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Spectral and Spatial Display
- Click on image pixel to display its corresponding spectrum
- Select image plane using displayed spectrum as reference, or with independent controls
- Display image plane intensity as a histogram and use the resulting statistical analysis for reproducible thresholding or as a direct quantitative metric
- Display multiple spectra in the same window or create multiple-graph windows
- Configure the image with per-pixel field of view size to see the dimensions of spatial features
- Display multiple images
- Zoom in and out in spectral and image windows using the mouse, or with specific coordinates
- Edit and annotate spectral plots
- Plot image planes against one another as scatter plots
Preprocessing Capabilities
- Standard Spectral Preprocessing
- Compute and correct baselines using polynomial functions
- Perform first and second derivatives and smoothing using the Savitsky-Golay algorithm
- Normalize spectra by choosing from a number of selectable options
- Mask non-sample areas or other sample features using image intensity values
- Perform FFTs and phase correction on FT-IR interferograms
- Calculate transmittance and absorbance image cubes using a single selected spectrum or entire background image cubes
- Calculate Kramers-Kronig and Kubelka-Munk transforms
- Truncate image cubes using selectable wavelength or frequency ranges, or across specified spatial limits
- Perform median filtering in the spatial or spectral dimension with selective criteria
- Bin individual images or entire image cubes to improve signal-noise ratio
- Average a selected region - store the result or use it to replace pixel spectra in the region
- Perform image and spectral interpolation, decimation or region averaging, convert between spectral units such as nm, cm -1.
- Interpolate / decimate spectra within entire image cube
- Perform Multiplicative Scatter Correction (MSC) or Standard Normal Variate (SNV) transform for diffuse reflectance data
- Correct for wavelength dependent path length variation in ATR chemical imaging data
- Data Cube Arithmetic
- Apply arithmetic operations to individual images, spectra, or entire image cubes
- Create spatial masks by combining a cube and a user-defined geometric mask
- Perform binary arithmetic operations between cubes
- Combine a cube and a spectrum
- Spatial Preprocessing
- Concatenate image data sets along any spatial or spectral direction
- Perform image convolutions using pre-defined or user-defined kernels
- Smooth data using Savitsky-Golay filters
- Fourier Filter in the spatial (image) dimension
- Spatially interpolate
- Bin pixels
- Image alignment / registration. Use binary images to register data cubes.
Library Creation and Management
- Define library (pure component) spectra by selecting individual spectra or regions within an image cube
- Define library by loading ASCII data derived from other experiments, or from single-point spectrometers
- Transfer libraries to new data sets in which they can undergo additional processing
- Save or load individual libraries
Standard Spectroscopic Analysis
- Peak Integration Mapping - generate a single-channel image from a cube based on the integral of each pixel spectrum between selectable limits
- Peak-Height Ratio Mapping - generate a single-channel image based on the ratio of each pixel spectrum at two specified wavelengths
- Create images based on the degree of spectral peak shift, peak variance, or other statistics computed from a chemical image data set
- Calculate Signal-to-Noise values of data using user selectable criteria
Chemometric Analysis Tools – Partial Listing
- Principal Component Analysis (PCA)
- PLS Regression (PLS)
- Multivariate Curve Resolution (MCR) with Alternating Least Squares (ALS)
- Principal Component Regression (PCR)
- Fuzzy C-Means, K-Means Clustering
- Cosine-coefficient Mapping
- Euclidean Distance Mapping
- Mahalanobis Distance Mapping
- Linear Discriminant Analysis (LDA)
- Multilinear Regression (Kmatrix)
Image Analysis Capabilities
- Display image plane intensity as a histogram and use the resulting statistical analysis for reproducible thresholding or as a direct quantitative metric
- Define contours for feature extraction and automated segmentation of image planes or cubes
- Morphologically filter images with operations such as open, close, dilate, erode, fill, clean, majority, remove, shrink, skeletonize, thicken, thin, watershed
- Automatically calculate size and distribution of chemically or morphologically distinct particles or domains with powerful statistical tools
- Determine spatial overlap between classification images utilizing logical operations on a stack of binary classification images
Visualizing Results
- Associate up to three single-channel intensity images to produce RGB images
- Create and view binary images created from image thresholding or pattern recognition techniques, and perform binary arithmetic operations
- Assign specific colors to any number of distinct chemical or morphological species and overlay them to produce component color maps
- Stretch and scale the color palette of individual images with brightness and contrast sliders
- Select from a variety of different color palettes and display the associated color bar
- Utilize advanced 3-D graphics to produce mesh and waterfall plots, and complex surface maps - save these as AVI movie files for presentation
- Change lighting effects and vary surface texture in 3-D images
- Interpolate across a surface in 2-D and 3-D images
Data import/export
Data is written and read in a proprietary file format, although seamless bi-directional file transfer to and from the following formats is supported:
- Near Infrared:
- Spectral Dimensions, Malvern - *.spf
- Perkin Elmer - *.fsm (Import only)
- Varian export to ENVI® - *.bip, *.bsq, *.bil, *.hdr
- Chemimage® - *.tif
- Mid Infrared:
- Thermo Omnic 6 - *.spa, *.spc, *.map (Import only)
- Varian export to ENVI® - *.bip, *.bsq, *.bil, *.hdr
- Perkin Elmer - *.fsm (Import only)
- Bruker export to ENVI® - *.bip, *.bsq, *.bil, *.hdr
- Raman:
- Horiba Jobin-Yvon - *.tsf., *.tvf, *.ngs, *.ngc
- Kaiser Optical – scandata.txt, *.spc
- Renishaw ® - *.wxd (Import only)
- Thermo - *.spa, *.spc, *.map (Import only)
- Witech ® export to ASCII - *.asc
- Chemimage® - *.tif (multipage tiff - Import only)
- Other instrument platform:
- Horiba Jobin Yvon XGT - *.rpl (Import only)
- EDAX Eagle XRF - *.spd (Import only)
- Remote sensing data export to ENVI® - *.bip, *.bsq, *.bil, *.hdr
- Generic file type:
- Grams® -*.spc
- Matlab® - *.mat
- ENVI® - *.bip, *.bsq, *.bil, *.hdr
- ASCII - *.asc
- Multi-page TIFF - *.tiff
- Standard Image Files - *.fts, *.jpg, *.tif, *.gif, *.bmp, *.png, *.hdf, *.pcx, *.xwd, *.ico, *.cur, *.ras, *.pbm, *.pgm, *.p
Computer specification
- Windows Vista, XP, 2000, NT
- 250 MB of disk space for program files and manual
- 256 MB minimum memory, although many applications perform better with 512 MB
- 2 GB of virtual memory (total page file size) is highly recommended
- 32 or 64 bit operating system, will currently run as 32 bit application on 64 bit OS
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