amira: A Highly Interactive System for Visual Data Analysis

Stalling, Detlev; Westerhoff, Malte; Hege, Hans‐Christian

doi:10.1016/b978-012387582-2/50040-x

Cited by 436 publications

(326 citation statements)

References 11 publications

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“…The projection images were aligned using cross-correlation procedures and reconstructed by a weighted back-projection algorithm as implemented in the EM and TOM software packages (31,32). Visualization and surface rendering was performed using the Amira software (33). Images were stitched together and adjusted for matching contrast and brightness using Adobe Photoshop CS4.…”

Section: Methodsmentioning

confidence: 99%

Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography

Rigort

Bäuerlein

Villa

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

389

306

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Cryoelectron tomography provides unprecedented insights into the macromolecular and supramolecular organization of cells in a close-to-living state. However because of the limited thickness range (< 0.5–1 μm) that is accessible with today’s intermediate voltage electron microscopes only small prokaryotic cells or peripheral regions of eukaryotic cells can be examined directly. Key to overcoming this limitation is the ability to prepare sufficiently thin samples. Cryosectioning can be used to prepare thin enough sections but suffers from severe artefacts, such as substantial compression. Here we describe a procedure, based upon focused ion beam (FIB) milling for the preparation of thin (200–500 nm) lamellae from vitrified cells grown on electron microscopy (EM) grids. The self-supporting lamellae are apparently free of distortions or other artefacts and open up large windows into the cell’s interior allowing tomographic studies to be performed on any chosen part of the cell. We illustrate the quality of sample preservation with a structure of the nuclear pore complex obtained from a single tomogram.

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Section: Methodsmentioning

confidence: 99%

Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography

Rigort

Bäuerlein

Villa

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

389

306

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“…For the skeletal muscles, the early detection of fascial disorders [3,4] is estimated as a promising field. Notably, for the realization of Part I and Part II, we use the software platform Amira [45,46]. Part III is dedicated to a -still Amira based -automation of the computational processing and a clinical study of about 20 -30 cases.…”

Section: E Project Scheme For Further Processingmentioning

confidence: 99%

Computer-assisted analysis of human upper arm flexion by 4D-visualization based on MRI

Kober

Gallo

Zeilhofer³

et al. 2011

Int J CARS

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“…where m [ω f ] was defined in (33). In this way we take the possible increase due to the normal step into account while avoiding any additional function evaluations.…”

Section: Acceptance Criteriamentioning

confidence: 99%

“…However the considerations in Section 3.1.3 mainly carry over to this setting. Now, tangential steps are computed as minimizers or at least directional minimizers along descent directions of (33). By orthogonality of the tangential and normal step, the trust region constraint on δx in (42) is equivalent to the trust region constraint…”

Section: Definition Of Globalized Stepsmentioning

confidence: 99%

An affine covariant composite step method for optimization with PDEs as equality constraints

Lubkoll

Schiela

Weiser

2016

Optimization Methods and Software

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AMS MSC 2000: 49M37, 90C55, 90C06We propose a composite step method, designed for equality constrained optimization with partial differential equations. Focus is laid on the construction of a globalization scheme, which is based on cubic regularization of the objective and an affine covariant damped Newton method for feasibility. We show finite termination of the inner loop and fast local convergence of the algorithm. We discuss preconditioning strategies for the iterative solution of the arising linear systems with projected conjugate gradient. Numerical results are shown for optimal control problems subject to a nonlinear heat equation and subject to nonlinear elastic equations arising from an implant design problem in craniofacial surgery.

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amira: A Highly Interactive System for Visual Data Analysis

Cited by 436 publications

References 11 publications

Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography

Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography

Computer-assisted analysis of human upper arm flexion by 4D-visualization based on MRI

An affine covariant composite step method for optimization with PDEs as equality constraints

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