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TeraStitcher specifications


Unique identifier OMICS_27778
Name TeraStitcher
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.10.12
Stability Stable
Maintained Yes




No version available



  • person_outline Alessandro Bria
  • person_outline Giulio Iannello
  • person_outline Roberto Valenti

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Publication for TeraStitcher

TeraStitcher citations


Automatic and adaptive heterogeneous refractive index compensation for light sheet microscopy

Nat Commun
PMCID: 5606987
PMID: 28931809
DOI: 10.1038/s41467-017-00514-7

[…] applied voltage on the slow-axis galvanometer mirror for each new position. because of local ri variation, it is possible that there are small mismatches in the axial location of adjacent stacks. terastitcher was designed to accommodate this mismatch, motivating its application here. by directly writing a compatible file structure to disk during acquisition, we were immediately able to load […]


Label free volumetric optical imaging of intact murine brains

Sci Rep
PMCID: 5388920
PMID: 28401897
DOI: 10.1038/srep46306

[…] confocal detection. images were acquired by synchronizing the focal plane of the detection objective and the position of the illumination light sheet. multiple image stacks were stitched with terastitcher (bria, bmc bioinformatics 2012) and visualized with imaris (bitplane). transverse sampling pitch was 2.32 μm and axial pitch was 5 μm. the total acquisition time was about 1 hrs., […]


Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high throughput image analysis

Front Neuroanat
PMCID: 4445386
PMID: 26074783
DOI: 10.3389/fnana.2015.00068

[…] written in labview (national instruments, austin, tx, usa) orchestrated all the hardware components of the microscope to perform automated imaging of the volume., to stitch the tiled raw image, the terastitcher tool () has been used. terastitcher is a free and fully automated 3d stitching tool specifically designed to match the special requirements coming out of teravoxel-sized tiled microscopy […]


A versatile clearing agent for multi modal brain imaging

Sci Rep
PMCID: 4423470
PMID: 25950610
DOI: 10.1038/srep09808

[…] labview code (national instruments) which coordinated the galvo scanners, the rolling shutter and the stack acquisition., in order to achieve a 3d image of the whole specimen from raw data, the terastitcher has been recently proposed, i.e. a stitching tool capable to deal with teravoxel-sized images. however, the terastitcher does not support input data acquired through the serial […]


Micron scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

PMCID: 3939053
PMID: 24145191
DOI: 10.3791/50696

[…] (figure 4c). this step is mandatory in order for the stitching software to deal with a complete cubic volume., launch vaa3d software (freely downloadable from http://www.vaa3d.org/) with the plugins terastitcher and teramanager installed., load the terastitcher plugin. select the directory containing the imaged volume, indicate the relative orientations of the axes (with respect to a reference […]

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TeraStitcher institution(s)
Center of Integrated Research, University Campus Bio-Medico di Roma, Roma, Italy; Department of Electrical and Information Engineering, University of Cassino and L.M., Cassino, Italy
TeraStitcher funding source(s)
Supported by the International Center of Computational Neurophotonics.

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