MIPS Molecular Imaging Program at Stanford
MIPS Quantitation Core

Image Quantitation, Analysis and Visualization Specialized Resource

Software

We provide technical support and individual or group training as needed for several software packages including both open Source/Free software packages and selected commercial software tools applicable for Molecular image analysis, quantification and visualization. Some of the most commonly used software tools in our facility are listed below along with brief summary of key features.

Selected Open Source Software Packages

Software Summary of key features

AMIDE

 

 

Supported File Formats: Raw, DICOM, GIF, Acr/Nema, MicroPET data, ECAT, Interfile, Analyze, NIFTI

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

Commercial/Instrument Software Packages

Software Summary of key features

MicroPET ASI Pro VMTM

 

MicroPET ASI Screenshot

 

Supported File Formats: MicroPET images (Analyze file format only) MicroPET instrument software

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

Living Image Screenshot

 

 

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

 

Amira Screenshot

 

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

 

CRi Maestro Screenshot

 

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

 

OsiriX

 

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

 

Other Online Free Software Resources

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