CytoSpec  an APPLICATION FOR HYPERSPECTRAL IMAGING 



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Chemical Imaging 

Chemical Imaging (or functional group mapping): This function permits to produce chemical images, which display defined spectral parameters such as absorbances at a given frequency as a function of the spatial position. Spectral parameters are color encoded according to the selected Colormap. In the CytoSpec program you can use the following methods for chemical imaging:
Method B: obtains the absorbance value at a given frequency P1 Method C: calculates the integrated area in the region P1, P2 (trapezoidal baseline correction) Method D: obtains a baseline corrected absorbance value at a given frequency P5. The baseline is obtained from the points P1 and P2 Methods AD/EH: calculate ratios using any combination of methods for two regions or absorbances at a given frequency


Chemical Movie 

increment [in wvs]: This allows to modify the the step size, in wavenumber unit steps (wvs), between frequency slices. If a value of '1' is indicated the step size of the animation will be 1 * 'wvs', with wvs being the wavenumber step (the point spacing between two frequency slices, see WVS  wavenumber step). The default value for 'increment' is '4'.
 
Frequency Imaging 

Frequency imaging: This function permits visualization of peak positions, and their variations, within hyperspectral maps. Band positions  either maxima or minima  are obtained and plotted as a function of the spatial coordinates. Band positions can be obtained from all types of data blocks, including also derivative spectra (for details refer to chapter Internal Data Organization). Two different methods of the 'frequency map' routine are available: Peak maxima/minima can be obtained from spectra contained in one of the four data blocks, or for overlapping bands from second derivative data blocks (this may also be second derivatives from spectra of the derivative data block!). The use of second derivatives for peak picking may be useful for the detection of peaks in the presence of strongly overlapping signals, i.e. when the band is only a small shoulder on a strong signal. To some extent 2nd derivatives compensate also for baseline effects. Derivatives should be used with care as noise is considerably amplified. The algorithm of the peak picking routine works as follows: A. If the option 'obtain peak positions from derivatives' was NOT selected:
2. If the option 'search maxima' was checked, the algorithm is then searching for the xpositions (frequencies) of the maxima within the spectral region indicated by the user. If minima are chosen, the program is searching for minima. IMPORTANT: If band positions are obtained from the data block of derivate spectra, maxima appear in second derivative spectra as minima and vice versa. There is no check for i) the order of the derivative and consequently ii), no compensation for the inversion of maxima and minima! 3. The frequency values of the maxima/minima are color scaled and plotted as a function of the spatial coordinates. If you wish to further analyze the band positions by other programs you can access the data matrix of frequency values by using the Export Maps function.
2. Derivative spectra are interpolated. For interpolation, the spline method is used. Interpolation is carried out in the frequency range indicated in the edit fields 'select spectral region for peak search'. Furthermore, a factor of interpolation can be selected. This factor indicates how many times the number of data points will be increased upon interpolation in the spectral region selected for peak picking. 3. If the option 'search maxima' was checked, the algorithm is then searching for the xpositions (frequencies) of the maxima within the spectral region indicated by the user. If minima are chosen, the program is searching for minima. IMPORTANT: If band positions are obtained from the data block of derivate spectra, maxima appear in second derivative spectra as minima and vice versa. There is no check for i) the order of the derivative and consequently ii) no compensation for the inversion of maxima and minima! 4. The frequency values of the maxima/minima are color scaled and plotted as a function of the spatial coordinates. If you wish to further analyze the band positions by other programs you can access the data matrix of frequency values by using the Export Maps function.


FWHM Imaging 

FWHM imaging: This is a new function of CytoSpec version 2.00.05 (Feb 2018). Suitable to create pseudocolor images based on the full width at half maximum (FWHM) of vibrational bands. The function requires the presence of a band in a given spectral interval, ideally in all spectra.
How to save spectral images as bitmaps? How to export the map data (absorbance/transmittance/Raman intensities) as ASCIItables? How to produce hyperspectral maps (Basics) Working with vibrational spectra  basic concepts


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