Biomedical Applications of Vibrational Spectroscopy - Hyperspectral Imaging - Chemometrics
 
 


Announcing a new version of our hyperspectral imaging software:
- CytoSpec 2.00.07 -



 
 

February 2021: CytoSpec 2.00.07 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 2.00.07?
  • CytoSpec 2.00.07 is the first version which is available also under the LINUX operating system, for details see CytoSpec for LINUX
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  • New imaging function available: MCR-ALS imaging (MCR-ALS: Multivariate Curve Resolution - Alternating Least Squares)
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  • New functionality added to the function composite images: 'plot single component images' and 'exclude components'
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  • The function imaging with distance values was completely re-designed
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  • The ROI selection tool has been revised (ROI - regions of interest)
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  • New options of the normalization spectral-domain preprocessing function added
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  • 3D-FSD function revised
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  • Fourier self-deconvolution in the spectral domain for resolution enhancement has been added.
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  • Function replace NaN pixel spectra slightly modified: A warning message is displayed if more than 15% of pixel spectra are to be replaced. The routine is aborted if this ratio exceeds a value of 34%.
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  • New options of the swap data block function available
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  • Many code improvements and bug fixes
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CytoSpec 2.00.06
CytoSpec 2.00.05
CytoSpec 2.00.04
  • New functionality of the PCA-based noise reduction routine
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  • New function edge-preserving denoising (EPD) available
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  • A node attenuation filter was added (developer version only). Node attenuation is considered a band narrowing filter avoiding artifical side lobes (like in Fourier-self deconvolution spectra, for example)
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  • The univariate imaging function FWHM imaging has been added (FWHM - full (band) width at half maximum). This functions permits visualization (imaging) of band widths variations.
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  • Many code improvements & bug fixes
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CytoSpec 2.00.03
  • New function n-findr multivariate imaging, an endmember extraction method.
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  • Function HCA of chemical images added: Unlike the function 'HCA imaging', which creates pseudo-color segmentation images based on spectral domain information, this functions allows hierarchical cluster analysis of chemical images, i.e. of image (spatial) domain information.
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  • Many code improvements & bug fixes
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CytoSpec 2.00.02
  • Import filter for Renishaw *.wdf spectra files. With version 2.00.02 CytoSpec supports importing of WiRE 4.0 *.wdf mapping data files.
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  • New import routine for Renishaw ASCII (*.txt) data files
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  • 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!
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  • 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!
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  • 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.
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  • New imaging function create composite images. This function is available from the context menus of CytoSpec's pseudo-color displays and allows superimposing up to 6 individual image layers.
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  • Many code improvements & bug fixes
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CytoSpec 2.00.01
  • First version of a 64-bit stand-alone version of CytoSpec. CytoSpec 64-bit requires installation of the free-of-charge Matlab Compiler Runtime (MCR) R2014a 64-bit. Matlab is not required anymore for using CytoSpec 64-bit.
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  • The graphical user interface has been redesigned and now features a cleaner look that makes it simpler and quicker to use.
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  • A new menu bar 'spatial preprocessing'' introduced that contains functions like 'crop', 'interpolate/binning','spatial filtering', 'edge-preserving denoising' (EPD, added later with v. 2.00.04),'3D-Fourier self-deconvolution' and 'replace NaNs' (added later with v. 2.00.05).
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  • Colormaps 'i-jet', 'i-hsv' and 'i-hot' allow displaying inverted colormaps which are useful to produce chemical images from second derivative spectra.
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  • The memory option 'compress' has been deactivated - this functionality became obsolete with the availability of CytoSpec 64-bit.
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  • With CytoSpec 2.00.01 functions chemical movie, frequency images and FWHM images were added to demo and commercial program versions.
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  • The figure display options has been removed - this functionality is now available from the redesigned graphical user interface of CytoSpec 2.0.
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  • Default folders containing the license key (cytospec.lic), 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 public user directory (C:\Users\Public\Documents\MATLAB) and usually offers full read/write access.
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  • Many code improvements & bug fixes
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