The CytoSpec program was originally developed in the year 2000 as a specialized software package for Fourier transform infrared (FT-IR) spectroscopic imaging. Since then, many pre-processing routines, imaging methods and import and export functions were added. Now, the program is widely used in a scientific environment (universities and research institutes) and was the workhorse in countless scientific studies in the area of vibrational spectroscopic (IR- and Raman) imaging. The CytoSpec software has been continuously developed over the past years and supports now most of the actual hardware platforms, including 64-bit environments.
 
How to obtain the program:
 
The full program (commercial version) can be ordered from CytoSpec. Please e-mail your request to CytoSpec (e-mail: order@cytospec.com). You can also obtain a free demo version (limited functionality) of CytoSpec (e-mail:service@cytospec.com).

To obtain the most recent version of the CytoSpec online help go to the CytoSpec web pages.

Introduction to the program/short description:
 
The software package available from CytoSpec is a program designed specifically for the analysis of vibrational spectroscopic (IR and Raman) imaging data sets. The major innovation of the CytoSpec software over competing software packages is its structure that manipulates (hyper-) spectral data cubes, rather than individual spectra. Thus, all operations carried out on the data affect every spectrum, with the number of spectra in the data set limited by the available memory.
 
The CytoSpec software is a stand-alone, comprehensive package that operates under Windows9x, Windows ME, and Windows 2000/XP. Hyperspectral data sets, in the format defined by the manufacturer of the infrared microspectrometer used by the researcher, are imported, converted to and stored in a data matrix format specific to the CytoSpec program.
 
The software permits the standard spectral manipulations customarily found in single spectra analysis software, such as expansion, smoothing, scaling, normalization, etc. Due to the fact that data sets often contain hundreds or thousands of spectra, a number of statistical approaches to the data are built in the software. These can be classified as uni- and multivariate statistical methods. Univarite methods of analysis, included in the software, consist of various mapping displays of hyperspectral data. In these, the user may select band intensities, integrated intensities, frequencies, intensity ratios, etc., to construct false color maps of the spectral data, which may be considered to be slices through the hyperspectral data cube.
 
The multivariate methods of data analysis create spectral correlations and maps by including not just one intensity or frequency point of a spectrum, but by utilizing the entire spectral information. These methods include Principal Component Analysis (PCA), and unsupervised and supervised methods of Cluster Analysis (HCA). The software is configured to permit output of the spectral data in the format used by other software packages, such as the NeuroDeveloper (Synthon), an artificial neural network simulator.
 

 
SYSTEM REQUIREMENTS:

INSTALLATION (Windows 2000 and XP):
 
(updated 12/01/2006)
 
Once you have received the CytoSpec CD, you are ready to install the program. During the install procedure CytoSpec's files will be automatically extracted from the cabinet and all necessary steps for starting CytoSpec will be taken.
 
IMPORTANT: In order to run CytoSpec an additional license key file ('keygen.gen') must be copied into CytoSpec's main directory. This individual license key is NOT included in the CytoSpec CD and can be obtained only by e-mailing a request to order@cytospec.com.
 

• Open the Windows File Manager or Explorer.


• Locate the CytoSpec setup file on the CD you received. The file is named 'setup.exe'


• To start the installation process just double click on setup.exe. The installation program will be started automatically.


• Determine the place on your hard disk where you want CytoSpec to be installed. Normally the proposed C:\program files\CytoSpec\CytoSpec will do fine.


• Then simply follow the instructions of the installation program.


• When setup is complete you can find a new program group and a CytoSpec shortcut on the desktop.


• You can copy now the license key file into CytoSpec's main directory (e.g. c:\program files\CytoSpec\CytoSpec)


• Start the program by double clicking on the CytoSpec icon.



Note: To manually update an older CytoSpec version you can simply overwrite the file 'ftir.exe' by the newer one.
 
view the readme file

 
The main window of the program shows three panels where the spectra and hyperspectral maps are displayed (cf. screen shot of the main window of the CytoSpec program below). The two panels to the right are used to display the spectral maps obtained from original spectral data (upper right panel) or from processed data (preprocessed data, derivatives, 3D-deconvolution data, cluster, PCA, and ANN maps: lower right panel.
 
The color scheme utilized to display spectral maps can be changed (see button 'set color' of the main window, cf. also the set colors option from the tools pull down menu). In addition, the CytoSpec program offers a lot of useful tools to adjust parameters such as image contrast and color scaling.
 
The CytoSpec program gives you easy access to the spectra. When clicking into a hyperspectral map (left mouse button) the
 

• spectrum with the pixel coordinates of the mouse pointer is displayed in the left window,


• the pixel coordinates of the active spectrum appear in editable text boxes, and


• some information of how the spectral map was produced is displayed in the field between both panels.
   


Many options for displaying spectra can be modified (button 'display options', option 'display options' of the tools pull down menu). For more details please refer to the chapter Working with Spectra - Basic Concepts.
 
One of the basic principles of this software is to ease data import of spectral data into other applications, and also from other programs into CytoSpec. To give an example, selecting individual spectra for ASCII export can be started by a simple click with the right mouse button (for details see chapter export).
 

 
 

When starting the CytoSpec program the main window (graphical user interface, gui) and a command line window appear. While the gui allows you to interact with the program, the command line windows shows you most of the distinct function parameters and displays non-standard errors. These messages are stored in a log-file (history.log), which can be found in the root directory of the CytoSpec program.

 
 
 
 
 

 
A number of icons is displayed CytoSpec's main window. The following table will give you a short overview about icons and associated CytoSpec functions.
 
Additionally CytoSpec provides many Hot Keys to help speed up image re-assembling and exporting data to other applications. You will find that you can save a lot of time by eliminating the need to move the mouse and to choose options from the pull down menus. Listed below are the Hot Keys for the CytoSpec program:
 

ICONS   clear all load spectral map save all print customize export ASCII spectra exit calculate derivatives quality tests batch mode chemical maps frequency maps HCA maps Synthon maps autoscale spectra display options display spectra set display limits manually grid on/off set color capture spectral plot capture upper image capture lower image edit help about

HOT KEYS   Control-X quit the program Control-H help Control-S save data Control-P plot Control-Z customize Control-Q clear all Control-F frequency maps Control-A about Control-E edit parameters Control-C edit colormaps Control-L load data Control-D display spectra Control-1 capture map of original data (bmp) Control-2 capture map of processed data (bmp) Control-O display options Control-3 capture spectral plot (bmp) Control-4 export mapping data (original data, ASCII) Control-5 export mapping data (processed data, ASCII) Control-H help

 
 

Internal data organization: Spectral data are stored in one file consisting of up to four distinct data blocks:
 

1. Original spectra: the first block is reserved exclusively for the original spectra, usually absorbance or transmission spectra, or Raman intensities in case of Raman maps. This block is usually not modified. Exceptions are the functions 'cut' and 'interpolate' of the preprocessing pull down menu and the functions 'swap data blocks', 'rotate', and 'flip' of the 'tools' pull down menu.
 

2. Preprocessed spectra: this data block contains the results of data manipulations on original spectra (e.g. preprocessed data).
 

3. Derivative spectra: the third data block is reserved for derivative spectra.
 

4. Deconvolution spectra: block number four contains the results of 3D-Fourier self deconvolution (FSD).
 

 
Preprocessing, multivariate analysis, and image re-assembling can be performed by choosing one of the existing data blocks (also called source blocks). The results of data manipulation are stored into so-called 'target data blocks'. Please note that existing target data blocks may be overwritten without warning! Target data blocks may vary for distinct functions (see synopsis below).


I. Preprocessing (except functions 'cut', 'interpolate',
'derivatives', 'baseline correction', and 'ABS <--> TR'):

source block		target block
original data	»»	preprocessed data
preprocessed data	»»	preprocessed data
derivative data	»»	derivative data
deconvolution data	»»	deconvolution data

II. Derivative calculation:

source block		target block
original data	»»	derivative data
preprocessed data	»»	derivative data
derivative data	»»	derivative data
deconvolution data	»»	derivative data

III. 'Cut', 'interpolate', 'rotate' & 'flip:

source block		target block
original data	»»	all data blocks
preprocessed data	»»	all data blocks
derivative data	»»	all data blocks
deconvolution data	»»	all data blocks

IV. Preprocessing: baseline correction & PCA
based noise reduction:

source block		target block
original data	»»	preprocessed data
preprocessed data	»»	preprocessed data
derivative data	»»	not possible
deconvolution data	»»	not possible

V. 'Swap data blocks':

source block		target block
original data	»»	preprocessed data
preprocessed data	»»	not changed
derivative data	»»	not changed
deconvolution data	»»	not changed

VI. 'ABS <--> TR':

source block		target block
original data	»»	original data
preprocessed data	»»	will be deleted!
derivative data	»»	will be deleted!
deconvolution data	»»	will be deleted!

VII. 'Dispersion correction':

source block		target block
original data	»»	preprocessed data
preprocessed data	»»	not possible
derivative data	»»	not possible
deconvolution data	»»	not possible

VIII. 'Subtraction':

source block		target block
original data	»»	preprocessed data
preprocessed data	»»	preprocessed data
derivative data	»»	derivative data
deconvolution data	»»	not possible

 
 
Since CytoSpec version 1.1.04 the presence/absence of data blocks is visualized by four LEDs located in the lower left corner of the main window. A red LED indicates the presence, a black LED the absence of the respective data block.
 
Memory management modes: CytoSpec offers three distinct memory management modes. This enables the user to perform highly memory consuming operations also with limited RAM resources.
 


1. 'speed' the fastest mode, but note that this mode is highly memory consuming! Recommended for performing HCA with files up to 64 x 64 arrays (512 MB of RAM required). In this mode all data are hold in memory as float64 values (8 byte precision).


2. 'intermediate' - relatively fast, but less memory consuming. This option is recommended for performing HCA with files up to 128 x 128 arrays (1 GB of RAM required). HCA of arrays of that size may take 10 hours and more. The spectral data are stored with 4 byte precision on disk. Only the required data block will be loaded and is stored during the calculations in memory. The distance matrix of cluster analysis will be held in RAM.


3. 'compression' - very slow, cluster analysis of very large maps possible (up to arrays sizes of 210 x 210). The distance matrix is stored on disk and may be of a size up to 4 GB. Attention: HCA of a 210 x 210 array will take weeks! Like for the memory settings 'intermediate' spectral data are stored as a temporary file on disk (CytoSpec's root directory). For cluster analysis, the distance matrix is stored in a separate temporary file (same directory).

 
 

Spectra of the mapping measurements are displayed in the left panel of the main window. Options for displaying the spectra can be selected from the 'display options' window. This window can be activated by pressing the button 'display options' (see Main Window - Basic Concepts ), or by selecting the menu Display Options from the 'tools menu'. To display spectra the following functions are available:

display interactively wavenumber and absorbance values (radio button 'show mode'   interactive expand/compress mode (radio button 'zoom mode')   interactive shift mode (radio button 'move mode')   set curves color (list box 'set color')   zoom window horizontally/vertically (sliders 'zoom spectra')   display multiple spectra (check box 'add mode')   x-y auto scale for active spectrum (check box 'auto scale')   clear window (button 'clear')

How to select spectra for display? There are two methods available to display spectra of active hyperspectral maps:
 
Method A: If you click into one of the hyperspectral maps ('show mode' activated) to the right the x/y pixel coordinates within the map are obtained and the respective spectrum is printed. Furthermore, pixel coordinates of the active spectrum are displayed in the text boxes of the main window (cf. x/y coordinates of active spectrum: Main Window - Basic Concepts ). Depending on the character of the map (map produced from original or processed data) the check box 'show work spectrum' is activated (or deactivated). If images re-assembled by multivariate imaging (PCA, HCA etc.) were activated CytoSpec displays an error message.
 
Method B: Alternatively, spectra can be selected by manually editing the edit fields 'coordinates, x or y' (see Main Window - Basic Concepts ) and/or by activating the check box 'show work spectrum'. If the corresponding map does not exist (e.g. there is no map of original absorbance spectra), an error message will be displayed.

 
 

The basic idea of hyperspectral imaging (or mapping) is to derive for each spectrum of a given set of spatially resolved spectra one single spectral parameter. This parameter is then color scaled and plotted as a function of the spatial (x,y) coordinates. There are a number of techniques, which can be used for hyperspectral mapping. The most frequently used technique is the so called chemical mapping technique. In chemical mapping (also referred to as functional group mapping) the absorbance, transmittance, Raman intensity, half-width, or the frequency of a given vibrational band is color encoded and plotted against the spatial (x,y) coordinates. This univariate imaging techniques permits to visualize the spatial distribution of functional groups, or specific chemical substances and is extensively applied in biomedical science, remote sensing and other research areas.
 
In the CytoSpec program you can create chemical maps by a number of different methods using the absorbance or transmittance, integral absorptions, Raman intensities, ratios etc. These methods are outlined in the chapter Chemical Maps
 
Furthermore, the CytoSpec software offers the opportunity to re-assemble so-called Frequency Maps. In this method, the maxima of specific bands are obtained and images are re-assembled by plotting the frequency values as a function of the spatial coordinates.
 
Other imaging techniques are based on multivariate methods of spectral data analysis. The CytoSpec program (v.1.05.06 , February 2003) offers six different methods of multivariate spectral imaging:

 
Principal Component Analysis (PCA) imaging
 
Imaging based on hierarchical cluster analysis: HCA imaging
 
k-means cluster imaging
 
Fuzzy C-means cluster imaging
 
Imaging based on ANN (Artificial Neural Network) analysis (SNNS imaging)
 
ANN Imaging based on ANN models developed by the help of Synthon's NeuroDeveloper software
 
3D-Fourier Self-Deconvolution (FSD) imaging: a combination of chemical imaging and a method for increasing the resolution in hyperspectral data.
 

These methods are extensively described in the respective chapters of the CytoSpec online help.

 
 

When starting the CytoSpec program the Main Window and a command line window (see screen shot below) appear. While the Main Window allows you to interact with the program, the command line window shows you most of the distinct function parameters and displays non-standard errors. These messages are stored in a log-file (history.log), which can be found in the root directory of the CytoSpec program.
 
Please note: Since CytoSpec 1.1.05 (August 2004) the history.log file of the previous CytoSpec session won't be overwritten upon the next initialization of the program.

 
 

 
Example of the command line window
 

Example of the content of the file 'history.log':
 
 


CytoSpec v.1.1.02 (July, 14th 2004)                       Hunter College CUNY
 
=================================================================================
CytoSpec: program for infrared imaging.     date: 07-Oct-2001,     time: 14:40:59
=================================================================================
 
                      Copyright 2000-2004 CytoSpec
 
log status is 'on'.
You can find the log file 'history.log' in the program's root directory
initializing ...
screensize 1024 x 768 detected
color depth: 24 bpp
file cell1.mat successfully loaded
chemical imaging ...
chemical map, method A, 1620 - 1680
calculating derivatives ...
derivative order: 2
number of smoothing points: 13
... finished. new block of derivative data created
normal end of program

 
 

 
 

How to obtain CytoSpec?

Ordering the full version:

The full program (commercial version) can be ordered from CytoSpec. Please e-mail your request to CytoSpec (e-mail: order@cytospec.com).


Downloading a demo version:

You can also download a free demo version (limited functionality) of CytoSpec. In order to run CytoSpec an additional license key file ('keygen.gen') must be copied into CytoSpec's main directory. This individual license key is NOT included in CytoSpec's zip archive and will be send to you on request. Please e-mail your request together with your name and an institutional address to the following e-mail address: service@cytospec.com.

Download CytoSpec's demo version 1.3.03: (built 303b, ZIP archive, ca. 27.9 MB)

You can also test an earlier demo version of CytoSpec.

Download CytoSpec's demo version 1.3.01: (built 289b, ZIP archive, ca. 27.9 MB)

Please note that you accept with downloading the following license conditions:

You are using the program at your own risk! CytoSpec does not take any responsibility for damages, problems etc. resulting from use of this program. CytoSpec also does not give any warranty for bug-free operation, fitness for a particular purpose or the appropriate behavior of the program.
The software is provided 'AS IS'. For your personal use you can make copies and run as many instances as required, but it is not allowed to further distribute this software.

View the complete license agreement
 
All trademarks mentioned are property of their owners.