TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

MessaoudiI, Cédric; Boudier, Thomas; Sorzano, C.O.S.; Marco, Sergio

doi:10.1186/1471-2105-8-288

Cited by 289 publications

(233 citation statements)

References 41 publications

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“…Each set of aligned single-axis tomogram tilts was reconstructed using the TomoJ software (component of ImageJ) (Messaoudii et al, 2007). For the reconstruction, 30 iterations of the SIRT algorithm, or 15 iterations of the ART algorithm, were applied (Messaoudii et al, 2007), depending on the quality of the reconstructed image stacks. Tomograms were displayed and analyzed with Imaris software to create the isosurface of the internal plastid membranes.…”

Section: Etmentioning

confidence: 99%

Three-Dimensional Visualization of the Tubular-Lamellar Transformation of the Internal Plastid Membrane Network during Runner Bean Chloroplast Biogenesis

et al. 2016

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Chloroplast biogenesis is a complex process that is integrated with plant development, leading to fully differentiated and functionally mature plastids. In this work, we used electron tomography and confocal microscopy to reconstruct the process of structural membrane transformation during the etioplast-to-chloroplast transition in runner bean (Phaseolus coccineus). During chloroplast development, the regular tubular network of paracrystalline prolamellar bodies (PLBs) and the flattened porous membranes of prothylakoids develop into the chloroplast thylakoids. Three-dimensional reconstruction is required to provide us with a more complete understanding of this transformation. We provide spatial models of the bean chloroplast biogenesis that allow such reconstruction of the internal membranes of the developing chloroplast and visualize the transformation from the tubular arrangement to the linear system of parallel lamellae. We prove that the tubular structure of the PLB transforms directly to flat slats, without dispersion to vesicles. We demonstrate that the grana/stroma thylakoid connections have a helical character starting from the early stages of appressed membrane formation. Moreover, we point out the importance of particular chlorophyll-protein complex components in the membrane stacking during the biogenesis. The main stages of chloroplast internal membrane biogenesis are presented in a movie that shows the time development of the chloroplast biogenesis as a dynamic model of this process.

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Section: Etmentioning

confidence: 99%

Three-Dimensional Visualization of the Tubular-Lamellar Transformation of the Internal Plastid Membrane Network during Runner Bean Chloroplast Biogenesis

et al. 2016

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“…Tomographic series (-40° to 40° with a constant tilt increment 1°) have been acquired using the Gatan Digital Micrograph tomography plugin at x3000 nominal magnification. Tomography reconstruction was performed using Tomo-J software (http://u759.curie.u-psud.fr/softwaresu759.html) 18 by applying ART reconstruction algorithm with 12 iterations and a relaxation coefficient of 0.1. Volume rendering has been performed using UCSF Chimera (www.cgl.ucsf.edu/chimera/).…”

mentioning

confidence: 99%

Involvement of HFq protein in the post-transcriptional regulation ofE. colibacterial cytoskeleton and cell division proteins

Zambrano¹,

Guichard²,

Bi³

et al. 2009

Cell Cycle

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“…It is useful to note that there are several popular software packages, such as TomoJ (Messaoudii et al, 2007), XMIPP (Sorzano et al, 2004), etc., offering various algorithms for tomographic reconstruction from standard transmission data. On the other hand, TXM-Wizard is designed to handle data from different X-ray microscopy systems such as diffraction-enhanced phase contrast imaging and grating-based X-ray phase contrast imaging (Zhu et al, 2010).…”

Section: Analytical and Iterative Tomographic Reconstructormentioning

confidence: 99%

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

et al. 2012

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Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available.

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TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

Cited by 289 publications

References 41 publications

Three-Dimensional Visualization of the Tubular-Lamellar Transformation of the Internal Plastid Membrane Network during Runner Bean Chloroplast Biogenesis

Three-Dimensional Visualization of the Tubular-Lamellar Transformation of the Internal Plastid Membrane Network during Runner Bean Chloroplast Biogenesis

Involvement of HFq protein in the post-transcriptional regulation ofE. colibacterial cytoskeleton and cell division proteins

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

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