Analyze Software System

Analyze is the product of more than 25 years of research, design and development at Mayo Clinic's Biomedical Imaging Resource (BIR). Since the early 1970's the BIR has been a world leader in the cutting edge design and implementation of computer-based techniques for the display and analysis of multidimensional biomedical images.

Analyze has matured into the most comprehensive, robust and productive software package available for 3D biomedical image visualization and analysis. The synergistic integration of comprehensive and generic tools for visualization, processing, and quantitative analysis of biomedical images in a highly operator-interactive, intuitive interface has allowed surgeons, physicians, and basic scientists to explore large multidimensional biomedical image volumes efficiently and productively.

Analyze is currently available on 5 Unix platforms, 6 windows platforms, and PC-based Linux operating systems. Functions that used to take several hours to perform, such as volume rendering, segmentation or surface generation, now take a matter of seconds. This increase in overall performance combined with overall price reductions in high-end hardware, has led to a dramatic increase in global Analyze usage over the past few years.

Analyze software system is entirely built upon a toolkit of optimized functions that are organized into a software development library called AVW. The AVW imaging library is a collection of over 600 functions that are accessible to software developers to build advanced image-based application solutions. Analyze is an integration of the full functionality represented in the AVW toolkit with an intuitive windows-based interface which makes it easy to learn and to use. The most important feature of Analyze is the paradigm in which it operates - a powerful software architecture that allows multiple volume images to be simultaneously accessed and processed by multiple programs in a multi-window interface. The user interface for Analyze is based on Tcl/Tk, which offers full compliance with interface standards across multivendor workstations and PCs.

Used by thousands of imaging researchers worldwide, Analyze represents a mature, feature-rich, tested and proven product with a long history and internationally recognized tradition of continuous innovative development and reliable support.

Computer Systems

Analyze is designed to run on all modern workstation platforms and today’s powerful “PC” systems. The effectiveness of Analyze on these platforms without requiring special hardware has significantly contributed to its worldwide, multi-disciplinary distribution, acceptance and utilization. Analyze is supported on the following computer platforms:

  • Sun Microsystems workstations running Solaris 2.5+
  • SGI workstations running IRIX 5.3+ and IRIX 6.2+
  • Hewlett-Packard workstations running HP-UX 10.02+
  • Compaq (DEC) Alpha workstations running Digital UNIX 4.0+
  • IBM RS/6000 workstations running AIX 4.2+
  • PC (Intel) systems running Linux (Red Hat 6.0+ or compatible)
  • PC systems running Windows 95, 98, NT 4.0 and 2000

Imaging Modalities

Analyze can be used effectively for almost any conceivable image visualization and/or analysis task, independent of the source of the image data. It is not restricted to biomedical images, having been successfully used for image processing and analysis tasks in non-biomedical fields such as geology, archeology, meteorology and photography, to name a few. However, it has been and is most commonly used in and provides procedural support for the following biomedical imaging modalities:

  • X-ray Computed Tomography (CT)
  • Magnetic Resonance Imaging (MRI)
  • Positron Emission Tomography (PET)
  • Single Photon Emission Computed Tomography (SPECT, ECT)
  • Ultrasound Imaging
  • Biomagnetic Imaging
  • Radiographic Imaging
  • Auto-radiographic Imaging
  • 2-D and 3-D Microscopy Imaging (Light, Electron, Confocal, Atomic Force)

Image File Formats

Analyze provides direct and automatic (user transparent) support for reading most standard computer image and picture formats, including the emergent DICOM standard for radiologic images. It also supports exporting (writing) image data in several of these formats. More formats are added continuously as they are identified and user demands dictate. For importing data of unknown format, a facility is provided in Analyze for users to generate their own format readers by designing a special template from a user-friendly fill-in-the-blanks program. The following is a list of supported formats:

Analyze Specific File Formats
AnalyzeAVW The new Analyze image file format - all data types, 2D, 3D and 4D
AnalyzeAVW Volume File A new format that enables lists of 2D files to form a 3D volume
Analyze Image (7.5) The old ANALYZE 7.5 image file format, i.e. .hdr & .img pairs
Analyze Object Maps Standard Analyze Object Maps (can be treated as image files)
Analyze Screen Files (7.5) The old ANALYZE 7.5 screen file format from the Screen Edit program
Standard Radiological File Formats
DICOM The current standard for all radiologic images (DICOM 3.0, Part 10)
ACR-NEMA The predecessor to the DICOM standard (1.0 and 2.0)
Papyrus  
Interfile A common nuclear nuclear medicine image file format
Vendor-Specific Radiological File Formats
GE Advantage GE format for CT and MRI
GE Signa MRI Older GE MRI format (Signa 4.x systems)
GE 9800 CT Old GE CT format
GE Advance PET GE Advance PET scanner format
GE Starcam Older GE nuclear medicine image file format
Siemens CT Old Siemens Somatom CT format (DR3)
Siemens MAGVIS Siemens Magnetom Vision MRI format
Siemens/CTI PET Siemens/CTI ECAT 6.X and 7.X PET file formats
Picker (Marcconi) MRI Old MRI image file format
IMATRON (EBCT) The Imatron EBCT image file format (Siemens)
SMIS A small-bore MRI Image file format (Bruker)
Common Raster File Formats
BMP Microsoft Windows Bitmap
GIF Common 2-D image file format (variable compression)
TIFF The Tagged Image File Format, a common 2-D format
PBM Portable Bitmap Library format
PGM A common 2-D image file format
PPM A common 2-D image file format
PNG Portable Network Graphics image file format
TARGA A common 2-D color image file format
PIC Image file format used by Softimage
SGI rgb An SGI 2-D image file format
Sun raster A 2-D image file format from Sun Microsystems
XBM An X-windows BitMap image file format
XWD X Windows dump image file format
Postscript The standard printer definition file format
Common Movie File Formats
Quicktime Very common movie file format (Apple)
SGI_Movie Common movie file format (SGI)
YUV A single frame color video file format

Cad File Formats

Analyze provides support for writing common CAD formats. Additional formats are added continuously as they are identified and user demands dictate. The following is a list of supported formats:

CAD File Formats
DXF Autocad ASCII format
OBJ Alias Wavefront ASCII format
HPGL Hewlett-Packard 3D plotter format
IGES Initial Graphics Exchange Specification
IV SGI Open Inventor version 2.1 format
POLY SGI Poly format
SLC 3D Systems Stereolithography slice format
STL 3D Systems Stereolithography polygonal format
WRL VRML version 1.0 format

What's New

  • SISCOM module
  • Multi-threaded Volume Rendering
  • Volume compositing
  • Increased Region of Interest functionality
  • Updated Model Viewer
  • Full DICOM support
  • Faster 2-D & 3-D registration

What's Coming

  • Calcium Scoring module
  • Volume DSA module
  • Virtual Endoscopic Sequencer
  • New image registration algorithms
    • gradient NMI registration
    • point-cloud registration
    • elastic registration
  • Active contour segmentation tools

Direct Collaboration With the Biomedical Imaging Resource

Our software is also made available to a limited number of qualified institutions and investigators who develop research collaborations with the Biomedical Imaging Resource. If you are an imaging researcher and are interested in developing an academic collaboration, please send a detailed proposal (uniqueness, relevance, specific aims, methods, expected results, mechanisms for collaboration, etc.) to the address below. The proposal will be reviewed for scientific merit and current relevance to our development and application goals. However, even meritorious proposals may not be accepted due to current emphasis, number of current collaborations and/or limited resources. Send proposals to:

  • Dr. Richard A Robb
  • Director, Biomedical Imaging Resource
  • Mayo Foundation
  • 200 First Street SW
  • Rochester, MN 55905
  • FAX: 507-284-1632