Biomedical Applications of Vibrational Spectroscopy - Hyperspectral Imaging - Chemometrics

We announce a new version of our hyperspectral imaging software:
CytoSpec 2.0


February 2018: CytoSpec 2.00.05 has finally been released and is now available for download.
What is CytoSpec?
The multivariate imaging software package CytoSpec represents a novel approach for creating pseudo-color displays of hyperspectral imaging data via statistical methods that utilize the entire spectral and spatial (image) information. It is laid out and optimized to work on 3-dimensional hyperspectral data sets from infrared (IR) or Raman spectroscopic imaging experiments. Native data formats from various instrument manufacturers can be analyzed.
What is new in CytoSpec 2.0?
  • A 64-bit stand-alone version of CytoSpec is available. CytoSpec 64-bit requires installation of the free Matlab Compiler Runtime (MCR) R2014a 64-bit. Matlab is not required anymore for using CytoSpec 64-bit.
  • The graphical user interface has been redesigned and now features a cleaner look that makes it simpler and quicker to use.
  • New or renamed functions for spatial preprocessing: 'crop', 'interpolate/binning', 'spatial filtering', 'edge-preserving denoising' (EPD, Chambolle algorithm), '3D-Fourier self-deconvolution', a blind deconvolution method and the function 'replace NaNs' have been added .
  • New function: baseline correction by asymmetric least squares (AsLS).
  • New function 'n-findr multivariate imaging', an endmember extraction method.
  • New imaging function 'create composite images'. This function is available from the context menus of the pseudo-color images and allows superimposing up to 6 different images.
  • Function 'cosmic spike correction' with new functionality and improved performance.
  • New function 'replace NaNs' (spatial pre-processing 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.
  • The import filter for Thermo/Atlus (*.spc) data files has been completely revised. This filter supports now importing of Atlus mapping version 7 data files.
  • New import routine for Thermo/Raman data files acquired by OMNICxi Raman imaging software (v. 1.00 and later). CytoSpec allows importing of Raman maps stored in the HDF5 data format (*.h5, hdf5 libraries version 1.6.4). Note that the *.h5 import filter is supported only by CytoSpec 64-bit.
  • Import filter for Renishaw *.wdf spectra files. With version 2.00.02 CytoSpec supports importing of WiRE 4.0 *.wdf mapping data files.
  • New import routine for Renishaw ASCII (*.txt) data files.
  • Updated import filter for WITec Raman data (*.txt, and *.mat [Matlab] format) produced by WITec Project v. 2.1 and WITec Project Four. Note that the Matlab *.mat import filter is supported only by CytoSpec 64-bit.
  • New function 'replace spectra': this function can be used to replace manually selected point spectra by averages of their neighbor spectra.
  • Function 'HCA of chemical images' added: Unlike the function 'HCA imaging', which creates pseudo color images based on spectral domain information, this functions allows hierarchical cluster analysis of chemical images, i.e. of image (spatial) domain information.
  • Colormaps 'i-jet', 'i-hsv' and 'i-hot' allow displaying inverted colormaps which are useful to produce chemical images from spectral second derivatives.
  • Hidden functionality of the 'quality test' function: Quality tests can be carried out directly from pre-processed spectra.
  • The memory option 'compress' has been deactivated - this functionality is obsolete with the availability of CytoSpec 64-bit.
  • With CytoSpec 2.0 the functions 'chemical movie', 'frequency images' and 'FWHM images' were added to the demo and commercial program versions.
  • The figure 'display options' has been removed - this functionality is now available from the redesigned graphical user interface of CytoSpec 2.0.
  • Default folders containing the license key (genkey.gen), log-files, temporary files and the color text file (color.txt) were modified. These files are are not anymore located in the CytoSpec program folder, but in the Windows User directory (C:\Users\Public\Documents\MATLAB), which gives users full read/write access to these files.
  • Many code improvements & bug fixes.



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