


CytoSpec's function 'replace NaNs' (NaN  not a number): This is a new function of CytoSpec version 2.00.05. Description to be continued


New function 'replace NaNs' (spatial preprocessing menu). The function can be used to replace NaN pixel spectra (i.e. 'bad spectra' from quality tests)
by interpolated spectra. These spectra represent averages from the neighboring pixel spectra and are obtained by an iterative procedure.


CytoSpec's function 'Edge preserving denoising': This is a new function of CytoSpec version 2.00.05. Description to be continued

Basics of 3DFSD and references to the literature:
This function allows Fourier selfdeconvolution in the two spatial dimensions (x and y) and the spectral/frequency dimensions (z) to be performed at the same time. The method can be applied to enhance the spectral and/or spatial resolution and to increase the image contrast. Adapted from the 1D algorithm described in:
J.K. Kauppinen, D.J. Moffat, H.H. Mantsch, D.G. Cameron, Fourier SelfDeconvolution: a method for resolving intrinsically overlapped bands. Appl Spectrosc. 35(3) 1981. 271276.
J.K. Kauppinen, D.J. Moffat, H.H. Mantsch, D.G. Cameron, Selfdeconvolution and first order derivatives using Fourier transforms. Anal Chem. 53(9) 1981. 14541457.
J.K. Kauppinen, D.J. Moffat, H.H. Mantsch, D.G. Cameron, Noise in Fourier selfdeconvolution. Appl. Opt. 20(3) 1981. 1866.
Procedure of 3DFSD:
 Spectra are baseline corrected.
 A 3D exponential curve, normalized to the point spacing, is generated.
 A 3D Bessel smoothing function is generated.
 The 3D data file is Fourier transformed.
 The result is multiplied by the product of the 3D exponential and smoothing functions.
 Finally, the result is inverse Fourier transformed to get the deconvoluted data file.
Constraints:
The kfactor must lie between 0 and 0.95: then larger k, then more the data are smoothed. You can apply different smoothing factors for the spatial (k factor x or y) and spectral dimensions (k factor z).
Gamma (the half width at half peak height, gamma > 0) is a parameter of the exponential part of the deconvolution function. The higher gamma, the higher the power of deconvolution.
The peak width value reported by this program actually refers to the REDUCTION in the width of the original peaks in the data. Therefore, a reported width value of 8 means that a peak of approx. width 10 before FSD, will have a width of 2 afterwards.
Example: This example shows the results of 3DFSD (data acquired by the use of a 64 x 64 midinfrared MCT focal plane array detector). For chemical imaging, the absorbance values at 1731 wavenumbers of the original spectral (upper plot) and of the FSD data block (lower panel) were color encoded and plotted as a function of (x,y) position. The panel to the left displays the original (blue) spectra and FSD spectra (red).
Important :
3D Fourier selfdeconvolution can be performed only on the original data (data block 1). This function is only suited for envelopes much broader than the spatial/spectral resolution. Avoid oscillatory patterns due to overdeconvolution!
Reference to the literature:
