Software forHyperspectral Imaging

Software forHyperspectral Imaging

Software forHyperspectral Imaging

Import Filters

Agilent Resolutions ProBruker OPUSGrams-3DMATLABPerkinElmer SpectrumSpotlightThermo-Nicolet AtlµsRenishaw WiRE 4.0WITec (ASCII), Kaiser-Holospec,Horiba Jobin-Yvon (ASCII)

TM

TM

TM

TM

TM

TM

TM

Chemical imagingHierarchical cluster imagingFrequency/ imagingPCA, n-findr & VCA imagingFuzzy C-means cluster imagingk-means cluster imagingANN imaging (SNNS)Imaging interface to theNeuroDeveloper (artificial neuralnetwork analysis)

FWHM

Savitzky-Golay derivativesSmoothingNormalizationAbsorbance/transmission conversionSpectral preprocessing: cut &interpolationPCA based noise reductionNon-linear baseline correctionWater vapor correctionSpectral quality testsCosmic ray removalSpatial preprocessing: crop & binningSpatial filtering, 3D-FSD

Preprocessing

imaging methods

download a demo version athttp://www.cytospec.com

for more informationInquire info at

info@cytospec.com

CytoSpecc/o Dr. P. Lasch

Parkstraße 29Berlin D-13086GERMANY

Fax: +49-321 21026149

CytoSpec Inc. http://www.cytospec.com CytoSpec Inc. http://www.cytospec.com CytoSpec Inc. http://www.cytospec.com

The Most PowerfulHyperspectral

ImagingSoftware Available

Rel. 2.0

absorbancehighlow

500 µm

Info at Info@CytoSpec .com internet: http://www.CytoSpec .comCytoSpec - software for hyperspectral imaging

Infrared class mean spectra as obtained by the 'calculateaverage spectra' option of CytoSpec's Hierarchical clusterimaging routine (6-class classification approach, see panel a).class mean spectra were obtained from original absorbancespectra (left) and first derivative spectra (Right). Spectra arecolor encoded in accordance to the color scheme used inPanel A.

FE

C

A B

D

1050115012501350

second derivatives

1

1202

1282

1336

13

14

11

21

10

44

10

79

1402

2

3

wavenumbers (cm )-1

1100130015001700

wavenumbers (cm )-1

absorbance

(AU

)

1- colonocytes2 - central parts of the crypts

(goblet cells, lumen)3 - lamina propria mucosae

1

2

3

EXAMPLE: IR imaging of a tissue specimen from thehuman colon mucosa. Panels A & B: IR images obtained byagglomerative hierarchical clustering (6 or 15 cluster).Panels C & D: Image reassembling based on k-means clustering(8 or 15 cluster). Panel E: Microphotograph of the tissuearea examined (1.34 x 1.39 mm2or 232 x 223 spectra).Panel F: Images as obtained by chemical imaging (area of thebaseline corrected amide I band 1620-1680 cm ).Preprocessing and image reassembling was carried out byusing the CytoSpec software package.

-1

What Is CytoSpec?

The multivariate imaging software packageCytoSpec represents a novel approach forcreating pseudo-color displays of spectral imagingdata via statistical methods that utilize the entirespectral information. It is laid out and optimizedto work on 3-dimensional spectral data sets fromimaging or mapping infrared or raman experiments.Native data formats from from various instrumentmanufacturers can be analyzed.

TM

What is new in CytoSpec 2.0?

CytoSpec̀ s graphical user interface has beenredesigned and now features a clean look thatmakes it simpler and quicker to use

New submenus for spectral preprocessing and spatialpreprocessing

New submenu 'image processing' that allows to performclustering of chemical images

New or renamed functions for spatial preprocessing:crop, binning, spatial filtering, 3D-Fourierself-deconvolution (FSD)

n-findr multivariate imaging function - an endmemberextraction method

New function FWHM maps (submenu univariate imaging)

The import filter for binary Thermo/Atlus data fileshas been completely revised. This filter supports nowimporting of Atlus mapping version 7 data files

Import filter for Renishaw *.wdf spectral maps. Withversion 2.00.02 CytoSpec supports importing of WiRE4.0 *.wdf mapping data files.

Colormaps i -jet, i -hsv and i -hot allow displayingcolormaps which are useful to produce

from spectral second derivatives

Memory option compress has been deactivated - thisfunctionality is obsolete with the 64-bit version ofthe CytoSpec software

With CytoSpec 2.0 the function chemical movie hasbeen added to the demo and commercial programversions

The figure display options has been removed - thisfunctionality is now available from the redesignedgraphical user interface of CytoSpec 2.0

Many code improvements & bug fixes

A trial version of CytoSpec canbe downloaded from the CytoSpecwebsite: http://www.cytospec.com

invertedchemical images

Software forHyperspectral Imaging