Amira (software)

Amira

Screenshot of Amira Window
Developer(s) Zuse Institute Berlin
FEI Visualization Sciences Group
Initial release October 1999 (1999-10)
Stable release
6.1.1 / May 1, 2016 (2016-05-01)
Written in C++
Operating system Microsoft Windows XP(SP3)/Vista/7, 32-bit and 64-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86_64 RHEL 5.5, 64-bit
Platform x86 & x86-64
Available in English language
Type 3D data visualization and processing
License Proprietary
Website www.amira.com

Amira (pronounce: Ah-meer-ah) is a software platform for 3D and 4D data visualization, processing, and analysis. It is being actively developed by Visualization Sciences Group, Bordeaux, France and the Zuse Institute Berlin (ZIB), Germany.

Overview

Amira[1] is an extendable software system for scientific visualization, data analysis, and presentation of 3D and 4D data. Amira is being developed and commercially distributed by FEI in cooperation with the Zuse Institute Berlin (ZIB). It is used by several thousand researchers and engineers in academia and industry around the world. Amira’s flexible user interface and its modular architecture make it a universal tool for processing and analysis of data from various modalities; e.g. micro-CT,[2] PET,[3] Ultrasound.[4] Its ever-expanding functionality has made it a versatile data analysis and visualization solution, applicable to and being used in many fields, such as microscopy in biology[5] and materials science,[6] molecular biology,[7] quantum physics,[8] astrophysics,[9] computational fluid dynamics (CFD),[10] finite element modeling (FEM),[11] non-destructive testing (NDT),[12] and many more. One of the key features, besides data visualization, is Amira’s set of tools for image segmentation[13] and geometry reconstruction.[14] This allows the user to mark (or segment) structures and regions of interest in 3D image volumes using automatic, semi-automatic, and manual tools. The segmentation can then be used for a variety of subsequent tasks, such as volumetric analysis,[4] density analysis,[15] shape analysis,[16] or the generation of 3D computer models for visualization,[17] numerical simulations,[18] or rapid prototyping[19] or 3D printing, to name a few. Other key Amira features are multi-planar and volume visualization, image registration,[20] filament tracing,[21] cell separation and analysis,[16] tetrahedral mesh generation,[22] fiber-tracking from diffusion tensor imaging (DTI) data,[23] skeletonization,[24] spatial graph analysis, and stereoscopic rendering[25] of 3D data over multiple displays including CAVEs (Cave automatic virtual environments).[26] As a commercial product Amira requires the purchase of a license or an academic subscription. A time-limited, but full-featured evaluation version is available for download free of charge.

History

1994–1998 Research Software

Amira’s roots go back to 1994 and the Department for Scientific Visualization, headed by Hans-Christian Hege at the Zuse Institute Berlin (ZIB). The ZIB is a research institute for mathematics and informatics. The Scientific Visualization department’s mission is to help solve computationally and scientifically challenging tasks in medicine, biology, and engineering. For this purpose, it develops algorithms and software for 2D, 3D, and 4D data visualization and visually supported exploration and analysis. At that time, the young visualization group at the ZIB had experience with the extendable, data flow-oriented visualization environments apE,[27] IRIS Explorer,[28] and Advanced Visualization Studio (AVS), but was not satisfied with these products’ interactivity, flexibility, and ease-of-use for non-computer scientists.

Therefore, in a subproject[29] within a medically oriented, multi-disciplinary collaborative research center[30] the development of a new software system was started in early 1994. The initial development was performed by Detlev Stalling, who later became the chief software architect. The software system was called “HyperPlan”, highlighting its initial target application  – a planning system for hyperthermia cancer treatment. The system was being developed on Silicon Graphics (SGI) computers, which at the time were the standard workstations used for high-end graphics computing. Software development was based on libraries such as OpenGL, SGI Open Inventor, and the graphical user interface libraries X11, Motif (software), and ViewKit. In 1998, X11/Motif/Viewkit were replaced by the Qt toolkit.

The HyperPlan framework served as the base for more and more projects at the ZIB and was used by a growing number of researchers in collaborating institutions. The projects included applications in neurobiology, confocal microscopy, flow visualization, molecule visualization and analysis and computational astrophysics.

1998–today Commercially Supported Product

The growing number of users of the system started to exceed the capacities that ZIB could spare for software distribution and support, as ZIB’s primary mission was algorithmic research. Therefore, the spin-off company Indeed, – Visual Concepts GmbH was founded by Hans-Christian Hege, Detlev Stalling, and Malte Westerhoff with the vision of making the extensive capabilities of the software available to researchers in industry and academia worldwide and to provide the product support and robustness needed in today’s fast-paced and competitive world.

In Feb 1998 the HyperPlan software was given the new, less application-specific name “Amira”. This name is not an acronym but was chosen for being pronounceable in different languages, starting with an ‘A’, and having an appropriate connotation: the Latin verb “admirare” (to admire), meaning “to look at” and “to wonder at”, describes a typical situation in data visualization.

A major re-design of the software was undertaken by Detlev Stalling and Malte Westerhoff in order to make it a commercially supportable product and to make it available on non-SGI computers as well. In March 1999, the first version of the commercial Amira was shown at the CeBIT tradeshow in Hannover, Germany on SGI IRIX and Hewlett-Packard UniX (HP-UX). Versions for Linux and Microsoft Windows followed within the following twelve months. Later Mac OS X support was added. Indeed, – Visual Concepts selected the Bordeaux, France and San Diego, United States based company TGS, Inc. as the worldwide distributor for Amira and completed five major releases (up to version 3.1) in the subsequent four years.

In 2003 both Indeed, as well as TGS were acquired by Massachusetts-based Mercury Computer Systems, Inc. (NASDAQ:MRCY) and became part of Mercury’s newly formed life sciences business unit, later branded Visage Imaging. In 2009, Mercury Computer Systems, Inc. spun off Visage Imaging again and sold it to Melbourne, Australia based Promedicus Ltd (ASX:PME), a leading provider of radiology information systems and medical IT solutions. During this time, Amira continued to be developed in Berlin, Germany and in close collaboration with the ZIB, still headed by the original creators of Amira. TGS, located in Bordeaux, France was sold by Mercury Computer systems to a French investor and renamed to Visualization Sciences Group (VSG). VSG continued the work on a complementary product named Avizo, based on the same source code but customized for material sciences.

In August 2012, FEI, to that date the largest OEM reseller of Amira, purchased VSG and the Amira business from Promedicus. In August 2013, Visualization Sciences Group (VSG) became a business unit of FEI. Amira and Avizo are still being marketed as two different products; Amira for life sciences and Avizo for materials science, but the development efforts are now joined once again. As in the beginning, the Amira roadmap continues to be driven by the interesting and challenging scientific questions that Amira users around the world are trying to answer, often at the leading edge in their fields.

Amira Options

Microscopy Option

DICOM Reader

Mesh Option

Skeletonization Option

Molecular Option

Developer Option

Neuro Option

VR Option

Very Large Data Option

Editors

Application Areas

Processing and Data Analysis

Visualization

Presentation

Supported File Formats

File Formats
Format Name Access Type Description
Amira Script read/write Amira Tcl script
Amira Script Object read/write Amira custom module written in Tcl
AmiraMesh Format read/write Amira's native general purpose format
AmiraMesh as LargeDiskData read/write access image data blockwise
Analyze 7.5 read/write 3D image data with separate header file
AnalyzeAVW read/write contains 2D and 3D medical image data
BMP Image Format read/write uncompressed Windows bitmap format
AutoCAD DXF read/write Drawing Interchange Format for AutoCAD 3D models
Encapsulated PostScript write for 2D raster images only
HTML read Hypertext document format
Hoc read/write Hoc file reader of morphometric models for NEURON environment
HxSurface read/write Amira's native format for triangular surfaces
Icol read/write ASCII format for colormaps with alpha channel
Interfile read Interfile file reader
JPEG Image Format read/write 2D image format with lossy compression
MATLAB Binary Format (.mat) read/write MATLAB matrices
MATLAB M-files Format (.m) read/write MATLAB script
Nifti read/write Nifti file reader
Open Inventor read/write standard file format for 3D models
PNG Image Format read/write portable network graphics format for 2D images
PNM Image Format read/write simple uncompressed 2D image format
PSI format read/write ASCII format for 3D points and associated data values
PLY Format read/write Stanford triangle format for points and surfaces
Raw Data read/write binary data as a 3D uniform field
Raw Data as LargeDiskData read/write access image data blockwise
SGI-RGB Image Format read/write 2D image format with run-length encoding
STL read/write simple format for triangular surfaces, no connectivity
SWC read/write interchange-file reader of morphometric models for neuroscience
Stacked-Slices read info file grouping together 2D images
TIFF Image Format read/write standard format for 2D and 3D image data
Tecplot read Tecplot ASCII and Binary file reader
VRML read/write virtual reality markup language for 3D models
Vevo Mode Raw Images read 2D and 3D ultrasound images from VisualSonics' Vevo 770
Wavefront Technologies 3D Geometry (.obj) write 3D geometries such as surfaces
AMBER read Assisted Model Building with Energy Refinement format
AMF read/write Amira Molecule Format
DX read APBS DX electrostatic field file
GROMACS read/write Groningen Machine for Chemical Simulations format
MAP read Autogrid interaction field file
MDL read/write MDL file format saving chemical structures
PDB read/write protein data base file format
PHI read Congen PHI Electrostatic field file (r)
PSF/DCD (CHARMM) read file format used by CHARMM
Tripos read/write file format used to save Tripos Sybyl mol2 molecules
UniChem read/write file format used by the UniChem molecular software
ZIB Molecular File Format read/write structured molecular file format
Amira Virtual Reality Option Config File read Amira Virtual Reality Option Config File (.cfg)
LDA read VolumeViz native file format
LargeDiskData read/write access image data blockwise
Stacked-Slices as LargeDiskData read access image data blockwise
AVS Field read/write stores data defined on regular grid
AVS UCD Format read/write stores unstructured cell data
Abaqus format write describes FEM grids and density data
FIDAP NEUTRAL read stores FEM meshes and solution data
Fluent / UNS read/write contains FEM meshes, boundary ids, solution data
HyperMesh read/write used by Altair HyperWorks FEM software
I-DEAS universal format read/write describes FEM grids and simulation data
Plot 3D Single Structured read/write stores curvilinear grids and associated data
Bio-Rad Confocal Format read simple uncompressed format for 3D image stacks
FEIStackedScalarField3 read scalar fields consisting of parallel slices (MRC format)
FEIUniformScalarField3 read scalar fields defined on a uniform lattice (MRC format)
Leica 3D TIFF read contains 3D image data with voxel sizes
Leica Binary Format (.lei) read 3D image stacks, time series, and meta information
Leica Image Format (.lif) read 3D image stacks, time series, and meta information
Leica Slice Series (.info) read contains list of 2D TIFF files and meta information
MRC read/write MRC file format for electron microscopy
Metamorph STK Format read special TIFF variant for 3D image stacks
Olympus (.oib/.oif) read file formats used by the Olympus FluoView 1000F
Zeiss LSM read 3D raster image format
ACR-NEMA read predecessor of the DICOM format for medical images
DICOM export write medical image export
DICOM import read standard file format for medical images

Release history

Amira versions
Version Release Date Supported Platforms
public
BETA
Dec 1998 SGI Irix 6.x
public
BETA
Mar 1999 SGI Irix 6.x
HP-UX 10.20
32-bit Linux: Red Hat 5.2, SuSE 6.0
(Linux: software rendering only)
2.0.0 Oct 1999 SGI Irix 6.5.x
HP-UX 10.20
32-bit Linux: Red Hat 6.0, SuSE 6.1
2.1.0 Mar 2000 Microsoft Windows 9x/NT4
32-bit Linux: Red Hat 6.x, SuSE 6.3
SGI Irix 6.5.x
HP-UX 10.20
Sun Solaris 7 (SunOS 5.7)
2.1.1 May 2000 Microsoft Windows 9x/NT4
32-bit Linux: Red Hat 6.x, SuSE 6.3
SGI Irix 6.5.x
HP-UX 10.20
Sun Solaris 7 (SunOS 5.7)
2.2.0 Sep 2000 Microsoft Windows 9x/NT4/2000
32-bit Linux: Red Hat 6.2, SuSE 6.3
SGI Irix 6.5.x
HP-UX 10.20
Sun Solaris 7 (SunOS 5.7)
2.3.0 Aug 2001 Microsoft Windows 9x/ME/NT4/2000, 32-bit
Linux: Red Hat 7.x, SuSE 7.x
SGI Irix 6.5.x
HP-UX 11.0
Sun Solaris 7 (SunOS 5.7)
3.0.0 Jul 2002 Microsoft Windows 98/ME/NT4/2000/XP, 32-bit
Linux: Red Hat 8.0
SGI Irix 6.5.x
Sun Solaris 8
HP-UX 11.0
3.1.0 Dec 2003 Microsoft Windows 98/ME/NT4/2000/XP, 32-bit
Linux IA64 (Red Hat AW 2.1), 64-bit
Linux Red Hat 8.0 (<=glibc-2.3.2), 32-bit
Linux SUSE 9.0 (x86-64), 64-bit
Sun Solaris 8/9, 32/64-bit
SGI Irix 6.5.x, 32/64-bit
HP-UX 11.0, 32/64-bit
3.1.1 Jun 2004 Microsoft Windows 98/ME/NT4/2000/XP, 32-bit
Linux IA64 (Red Hat AW 2.1), 64-bit
Linux Red Hat 8.0 (<=glibc-2.3.2), 32-bit
Linux SUSE 9.0 (x86-64), 64-bit
Sun Solaris 8/9, 32/64-bit
SGI Irix 6.5.x, 32/64-bit
HP-UX 11.0, 32/64-bit
4.0.0 Dec 2005 Microsoft Windows XP 2003 (x86-64), 64-bit
Microsoft Windows 2000/XP, 32-bit
Linux IA64 (RHEL 3.0, Itanium 2), 64-bit
Linux x86-64 (RHEL 3.0), 64-bit
Linux x86 (RHEL 3.0), 32-bit
Mac OS X 10.4(Tiger), 32-bit
Sun Solaris 8, 32/64-bit
SGI Irix 6.5.x, 32/64-bit
HP-UX 11.0, 32/64-bit
4.1.0 May 2006 Microsoft Windows XP 2003 (x86-64), 64-bit
Microsoft Windows 2000/XP, 32-bit
Linux IA64 (RHEL 3.0, Itanium 2), 64-bit
Linux x86-64 (RHEL 3.0), 64-bit
Linux x86 (RHEL 3.0), 32-bit
Sun Solaris 8, 32/64-bit
SGI Irix 6.5.x, 32/64-bit
HP-UX 11.0, 32/64-bit
4.1.1 Oct 2006 Microsoft Windows XP 2003 (x86-64), 64-bit
Microsoft Windows 2000/XP, 32-bit
Linux IA64 (RHEL 3.0, Itanium 2), 64-bit
Linux x86-64 (RHEL 3.0), 64-bit
Linux x86 (RHEL 3.0), 32-bit
Mac OS X 10.4 (Tiger), 32-bit
Sun Solaris 8, 32/64-bit
SGI Irix 6.5.x, 32/64-bit
HP-UX 11.0, 32/64-bit
4.1.2 Feb 2007 Microsoft Windows XP 2003 (x86-64), 64-bit
Microsoft Windows 2000/XP, 32-bit
Linux IA64 (RHEL 3.0, Itanium 2), 64-bit
Linux x86-64 (RHEL 3.0), 64-bit
Linux x86 (RHEL 3.0), 32-bit
Mac OS X 10.4 (Tiger), 32-bit
Sun Solaris 8, 32/64-bit
SGI Irix 6.5.x, 32/64-bit
HP-UX 11.0, 32/64-bit
5.0.0 May 2008 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
5.0.1 Jun 2008 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
5.2.0 Nov 2008 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Linux x86-64 (RHEL 5.2), 64-bit
5.2.1 Mar 2009 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Linux x86-64 (RHEL 5.2), 64-bit
5.2.2 Jul 2009 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Linux x86-64 (RHEL 5.2), 64-bit
5.3.0 Jun 2010 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.3.1 Jul 2010 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.3.2 Oct 2010 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.3.3 Dec 2010 Microsoft Windows 2000/XP/Vista (x86-64), 64-bit
Microsoft Windows 2000/XP/Vista, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.4.0 Oct 2011 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.4.1 Dec 2011 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.4.2 Mar 2012 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.4.3 Oct 2012 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.4.4 Mar 2013 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.4.5 Mar 2013 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.5 (Leopard), 32-bit
Mac OS X 10.6 (Snow Leopard), 32-bit
Mac OS X 10.7 (Lion), 32-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.5.0 Oct 2013 Microsoft Windows XP/Vista/7 (x86-64), 64-bit
Microsoft Windows XP/Vista/7, 32-bit
Mac OS X 10.7 (Lion), 64-bit
Mac OS X 10.8 (Mountain Lion), 64-bit
Linux x86-64 (RHEL 5.5), 64-bit
5.6.0 Apr 2014 Microsoft Windows XP/Vista/7/8 (x86-64), 64-bit
Microsoft Windows XP/Vista/7/8, 32-bit
Mac OS X 10.7/10.8 (Lion), 64-bit
Mac OS X 10.8 (Mountain Lion), 64-bit
Linux x86-64 (RHEL 5.5), 64-bit
6.0 Jan 2015 Microsoft Windows 7/8 (x86-64), 64-bit
Microsoft Windows 7/8, 32-bit
Mac OS X 10.7 (Lion), 64-bit
Mac OS X 10.8 (Mountain Lion), 64-bit
Mac OS X 10.9 (Mavericks), 64-bit
Linux x86-64 (RHEL 6), 64-bit
6.0.1 Jul 2015 Microsoft Windows 7/8 (x86-64), 64-bit
Microsoft Windows 7/8, 32-bit
Mac OS X 10.7 (Lion), 64-bit
Mac OS X 10.8 (Mountain Lion), 64-bit
Mac OS X 10.9 (Mavericks), 64-bit
Linux x86-64 (RHEL 6), 64-bit
6.1.1 May 2016 Microsoft Windows 7/8/10 (x86-64), 64-bit
Microsoft Windows 7/8/10, 32-bit
Mac OS X 10.7 (Lion), 64-bit
Mac OS X 10.8 (Mountain Lion), 64-bit
Mac OS X 10.9 (Mavericks), 64-bit
Linux x86-64 (RHEL 6), 64-bit

References

  1. Stalling, D.; Westerhoff, M.; Hege, H.-C. (2005). C.D. Hansen and C.R. Johnson, ed. "Amira: A Highly Interactive System for Visual Data Analysis". The Visualization Handbook. Elsevier: 749–767. CiteSeerX 10.1.1.129.6785Freely accessible.
  2. Adam, R.; Smith, A.R.; Sieren, J.C.; Eggleston, T.; McLennan, G. (2010). "Characterization Of The Airways And Lungs For The FABP/CFTR-Knockout Mouse Using Micro-Computed Tomography And Large Image Microscope Array" (PDF). American Journal of Respiratory and Critical Care Medicine. Am Thoracic Soc. 181: A6264. doi:10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a6264.
  3. Awasthi, V.; Holter, J.; Thorp, K.; Anderson, S.; Epstein, R. (2010). "F-18-fluorothymidine-PET evaluation of bone marrow transplant in a rat model". Nuclear Medicine Communications. 31 (2): 152–158. doi:10.1097/mnm.0b013e3283339f92.
  4. 1 2 Ayers, G.D.; McKinley, E.T.; Zhao, P.; Fritz, J.M.; Metry, R.E.; Deal, B.C.; Adlerz, K.M.; Coffey, R.J.; Manning, H.C. (2010). "Volume of Preclinical Xenograft Tumors Is More Accurately Assessed by Ultrasound Imaging Than Manual Caliper Measurements". Journal of Ultrasound in Medicine. Am inst Ultrasound Med. 29 (6): 891.
  5. Dlasková, A.; Spacek, T.; Santorová, J.; Plecitá-Hlavatá, L.; Berková, Z.; Saudek, F.; Lessard, M.; Bewersdorf, J.; Jezek, P. (2010). "4Pi microscopy reveals an impaired three-dimensional mitochondrial network of pancreatic islet beta-cells, an experimental model of type-2 diabetes.". Biochimica et Biophysica Acta (BBA) - Bioenergetics. Elsevier. 1797: 1327–1341. doi:10.1016/j.bbabio.2010.02.003.
  6. Clark, N.D.L.; Daly., C. (2010). "Using confocal laser scanning microscopy to image trichome inclusions in amber" (PDF). Journal of Paleontological Techniques. 8.
  7. Amstalden van Hove, E.R.; Blackwell, T.R.; Klinkert, I.; Eijkel, G.B.; Heeren, R.; Glunde, K. (2010). "Multimodal Mass Spectrometric Imaging of Small Molecules Reveals Distinct Spatio-Molecular Signatures in Differentially Metastatic Breast Tumor Models". Cancer Research. AACR. 70 (22): 9012–9021. doi:10.1158/0008-5472.can-10-0360.
  8. Sherman, D.M. (2010). "Metal complexation and ion association in hydrothermal fluids: insights from quantum chemistry and molecular dynamics.". Geofluids. John Wiley & Sons. 10 (1-2): 41–57. doi:10.1002/9781444394900.ch4.
  9. O'Neill, S.M.; Jones, T.W. (2010). "Three-Dimensional Simulations of Bi-Directed Magnetohydrodynamic Jets Interacting with Cluster Environments.". The Astrophysical Journal. IOP Publishing. 710 (1): 180–196. arXiv:1001.1747Freely accessible. Bibcode:2010ApJ...710..180O. doi:10.1088/0004-637x/710/1/180.
  10. Baharoglu, M.I.; Schirmer, C.M.; Hoit, D.A.; Gao, B.L.; Malek, A.M. (2010). "Aneurysm Inflow-Angle as a Discriminant for Rupture in Sidewall Cerebral Aneurysms". Morphometric and Computational Fluid Dynamic Analysis. Stroke, Am Heart Assoc.
  11. Bardyn,, T.; Gédet, P.; Hallermann, W.; Büchler., P. (2010). "Prediction of dental implant torque with a fast and automatic finite element analysis: a pilot study.". Oral Surgery, Oral Medicine, Oral Pathology, Oral Radiology, and Endodontology. Elsevier. 109: 594–603. doi:10.1016/j.tripleo.2009.11.010.
  12. Shearing, P.R.; Gelb, J.; Yi, J.; Lee, W.K.; Drakopolous, M.; Brandon, N.P. (2010). "Analysis of Triple Phase Contact in Ni-YSZ Microstructures Using Non-destructive X-ray Tomography with Synchrotron Radiation". Electrochemistry Communications. Elsevier. 12: 1021–1024. doi:10.1016/j.elecom.2010.05.014.
  13. Jährling, N.; Becker, K.; Schönbauer, C.; Schnorrer, F.; Dodt, H.U. (2010). "Three-dimensional reconstruction and segmentation of intact Drosophila by ultramicroscopy". Frontiers in Systems Neuroscience. Frontiers Research Foundation. 4: 1. doi:10.3389/neuro.06.001.2010. PMC 2831709Freely accessible. PMID 20204156.
  14. Zheng, G. (2010). "Statistical shape model-based reconstruction of a scaled, patient-specific surface model of the pelvis from a single standard AP x-ray radiograph.". Medical Physics. 37: 1424. Bibcode:2010MedPh..37.1424Z. doi:10.1118/1.3327453.
  15. Rodriguez-Soto, A.E.; Fritscher, K.D.; Schuler, B.; Issever, A.S.; Roth, T.; Kamelger, F.; Kammerlander, C.; Blauth, M.; Schubert, R.; Link, T.M. (2010). "Texture Analysis, Bone Mineral Density, and Cortical Thickness of the Proximal Femur: Fracture Risk Prediction.". Journal of Computer Assisted Tomography. 34 (6): 949–957. doi:10.1097/rct.0b013e3181ec05e4.
  16. 1 2 Leischner, U.; Schierloh, A.; Zieglgänsberger, W.; Dodt, H.U. (2010). "Formalin-Induced Fluorescence Reveals Cell Shape and Morphology in Biological Tissue Samples". Public Library of Science. 5 (4): e10391. Bibcode:2010PLoSO...510391L. doi:10.1371/journal.pone.0010391. PMC 2861007Freely accessible. PMID 20436930.
  17. Felts, R.L.; Narayan, K.; Estes, J.D.; Shi, D.; Trubey, C.M.; Fu, J.; Hartnell, L.M.; Ruthel, G.T.; Schneider, D.K.; Nagashima, K. (2010). "3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells.". Proceedings of the National Academy of Sciences of the United States of America. National Acad Sciences. 107 (30): 13336–13341. Bibcode:2010PNAS..10713336F. doi:10.1073/pnas.1003040107.
  18. Taylor, D.J.; Doorly, D.J.; Schroter, R.C. (2010). "Inflow boundary profile prescription for numerical simulation of nasal airflow.". Journal of the Royal Society Interface. The Royal Society. 7 (44): 515–527. doi:10.1098/rsif.2009.0306.
  19. Lucas, B.C.; Bogovic, J.A.; Carass, A.; Bazin, P.L.; Prince, J.L.; Pham, D.L.; Landman, B.A. (2010). "The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software" (PDF). Neuroinformatics. Springer. 8 (1): 5–17. doi:10.1007/s12021-009-9061-2.
  20. Dasgupta, S.; Feleppa, E.; Ramachandran, S.; Ketterling, J.; Kalisz, A.; Haker, S.; Tempany, C.; Porter, C.; Lacrampe, M.; Isacson, C. (2007). "8A-4 Spatial Co-Registration of Magnetic Resonance and Ultrasound Images of the Prostate as a Basis for Multi-Modality Tissue-Type Imaging": 641–643.
  21. Oberlaender, M.; Bruno, R.M.; Sakmann, B.; Broser, P.J. (2007). "Transmitted light brightfield mosaic microscopy for three-dimensional tracing of single neuron morphology.". Journal of Biomedical Optics. 12: 064029. Bibcode:2007JBO....12f4029O. doi:10.1117/1.2815693.
  22. Lamecker, H.; Mansi, T.; Relan, J.; Billet, F.; Sermesant, M.; Ayache, N.; Delingette., H. (2009). "Adaptive Tetrahedral Meshing for Personalized Cardiac Simulations.". Citeseer.
  23. Boretius, S.; Michaelis, T.; Tammer, R.; Ashery-Padan, R.; Frahm, J.; Stoykova, A. (2009). "In vivo MRI of altered brain anatomy and fiber connectivity in adult pax6 deficient mice.". Cerebral Cortex. Oxford University Press. 19 (12): 2838–2847. doi:10.1093/cercor/bhp057.
  24. Kohjiya, S.; Katoh, A.; Suda, T.; Shimanuki, J.; Ikeda, Y. (2006). "Visualisation of carbon black networks in rubbery matrix by skeletonisation of 3D-TEM image.". Polymer. Elsevier. 47 (10): 3298–3301. doi:10.1016/j.polymer.2006.03.008.
  25. Clements, R.J.; Mintz, E.M.; Blank, J.L. (2009). "High resolution stereoscopic volume visualization of the mouse arginine vasopressin system.". Journal of neuroscience methods. Elsevier. 187: 41–45. doi:10.1016/j.jneumeth.2009.12.011.
  26. Ohno, N.; Kageyama., A. (2009). "Region-of-interest visualization by CAVE VR system with automatic control of level-of-detail.". Computer Physics Communications. Elsevier. 181: 720–725. Bibcode:2010CoPhC.181..720O. doi:10.1016/j.cpc.2009.12.002.
  27. Dyer, D.S. (1990). "A dataflow toolkit for visualization.". Computer Graphics and Applications. IEEE. 10: 60–69. doi:10.1109/38.56300.
  28. Foulser, D. (1995). "IRIS Explorer: A framework for investigation.". Computer Graphics. ACM SIGGRAPH. 29: 13–16. doi:10.1145/204362.204365.
  29. "DFG Project: Algorithmen zur Planung und Kontrolle von Hyperthermiebehandlungen". DFG Deutsche Forschungsgemeinschaft. Retrieved 28 January 2015.
  30. "DFG Project SFB 273: Hyperthermia: Methodics and Clinics". DFG Deutsche Forschungsgemeinschaft. Retrieved 28 January 2015.
  31. 1 2 3 de Boer, B.A.; Soufan, A.T.; Hagoort, J.; Mohun, T.J.; van den Hoff, M.J.B; Hasman, A.; Voorbraak, F.P.J.M.; Moorman, A.F.M.; Ruijter, J.M. (2011). "The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format.". Development. 138 (1): 159–167. doi:10.1242/dev.051086.
  32. Specht, M.; Lebrun, R.; Zollikofer, C.P.E. (2007). "Visualizing shape transformation between chimpanzee and human braincases." (PDF). The Visual Computer: International Journal of Computer Graphics archive. 23 (9): 743–751. doi:10.1007/s00371-007-0156-1.
  33. 1 2 3 Gaemers, I.C.; Stallen, J.M.; Kunne, C.; Wallner, C.; van Werven, J.; Nederveen, A.; Lamers, W.H. (2011). "Lipotoxicity and steatohepatitis in an overfed mouse model for non-alcoholic fatty liver disease.". Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease. Elsevier. 1812: 447–458. doi:10.1016/j.bbadis.2011.01.003.
  34. 1 2 Kudryashev, M; Cyrklaff, M.; Alex, B.; Lemgruber, L.; Baumeister, W.; Wallich, R.; Frischknecht, F. (2011). "Evidence of direct cell-cell fusion in Borrelia by cryogenic electron tomography.". Cellular Microbiology. Wiley Online Library. 13: 731–741. doi:10.1111/j.1462-5822.2011.01571.x.
  35. Meisslitzer-Ruppitsch, C.; Röhrl, C.; Ranftler, C.; Neumüller, J.; Vetterlein, M.; Ellinger, A.; Pavelka, M. (2011). "The ceramide-enriched trans-Golgi compartments reorganize together with other parts of the Golgi apparatus in response to ATP-depletion.". Histochemistry and Cell Biology. Springer. 135 (2): 159–171. doi:10.1007/s00418-010-0773-z.
  36. Bevan, R.L.T.; Sazonov, I.; Saksono, P.H.; Nithiarasu, P.; van Loon, R.; Luckraz, H.; Ashral, S. (2011). "Patient-specific blood flow simulation through an aneurysmal thoracic aorta with a folded proximal neck.". Numerical Methods in Biomedical Engineering. Wiley. 27 (8): 1167–1184. doi:10.1002/cnm.1425.
  37. Bujotzek, A.; Shan, M.; Haag, R.; Weber, M. (2011). "Towards a rational spacer design for bivalent inhibition of estrogen receptor". Journal of Computer-Aided Molecular Design. 25 (3): 253–262. Bibcode:2011JCAMD..25..253B. doi:10.1007/s10822-011-9417-1.
  38. 1 2 Cai, W.; Lee, E.Y.; Vij, A.; Mahmood, S.A.; Yoshida, H. (2011). "MDCT for Computerized Volumetry of Pneumothoraces in Pediatric Patients.". Academic Radiology. Elsevier.
  39. 1 2 Irving, S.; Moore, D.R.; Liberman, M.C.; Sumner, C.J. (2011). "Olivocochlear Efferent Control in Sound Localization and Experience-Dependent Learning.". Journal of Neuroscience. Soc Neuroscience. 31 (7): 2493–2501. doi:10.1523/jneurosci.2679-10.2011.
  40. 1 2 Obenaus, A.; Hayes, P. (2011). "Drill hole defects: induction, imaging, and analysis in the rodent.". Methods in molecular biology. Springer. 690: 301–314. doi:10.1007/978-1-60761-962-8_20.
  41. Ertürk, A.; Mauch, C.P.; Hellal, F.; Förstner, F.; Keck, T.; Becker, K.; Jährling, N.; Steffens, H.; Richter, M.; Hübener, M.; Kramer, E.; Kirchhoff, F.; Dodt; Bradke, F. (2011). "Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury.". Nature Medicine. 18: 166–171. doi:10.1038/nm.2600.
  42. Carlson, K.J.; Wrangham, R.W.; Muller, M.N.; Sumner, D.R.; Morbeck, M.E.; Nishida, T.; Yamanaka, A.; Boesch, C. (2011). "Comparisons of Limb Structural Properties in Free-ranging Chimpanzees from Kibale, Gombe, Mahale, and Tai Communities.". Primate Locomotion. Springer: 155–182. doi:10.1007/978-1-4419-1420-0_9.
  43. Hartwig, T.; Streitparth, F.; Gro, C.; Müller, M.; Perka, C.; Putzier, M.; Strube, P. (2011). "Digital 3-Dimensional Analysis of the Paravertebral Lumbar Muscles After Circumferential Single-level Fusion.". Journal of Spinal Disorders & Techniques.
  44. Lee, J.; Eddington, D.K.; Nadol, J.B. (2011). "The Histopathology of Revision Cochlear Implantation.". Audiology and Neurotology. 16 (5): 336–346. doi:10.1159/000322307.
  45. Han, M.; Kim, C.; Mozer, P.; Schafer, F.; Badaan, S.; Vigaru, B.; Tseng, K.; Petrisor, D.; Trock, B.; Stoianovici, D. (2011). "Tandem-robot Assisted Laparoscopic Radical Prostatectomy to Improve the Neurovascular Bundle Visualization: A Feasibility Study." (PDF). Urology. 77 (2): 502–6. doi:10.1016/j.urology.2010.06.064.

External links

This article is issued from Wikipedia - version of the 11/9/2016. The text is available under the Creative Commons Attribution/Share Alike but additional terms may apply for the media files.