March 2024: CytoSpec 2.10.01 has finally been released and is now available.
 
What is CytoSpec?
 
The CytoSpec multivariate imaging software package is a comprehensive software solution for creating pseudo-color representations of hyperspectral imaging (HSI) data using statistical and machine learning methods that exploit the full spectral and spatial (image) information. It is designed and optimized to work with 3-dimensional hyperspectral data matrices from infrared (IR) or Raman spectroscopic imaging experiments. Native data formats from different instrument vendors can be analyzed.
 
What is new in CytoSpec 2.10.01?

• New import filter for Photothermal *.ptir (hdf5) PTIR / Raman files
 

• New preprocessing function of Kramers-Kronig transform (KKT) to transform FTIR specular reflection data into absorbance-like data
 

• Function subtraction revised: tooltips added, improved usability, dialog box revised
 

• Instead of instead of Matlab Component Runtime (MCR) R2014a 64-bit, CytoSpec standalone Windows version 2.10.01 requires the MCR R2023b 64-bit environment to be installed
 

• Function water vapor correction slightly modified: tooltips added, etc.
 

• Many code improvements and bug fixes
 

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
 

• New imaging function available: MCR-ALS imaging (MCR-ALS: Multivariate Curve Resolution - Alternating Least Squares)
 

• New functionality added to the function composite images: 'plot single component images' and 'exclude components'
 

• The function imaging with distance values was completely re-designed
 

• The ROI selection tool has been revised (ROI - regions of interest)
 

• New options of the normalization spectral-domain preprocessing function added
 

• The 3D-FSD function has been revised
 

• Fourier self-deconvolution in the spectral domain for resolution enhancement has been added.
 

• 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%.
 

• New options of the swap data block function available
 

• Extended support for importing Thermo/Raman (OMNICxi) *.h5 files
 

• Many code improvements and bug fixes
 

CytoSpec 2.00.06

• 2D-COS Two-dimensional correlation analysis functionality from the developer version unlocked. The 2D-COS function is now available in the commercial and demo versions.
 

• The license key handling concept has been re-designed.
 

• Support for importing OPUS 64-bit files added.
 

• Many code improvements & bug fixes
 

CytoSpec 2.00.05

• New function replace NaNs (spatial preprocessing). This function can be used to replace NaN pixel spectra (i.e. 'bad spectra' from quality tests) by interpolated spectra. Replaced spectra can be considerd average of neighboring pixel spectra and are obtained by an iterative procedure.
 

• Function cosmic spike correction with new functionality and improved performance
 

• Redesign of the function imaging with distance values
 

• New function for baseline correction baseline correction by asymmetric least squares (AsLS) added
 

• Batch preprocessing function revised
 

• Many code improvements & bug fixes
 

CytoSpec 2.00.04

• New functionality of the PCA-based noise reduction routine
 

• New function edge-preserving denoising (EPD) available
 

• 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)
 

• 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.
 

• Many code improvements & bug fixes
 

CytoSpec 2.00.03

• New function n-findr multivariate imaging, an endmember extraction method.
 

• 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.
 

• Many code improvements & bug fixes
 

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.
 

• 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 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!
 

• 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 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.
 

• Many code improvements & bug fixes
 

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.
 

• The graphical user interface has been redesigned and now features a cleaner look that makes it simpler and quicker to use.
 

• 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).
 

• Colormaps 'i-jet', 'i-hsv' and 'i-hot' allow displaying inverted colormaps which are useful to produce chemical images from second derivative spectra.
 

• The memory option 'compress' has been deactivated - this functionality became obsolete with the availability of CytoSpec 64-bit.
 

• With CytoSpec 2.00.01 functions chemical movie, frequency images and FWHM images were added to 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 (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.
 

• Many code improvements & bug fixes
 

• CytoSpec's web site
 

• Introduction
 

• Installation
 

• System Requirements
 

• Basic Concepts
 

• Download a trial version
 

• Ordering the Program, License, Disclaimer