Automated Correlation and Averaging of Three-Dimensional Reconstructions Obtained by Electron Tomography

Öfverstedt, Lars-Göran; Zhang, Kan; Isaksson, Leif A.; Bricogne, G.; Skoglund, Ulf

doi:10.1006/jsbi.1997.3915

Cited by 15 publications

(13 citation statements)

References 38 publications

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“…To refine the shifts and ϕ values and to determine θ and ψ, reference free alignment algorithms, used for single particle approaches [36,37], can be adapted in 3D. This approach has been successfully tested in the case of ribosomes, leading to a significant resolution improve ment [47].…”

Section: Improving Tomogram Resolutionmentioning

confidence: 99%

Electron tomography of biological samples

Marco

Boudier

Messaoudi

et al. 2004

Biochemistry (Moscow)

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Electron tomography allows computing three-dimensional (3D) reconstructions of objects from their projections recorded at several angles. Combined with transmission electron microscopy, electron tomography has contributed greatly to the understanding of subcellular structures and organelles. Performed on frozen-hydrated samples, electron tomography has yielded useful information about complex biological structures. Combined with energy filtered transmission electron microscopy (EFTEM) it can be used to analyze the spatial distribution of chemical elements in biological or material sciences samples. In the present review, we present an overview of the requirements, applications, and perspectives of electron tomography in structural biology.

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Section: Improving Tomogram Resolutionmentioning

confidence: 99%

Electron tomography of biological samples

Marco

Boudier

Messaoudi

et al. 2004

Biochemistry (Moscow)

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“…(1,2,8,10,11) With reference to 0° tilt, let ∅ represent the microscope mechanical rotation angle, while θ represents the specimen tilt angle, Ω represents the rotation angle of projection, and s represents the relative scaling factor. Let xs, ys represent the center shift along X and Y coordinate axes in a tilt's projection.…”

Section: Geometry Modelmentioning

confidence: 99%

“…In order to make shift prediction more stable and accurate in noisy datasets, pre-processing methods (1), (2), and (3) and post-processing methods (4) and (5) are used:…”

Section: Predicting the Shiftmentioning

confidence: 99%

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Xpix2: Software to Pick the Fiducial Markers Semi-Automatically in Electron Tomography Tilt Images

Tian

Öfverstedt

Skoglund

2016

Proceedings of the 4th IIAE International Conference on Intelligent Systems and Image Processing 2016

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In electron microscope tomography, alignment of tilt series images is a major determinant of resolution in 3D reconstructions. One alignment method uses gold beads deposited on or in the specimen as fiducial markers. We have developed software called "xpix2" that picks markers semi-automatically. It uses a cross-correlation function to determine the shift between tilt images and predicts marker positions. Then it refines them in a local search area, and detects and corrects wrongly picked markers automatically. xpix2 checks its own status and pauses to ask the operator to intercede if it finds that most markers are wrongly picked. xpix2 is more accurate than manual picking. We now use this software in our research unit.

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“…One of the standard technique of reducing image noise is to record a rapid series of images and average the signal over the images in the series. [6][7][8][9][10][11][12][13][14][15] Swindell and Mosleh-Shirazi have analysed the theoretical improvement that can be achieved by averaging serial images to reduce SNR 13 and found that the improvement is proportional to the square root of the number of images. However, in ophthalmic imaging applications eye motions limit the number of images that can be included.…”

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confidence: 99%

Improved visualisation of choroidal neovascularisation by scanning laser ophthalmoscope using image averaging

Bartsch

2005

British Journal of Ophthalmology

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Aims: To improve visualisation of angiographic features in patients with age related macular degeneration associated with choroidal neovascularisation (CNV) and related complications. To evaluate if image averaging can achieve this goal. Methods: 27 eyes of 20 sequential patients with age related macular degeneration over a 3 month period were studied. Indocyanine green angiograms (ICGA), fluorescein angiograms (FA), and oral fluorescein angiograms were recorded with a confocal scanning laser ophthalmoscope. Software was used to average multiple images from a 10-20 image series (over 0.5-1.0 seconds). Image quality was assessed by two masked observers and graded on a scale of 0-3. A more quantifiable grading method was devised by adding a variable amount of Gaussian noise to the improved image until the original and image averaged image appeared equal. Results: Masked review showed mild to strong improvement of visualisation of structures including borders of CNV. Improvement varied depending on the type and phase of the angiogram. Improvement was highest in late phase FA, mid and late phase ICGA, and all phases of oral FA. Conclusion: Image averaging using software based algorithms improves the quality of angiographic images, particularly late ICGA images and oral FAs. This method may assist in the visualisation of choroidal neovascularisation in age related macular degeneration.

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Automated Correlation and Averaging of Three-Dimensional Reconstructions Obtained by Electron Tomography

Cited by 15 publications

References 38 publications

Electron tomography of biological samples

Electron tomography of biological samples

Xpix2: Software to Pick the Fiducial Markers Semi-Automatically in Electron Tomography Tilt Images

Improved visualisation of choroidal neovascularisation by scanning laser ophthalmoscope using image averaging

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