TxBR statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Data format conversion chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Download


Versioning


Add your version

Maintainer


  • person_outline Mark Ellisman <>

Publications for TxBR

TxBR in publications

 (5)
PMCID: 5119941
PMID: 27872255
DOI: 10.1083/jcb.201607099

[…] 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) […]

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

[…] 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, […]

PMCID: 3754886
PMID: 24013648
DOI: 10.1371/journal.pbio.1001640

[…] at +/−60° with 1° intervals and a pixel size of 0.5 nm (at 18k). images were captured using a 4k×4k gatan ultrascan 4000 camera. reconstruction was accomplished using a combination of imod and txbr reconstruction packages. rough alignment of the two tilt series was done with imod software package, and fine alignment and reconstruction was done using the txbr package., we are grateful […]

PMCID: 3446896
PMID: 23028948
DOI: 10.1371/journal.pone.0045344

[…] down two times by averaging adjacent pixels so that the final pixel resolution was 2.4 nm. the imod software package was used for the complete image processing unless there were problems, and then txbr software was used to refine the alignment and reconstruction . five nc and five ha mitochondrial volumes were generated. volume segmentation was performed by manual tracing in the planes […]

PMCID: 5415345
PMID: 28479932
DOI: 10.1016/j.procs.2012.04.175

[…] users can launch their computation-intensive program easily., the “integrated imaging workflow” actor () encapsulates various software packages in the processing pipeline. those packages, such as txbr, are accessed through a unified protocol for application integration with a kepler workflow engine. txbr is an advanced electron tomography code. this code contains alignment, image correction, […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

TxBR reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review TxBR