Limited angle STIM and PIXE tomography of single cells

Andrea, T.; Rothermel, Martin; Werner, Ronald; Butz, T.; Reinert, Tilo

doi:10.1016/j.nimb.2010.02.049

Cited by 21 publications

(8 citation statements)

References 20 publications

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“…3. As discussed above, this method could facilitate the reconstruction of limited angle tomography data and could constitute an alternative to the option proposed by Andrea et al [17].…”

Section: Reconstruction Algorithmmentioning

confidence: 99%

“…An innovative approach was proposed by Andrea et al [17] for limited angle tomography of single cells, over an angular range of 120°. In this study, the missing STIMT projections, over the 60° angle range not covered by the beam, were interpolated using a back and forth numerical guess of the complete sinogram, based on a FBP method.…”

Section: Current Limitations and Prospectsmentioning

confidence: 99%

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Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

Habchi

Gordillo

Bourret

et al. 2013

Nuclear Instruments and Methods in Physics Research Section B:

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A new version of the TomoRebuild data reduction software package is presented, for the reconstruction of scanning transmission ion microscopy tomography (STIMT) and particle induced X-ray emission tomography (PIXET) images. First, we present a state of the art of the reconstruction codes available for ion beam microtomography. The algorithm proposed here brings several advantages. It is a portable, multi-platform code, designed in C++ with well-separated classes for easier use and evolution. Data reduction is separated in different steps and the intermediate results may be checked if necessary. Although no additional graphic library or numerical tool is required to run the program as a command line, a user friendly interface was designed in Java, as an ImageJ plugin. All experimental and reconstruction parameters may be entered either through this plugin or directly in text format files. A simple standard format is proposed for the input of experimental data. Optional graphic applications using the ROOT interface may be used separately to display and fit energy spectra. Regarding the reconstruction process, the filtered backprojection (FBP) algorithm, already present in the previous version of the code, was optimized so that it is about 10 times as fast. In addition, Maximum Likelihood Expectation Maximization (MLEM) and its accelerated version Ordered Subsets Expectation Maximization (OSEM) algorithms were implemented. A detailed user guide in English is available. A reconstruction example of experimental data from a biological sample is given. It shows the capability of the code to reduce noise in the sinograms and to deal with incomplete data, which puts a new perspective on tomography using low number of projections or limited angle.

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“…3. As discussed above, this method could facilitate the reconstruction of limited angle tomography data and could constitute an alternative to the option proposed by Andrea et al [17].…”

Section: Reconstruction Algorithmmentioning

confidence: 99%

Section: Current Limitations and Prospectsmentioning

confidence: 99%

Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

Habchi

Gordillo

Bourret

et al. 2013

Nuclear Instruments and Methods in Physics Research Section B:

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show abstract

“…We have shown that in principle IBA-T (that is, using the BS signals as well as the PIXE signals) is already achievable in principle, and should be significantly more efficient (and therefore much faster) than pure PIXE-T since a single slice already has (nearly) complete 3-D information. This is important since tomography is rather slow, and its importance is increased since it seems that beam damage limits the use of a pure PIXE-T for important classes of samples [85]. In principle, using the depth information available explicitly in IBA-T (from the particle signals) must be quicker than unfolding the depth information available only implicitly (and at much lower resolution) in the PIXE signals.…”

Section: Iba For Blind Samplesmentioning

confidence: 99%

“Total IBA” – Where are we?

Jeynes

Bailey

Bright

et al. 2012

Nuclear Instruments and Methods in Physics Research Section B:

120

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“…The samples must be prepared free-standing as far as possible in order to avoid further source of inaccuracy due to the mounting media. On the other hand, a free-standing sample would deteriorate readily as a result of high fluences employed in PIXE-T. Andrea et al 7 performed limited angle tomography of single cells grown on a substrate to overcome the sample preparation limitations. They used an average fluence of 500 pC/µm² per map to avoid the sample deterioration.…”

Section: Introductionmentioning

confidence: 99%

3d Analysis of an Induced Atherosclerotic Lesion in a Murine Artery by Pixe Stacking

et al. 2012

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Quantitative three dimensional analysis is possible, in principle, by PIXE tomography. But, the inherent problems in quantitation, restrictions on the sample geometry and preparation, and specimen damage due to high fluences make this method unsuitable for many biological samples. The specimen under investigation, a murine artery, was around a millimeter in diameter and the induced atherosclerotic lesion was spread few hundreds of micrometers across the length of the artery. Since no tomographic experiments were possible, we chose to do the 3D quantitative analysis by means of PIXE Stacking. Herein, thin serial sections of the specimen are prepared and measured by conventional ion beam techniques. The resultant two dimensional quantitative element maps are stacked and aligned to reconstruct a quantitative volume of the specimen. Although the reconstructed dimension has poorer spatial resolution as compared with the measured dimensions, new information can still be gained from it. The three dimensional element distribution of the atherosclerotic lesion shows calcification on the outer surface of the artery, which otherwise would not have been easily visible in the two dimensional analysis.

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Limited angle STIM and PIXE tomography of single cells

Cited by 21 publications

References 20 publications

Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

Beyond filtered backprojection: A reconstruction software package for ion beam microtomography data

“Total IBA” – Where are we?

3d Analysis of an Induced Atherosclerotic Lesion in a Murine Artery by Pixe Stacking

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