August 2023: CytoSpec 2.00.07 (build 372) has finally been released and is now available for
download
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 2.00.07?
- CytoSpec 2.00.07 is the first version which is available also under the LINUX operating system, for details see
CytoSpec for LINUX
- New 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
- 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
- 3D-FSD function 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
- New spectral preprocessing function of Kramers-Kronig transformation added
- Many code improvements and bug fixes
CytoSpec 2.00.06
CytoSpec 2.00.05
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
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