Image Quantitation, Analysis and Visualization Specialized Resource

Multi-data file loading and visualization

Standard 2D orthognal (trans, coronal, saggital), Volume rendering

ROI defintion and quantitation:

2D and/or 3D (Ellipsoid, Cylindrical, box, iso-contour and freehand), ROI Statistics outputs(mean, min, max, median, s.d) in units (%ID/g, SUV) of the underlying image pixel value

Export capability (image and/or analysis outputs):

ROI result to txt, image views to jpeg, image data to any supported file formats

Other features:

Co-registration using Fuducial Marker, Image fusion, Cropping, fly-through, line profile, math, filter and factor analysis.

GE Micro View

Supported File Formats: Raw, DICOM, JPEG, ECAT, Analyze,  Vtk, HFH,     MINC, TIFF,     BMP, PNG,      VFF and Pixmap format

Data loading and visualization

Robust single data 2D viewing (trans, coronal, saggital), Volume rendering, Surface rendering (isosurface), Sub-volume viewing, Gray scale only

ROI defintion and quantitation:

ROIs (Box, cylinder), Image Statistics (Mean, max, s.d), Bone Measurements (Bone Mineral Density and Bone Volume Fraction (BVF)),Stereological parameters, Line measurement,

Export capability (image and/or analysis outputs):

uses export/save as from file menu to convert image data to different file format

Other features:

Zoom, Pan, Rotate, Line Profile, Histogram Plotting, Display window/Level control, Arbitrary oblique slicing, Image registration & fusion (commercial version available for Stanford users)

ImageJ

Supported File Formats: All standard file formats (jpeg, tiff, dicom, Fits, pgm avi, text images, avi, raw and image sequences) and more

Data loading and visualization

Multiple data loading, Default 2D display with slice image scroll bar, Plugins available for 3D view (volume, surface rendering), Orthogonal view (axial, coronal, saggital)

ROI defintion and quantitation:

ROIs: Rectangular, elliptical, plogon, freehand, line, point, Measurement: roi statistics, area and volume, Histogram, Line profile, surface profile, Gel analysis tools, ROI manager tools

Export capability (image and/or analysis outputs):

Save As to export image data to different file format

Other features

Many other tools such as Cut, copy, past, crop, size, scale, rotate, Macros & plugins for extended features, Smoothing, sharpening, edge detection and median filtering

RT_image

Supported File Formats: DICOM complainant, Imports: MicroCT, MicroPET (Static & Dynamic), IVIS (2D/3D), BMP, JPG, TIF, Avi, interfile and Raw.

Data loading and visualization

Multiple data loading, Orthogonal viewing of 3D volume, 3D MIP, Volume and surface rendering

ROI defintion and quantitation:

ROIs: freehand, Rec. elliptical, ellipsoid, intensity contour, region grow, line, ROI analysis: Grouping, Splitting & pixel statistics, histogram, MRI T1/T2 fitting, Dynamic PET time activity curve (TAC)

Export capability (image and/or analysis outputs):

Export image data to 2D/3D DICOM file format, image slice view and animations

Other features

Image Fusion, Filtering, Masking, registration, Normalization, Math, Re-sampling and ROI (cut, copy, & past capability

OsiriX

Supported File Formats: DICOM complian, Imports: TIFF(8,16,32 bits) JPEG, ANALYZE, PNG, JPEG, QuickTime, AVI, MPEG and Raw

Data loading and visualization

Query/Retrieve from any PACS, Exclusive navigation and visualization of multimodality and multidimensional images, 2D, 3D, 4D and 5D viewers) , All advanced rendering modules: Multiplanar reconstruction (MPR), curved-MPR, Maximum Intensity Projection (MIP), Volume rendering, surface rendering

ROI defintion and quantitation:

ROIs: Polygons, Oval, Recg. Region grow, Length, Angle, Point, Grouping ROIs to form 3D ROIs, Pixel statistics, Polygon measurements, Volume measurement, Ejection fraction, T2 fit map and analysis using plug-in module

Export capability (image and/or analysis outputs):

Export file, Images views and movie capability

Other features

Image registration and fusion tools, Many Image processing tools (Convolution/Filter), VOI cutter, Plug-Ins architecture, advanced Image navigation and manipulation tools

Data loading and visualization

Multi-data loading (static or dynamic, Synchronized 2D Viewing (trans, coronal, saggital), Sine movie (over space or over time)

ROI defintion and quantitation:

ROIs: Ellipse, Rec and trace, Region grow (2D or 3D), Time Activity curve (TAC), ROI measurement: Area, Volume, Min, Max, Mean, Median and Total, Line Profile.

Export capability (image and/or analysis outputs):

Save Volume (Analyze format), Save views to tiff

Other features:

Sum frames, Projections and transforms, Flip about Z, Smoothing tools, Clipping, Bed Sticher, Annotate, Registration and Fusion tool, and Compartment Modeling

Living Image

Supported File Formats: IVIS image data only (tif, txt), IVIS imaging system instrument software

Data loading and visualization

Multi-image data loading, Photographic and bioluminescent overlay image display, Image adjust, Correction/Filtering

ROI defintion and quantitation:

ROI: Circle, rectangle, auto, freehand, Measurement: ROI statistics of Count or Photon, Image information, Line profile, histogram

Export capability (image and/or analysis outputs):

Saves images as tif file format

Other features:

Planar image analysis, Image math, Spectral Unmixing, Point source fitting, 3D Fluorescence imaging tomography (FLIT), 3D Diffuse Luminescence tomography (DLIT)

Amira

Supported File Formats: TIFF (multichannel and multiframes), BMP, JPEG, PNG, SGI, Leica, Zeiss, BioRad, Olympus, MRC, DICOM, Analyze 3D, Nifti, HOC, SWC, FIDAP, I-DEAS, Fluent,Geometric modeling and CAD: DXF, STL, VRML, Inventor, CATIA 4/5, IGES

Full flexibility and extensibility

Data loading and visualization

Orthogonal and oblique slicing, Volume rendering, Surface rendering, Isolines and isosurfaces, Multichannel imaging, Image fusion, Vector and tensor visualization,Structured network visualization, Support of structured / unstructured grids,Molecular simulation and visualization

ROI defintion and quantitation:

Volume, area, and distance measurements,Densitometry (gray value statistics),Filament network statistics,Co-localization analysis,Component separation and counting,Arithmetic operations on images, vector fields,and unstructured grids,Direct integration of the MATLAB® compute engine

Export capability (image and/or analysis outputs):

Save As to export image data to different file format

Other features

2D and 3D image filtering,Surface generation, FEM grid generation,Interactive/automatic segmentation,Interactive/automatic slice alignment,Image registration and morphing,Tensor computation,Skeletonization and tracing of neural and vascular networks,Deconvolution and Z-drop correction,Dedicated editors for segmentation, tracing and filtering

CRi Maestro, Fluorescence Imaging

Supported File Formats: Cri Maestro image cube data, Maestro fluorescence imaging instrument software

Data loading and visualization

Loading image cube,Auto and Manual unmix,Adjusting Brightness and Contrast Levels,Applying Overlays,Adjusting a Cube's RGB,Changing Components in a Composite Image,Advanced Display Controls

Displaying the Intensity Legend

ROI defintion and quantitation:

Auto threshold segmentation region finding,Manual drawing, modifying and cloning region of interest,Defined region quantification

Export capability (image and/or analysis outputs):

Saving An Unmixed Result Set

Other features

Working With Saved Result Sets, Checking Spectral Library,Using Line Profiles to Analyze Signals,Comparing Multiple Images, Processing a Batch of image data

ART OptiView

Supported File Formats: TD file scan data of fluorescence

Data loading and visualization

Multi-data file loading,Display of scan data images, data information, intensity map, Display windows for different data analysis tasks

ROI defintion and quantitation:

Intensity, lifetime and lifetime error maps,Measuremnt of distances,Perform selections and compute the average, standard deviation of ROIs

Other features

Depth, concentration and quality factor analysis,Topographic representation of depth superimposed on the specimen profile