TxBR montage reconstruction for large field electron tomography
Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a conse...
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| Published in: | Journal of structural biology Vol. 180; no. 1; pp. 154 - 164 |
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| Abstract | Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a consequence, are rather difficult to generate directly. Various techniques have been developed towards generating those views, from increasing the sensor array size to implementing serial sectioning and montaging. Datasets and reconstructions obtained by the latter techniques generate multiple three-dimensional (3D) reconstructions, that need to be combined together to provide all the multiscale information. In this work, we show how to implement montages within TxBR, a tomographic reconstruction software package. This work involves some new application of mathematical concepts related to volume preserving transformations and issues of gauge ambiguity, which are essential problems arising from the nature of the observation in an electron microscope. The purpose of TxBR is to handle those issues as generally as possible in order to correct for most distortions in the 3D reconstructions and allow for a seamless recombination of ET montages. |
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| AbstractList | Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a consequence, are rather difficult to generate directly. Various techniques have been developed towards generating those views, from increasing the sensor array size to implementing serial sectioning and montaging. Datasets and reconstructions obtained by the latter techniques generate multiple three-dimensional (3D) reconstructions, that need to be combined together to provide all the multiscale information. In this work, we show how to implement montages within TxBR, a tomographic reconstruction software package. This work involves some new application of mathematical concepts related to volume preserving transformations and issues of gauge ambiguity, which are essential problems arising from the nature of the observation in an electron microscope. The purpose of TxBR is to handle those issues as generally as possible in order to correct for most distortions in the 3D reconstructions and allow for a seamless recombination of ET montages. |
| Author | Terada, Masako Phan, Sébastien Lawrence, Albert Berlanga, Monica Kulungowski, Alexander Ellisman, Mark Obayashi, James Lanman, Jason Molina, Tomas |
| Author_xml | – sequence: 1 givenname: Sébastien surname: Phan fullname: Phan, Sébastien – sequence: 2 givenname: Albert surname: Lawrence fullname: Lawrence, Albert – sequence: 3 givenname: Tomas surname: Molina fullname: Molina, Tomas – sequence: 4 givenname: Jason surname: Lanman fullname: Lanman, Jason – sequence: 5 givenname: Monica surname: Berlanga fullname: Berlanga, Monica – sequence: 6 givenname: Masako surname: Terada fullname: Terada, Masako – sequence: 7 givenname: Alexander surname: Kulungowski fullname: Kulungowski, Alexander – sequence: 8 givenname: James surname: Obayashi fullname: Obayashi, James – sequence: 9 givenname: Mark surname: Ellisman fullname: Ellisman, Mark email: mark@ncmir.ucsd.edu |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22749959$$D View this record in MEDLINE/PubMed |
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| Keywords | Electron tomography Montaging 3D reconstruction TxBR Whole cell tomography Section flattening |
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| SubjectTerms | 3D reconstruction Algorithms Animals Brain - cytology Drosophila - cytology Drosophila - virology Electron Microscope Tomography - methods Electron tomography Imaging, Three-Dimensional - methods Insect Viruses - physiology Mice Montaging Neurons - ultrastructure Section flattening Software TxBR Whole cell tomography |
| Title | TxBR montage reconstruction for large field electron tomography |
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