• 2D stitching (single slice images) supported
• regular expression based matching for image file names
• data subset selection
• sparse data support
• i/o plugin-based architecture
• stitching of multi-channel images
• support for big tiff files (> 4 GB)
• HDF5-based formats
• parallelization on multi-core platform
• fast alignment computation on NVIDIA GPUs

News

2018-08-31. Added support for executing the computation intensive alignment step on NVIDIA GPUs See the this page for a demo of this feature.

2018-08-31. Added parallel execution of multiple TeraStitcher instances with MPI and the MPI Python inteface mpi4py. See the this page for a demo of this feature.

2018-04-07. New version 1.10.12 improves the loading of unstitched subvolumes. See the latest binary release!

2018-03-01. New version 1.10.11 improves the precision of computed tile displacements. See the latest binary release!

2017-10-13. New version 1.10.8 fixes a bug that could cause to generate incorrect Big TIFFs. See the latest binary release!

2017-06-19. New version 1.10.3 fixes a major bug of previous versions 1.10.x that might cause the Merge step to crash when using the GUI executable. See the latest binary release!

2017-05-04. New version 1.10.0 comes along with a re-designed Merge step (multi-channel stitching, X,Y,Z,C(hannel) volume-of-interest selection), major changes to the GUI (easier Import step, and more options in the Merge step) and more supported formats in output (Imaris HDF5, BigDataViewer HDF5). See the latest binary release!

2017-04-13. New version 1.9.70 fixes many bugs related to big tiffs and multi-channel images (some bugs were signaled directly by users: thanks!). See the latest binary release!

2016-09-30. New version 1.9.63 adds support for Big TIFF (tif files larger than 2 GB) and fixes a RAM allocation issue in the GUI when doing 2D stitching. See the latest binary release!

2016-09-06. New version 1.9.62 adds advanced libtiff compression options --libtiff_uncompress and --libtiff_rowsperstrip and fixes a bug in the GUI when doing 2D stitching. See the latest binary release!

2016-05-03. Support for parallel execution of TeraConverter, see --parallel option.

2016-04-18. New version 1.9.61 with standalone installers for Windows, Linux and MacOS! See the latest binary release!

2015-12-21. New version 1.9.5 with Qt-based GUI! See the latest binary release!

2015-01-18. New version 1.9.1 allows importing bunches of image files stored in one single folder and, more generally, any other customized tiles arrangement! See the new IMG_REGEX xml attribute and download the latest release!.

2014-12-11. New version 1.8.0 is out! See the changelog and download the latest release!

2014-12-11. Removed dependency from OpenCV library! The build process has never been so smooth (no 3rd party library dependencies)!

2014-11-11. Added TeraConverter utility.

Contributors

Alessandro Bria (a.bria@unicas.it)
Post-doctoral Fellow at University of Cassino and L.M. (Italy)
Main developer and Website Maintainer

Giulio Iannello (g.iannello@unicampus.it)
Full Professor at University Campus Bio-Medico of Rome (Italy)
Supervisor and co-developer

Roberto Valenti (r.valenti@unicampus.it)
Software Developer at University Campus Bio-Medico of Rome (Italy)
Co-developer