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TxBR specifications

Information


Unique identifier OMICS_27814
Name TxBR
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Python
Computer skills Advanced
Version 3.0.1
Stability Beta
Requirements
Enthought Python Distribution, Class Library for Numbers, GiNaC symbolic package, python swiginac bindings, fftw3, OpenCV, libtiff, IMOD EM
Source code URL https://confluence.crbs.ucsd.edu/download/attachments/12648600/TxBR-beta-3.0.1.tar.gz
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Mark Ellisman

Publications for TxBR

TxBR citations

 (10)
library_books

Proteolipid protein–deficient myelin promotes axonal mitochondrial dysfunction via altered metabolic coupling

2016
PMCID: 5119941
PMID: 27872255
DOI: 10.1083/jcb.201607099

[…] 2° angles from −60° to 60°. Negatives were digitized to produce images with 1.41 nm/pixel. The IMOD package () was used for rough alignment, with fine alignment and reconstruction performed using the TxBR package (). Volume segmentation was performed by manual tracing using Xvoxtrace (), and reconstructions were visualized using Analyze (Mayo Foundation), Synu (), and Amira (Mercury/TGS) software. […]

library_books

3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography

2016
PMCID: 4972035
PMID: 27547706
DOI: 10.1186/s40679-016-0021-2

[…] To produce a high-quality reconstruction, the projection images must be aligned accurately. In TxBR [], a reconstruction package developed at NCMIR, this is done with a non-linear bundle adjustment scheme that optimizes the micrograph registration to the final volume with the 3D distribution of […]

library_books

A split horseradish peroxidase for detection of intercellular protein protein interactions and sensitive visualization of synapses

2016
Nat Biotechnol
PMCID: 4942342
PMID: 27240195
DOI: 10.1038/nbt.3563

[…] pe (FEI Titan) operating at 300 kV, while sections were tilted every 0.5° (from −60° to +60°) in a 4-tilt series scheme. The final 3D representations were built from the projection sets following the TxBR alignment protocol and using iterative procedures (weighted SIRT). Volumes are displayed with IMOD, and animations created with AMIRA. Tomograms reported in this paper were all acquired at a magn […]

library_books

Nuclear pore complex remodeling by p75NTR cleavage controls TGF β signaling and astrocyte functions

2015
Nat Neurosci
PMCID: 4878404
PMID: 26120963
DOI: 10.1038/nn.4054

[…] controlled goniometer. The pixel dimensions of the CCD camera were 3448 × 3448 and the pixel resolution was 0.865 nm. The IMOD software package was used for rough alignment of the tilt series and the TxBR software package was used for fine alignment and reconstruction. Nuclear pore diameter measurements were made using NIH ImageJ. Measurements were taken in the XY plane of multiple slices about th […]

library_books

Pannexin2 oligomers localize in the membranes of endosomal vesicles in mammalian cells while Pannexin1 channels traffic to the plasma membrane

2015
PMCID: 4313697
PMID: 25698922
DOI: 10.3389/fncel.2014.00468

[…] lt series was calculated using the IMOD package (Kremer et al., ). Fine alignment of projections and combination of the three tilt series data for the final 3D reconstruction were performed using the TxBR reconstruction package (Lawrence et al., ). Reconstructed volumes were viewed and vesicles segmented using the automated thresholding algorithm in Amira (FEI Visualization Sciences Group, Burling […]

library_books

Liprin α/SYD 2 determines the size of dense projections in presynaptic active zones in C. elegans

2013
PMCID: 3857474
PMID: 24322429
DOI: 10.1083/jcb.201302022

[…] specimen deformation during the image collection process. Rough alignment of the two tilt series was performed with IMOD software package (). Fine alignment and reconstruction was performed using the TxBR package (). Volume segmentation was performed by manual tracing using Amira (FEI). […]

Citations

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TxBR institution(s)
National Center for Microscopy and Imaging Research, University of California, San Diego, CA, USA
TxBR funding source(s)
Supported by grants from the NIH National Center for Research Resources (NCRR) under Award Number P41RR008605, The National Biomedical Computation Resource, and Award Number P41RR004050, The National Center for Microscopy and Imaging Research.

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