Help is available for the following functions of the 'file' pull down menu:
 

load
save
save Matlab
import ASCII
import binary
export
delete
clear
plot
customize
batch multiple files
exit

 

The workspace, i.e. the spectral hypercube containing the original spectral data as well as all processed data (up to 4 different 3D data blocks) and the instrument-, data acquisition-, and additional data parameters can be stored/loaded in form of one single file. This file can be loaded/stored by choosing the 'load' (or 'save') option of the 'file' pull down menu. A standard Windows dialog box allows you to browse the directory structure and to select an appropriate data file name.
 
To save disk space, data are stored as single precision values (float32) while all calculations are carried out with floating 64 bit point numbers.
 
Please note: The default file name extension of binary CytoSpec workspace files is '*.cyt'. Files ending with '.dis', '.cls', or '.pca' contain results of HCA, or PCA and have a different format than standard CytoSpec workspace files. These files cannot be loaded by the 'load' function of the 'file' pull down menu. Please note also that CytoSpec's (ver. 1.05.09 and older) older data files ('.mat') or obsolete. To load these files use the 'import' option.
 

 
 

Example: saving the workspace of a focal plane array detector experiment.

 
 

 

This option permits to save the spectral hypercube into a Matlab (The Mathworks Inc., Natick, MA) compatible data format.
 
To open the file 'Matlab.mat' cd to the directory where this file resides and type type 'load Matlab' in the Matlab command line window. This will cause Matlab to open the file. As a result you will get access to the variable 'C' - the spectral hypercube (a 4D array of double precision or float64 values).
 
The array 'C' will have the following dimensions: xdim x ydim x zdim x data block number (1: original data, 2: preprocessed data, 3: derivative data, 4: 3D-FSD data, for details see also the chapter Internal Data Organization.
 
The second variable 'Info' is a structure array of the following fields:
 

• Info.File: [74x64 char], i.e a character array of strings. This character array contains the entries for the spectral parameters described in the chapter Edit Parameters.
 

• Info.Org: string describing the manipulations performed so far with the data block of original spectra
 

• Info.Pre: string describing the manipulations performed so far with the data block of pre-processed spectra
 

• Info.Der: string describing the manipulations performed so far with the data block of derivative spectra
 

• Info.Dec: string describing the manipulations performed so far with the data block of 3D-FSD spectra
 

 

 

Help is available for the following import ASCII options:
 

Import Single Column ASCII Spectra
Import Double Column ASCII Spectra
Import xyz ASCII (option 1) Spectra
Import xyz ASCII (option-2) Spectra

 

Data format: Single column ASCII data contain one column of absorbance/transmittance/Raman intensity data (see example below) from high to low wavenumbers, or frequencies. The user is prompted to enter the high (upper wvn limit) and low (lower wvn limit) value of the IR spectra (in wavenumbers). Upon loading the data, the program determines the wavenumber step increment and the number of data points from the data file.
 

Single column ASCII data - data structure:   0.0061677871 ---> absorbance value at the highest wavenumber 0.0065018409 0.0068493136 0.0071548000 0.0073572793 0.0074029630 0.0072586290 . . . . . . . . . . . . . . . . . . . . . . . . 0.0069211922 0.0064206994 0.0058157393 0.0051814606 0.0045940578 0.0041149510 0.0037795175 ---> absorbance value at the lowest wavenumber

 

xdim & ydim: the dimensions of the map to be imported (in pixel). In the example files (see directory CytoSpecRootDir\Testdata\ASCII\y\) these are xdim x xydim = 11 x 16 (176 spectra). In order to import all ASCII spectra, the files must reside in one single directory. Please make sure that all data files contain the same number of lines.
 
Wavenumber values: Please indicate the highest (upper wvn limit) and the lowest (lower wvn limit) wavenumber values. Please note that CytoSpec assumes a constant (equidistant) wavenumber step.
 
Increment extension: The checkbox marked 'increment extension' determines the complete file names of the files to be read. You can either import single column ASCII data incremented by file extension (e.g. spec.0, spec.1 ... spec.999) or you can import files in which a numeric part of the filename is incremented (for example spec00001.0, spec0002.0, spec0003.0, ..... , spec9999.0). For the former option, check the 'increment extension' option box. Up to 1000 spectra can be loaded using this method. If the file number is encoded by the filename, it is possible to load maximally 10.000 spectra. The fields xdim and ydim determine the number of x- and y- data points of the mapping experiment ((x,y) dimensions of the map). They determine which of the consecutively read spectra defines a new row in the map.
 
After pressing the 'load' button, a standard file window will appear, in which you may browse the directory structure of your computer or network connections. Select the first ASCII data file of the map. A progress indicator shows you then the progress of loading the data files. If problems are encountered during loading of single column ASCII files, try first to import the data of the CytoSpecRootDir/Testdata/ASCII/y/.. directory of the program CD before contacting CytoSpec.
 

 

 

Data format: Double column ASCII data contain the wavenumber/frequency values in the first column and the absorbance/transmittance/Raman intensity values in the second column (see example below, in which data are comma delimited.
 

Double column ASCII data - data structure:   3999.91862793 ,   0.00158696 3997.99002686 ,   0.00158500 3996.06142578 ,   0.00167975 3994.13282471 ,   0.00180794 3992.20422363 ,   0.00191176 3990.27562256 ,   0.00198500 3988.34702148 ,   0.00204885 3986.41842041 ,   0.00210202 3984.48981934 ,   0.00211902 3982.56121826 ,   0.00209280 3980.63261719 ,   0.00205204 3978.70401611 ,   0.00202350 3976.77541504 ,   0.00199000 3974.84681396 ,   0.00190918 . . . . . . . . . ,  . . . . . . . . . . . . . . . . . . ,  . . . . . . . . . . . . . . . . . . ,  . . . . . . . . . 918.01411133 ,   0.00025236 916.08551025 ,   0.00055385 914.15690918 ,   0.00066521 912.22830811 ,   0.00064084 910.29970703 ,   0.00069492 908.37110596 ,   0.00094159 906.44250488 ,   0.00125682 904.51390381 ,   0.00141472 902.58530273 ,   0.00132679 900.65670166 ,   0.00110762

 

xdim & ydim: the dimensions of the map to be imported (in pixel). In the example files (see directory CytoSpecRoot\testdata\ASCII\xy\) these are xdim x xydim = 11 x 16 (176 spectra). In order to import all ASCII spectra, the files must reside in one single directory. Please make sure that all data files contain the same number of lines.
 
Wavenumber values: These options are not available in the double column ASCII import routine as these data are directly obtained from the spectral data files. Please note that CytoSpec assumes a constant (equidistant) wavenumber step.
 
Delimiter format: You can choose between the following delimiters: comma, space, tab, and semicolon.
 
Lines to skip: Some data formats may contain header lines (text), which cannot be loaded by the CytoSpec program. To avoid errors upon loading please indicate the number of lines, which should be skipped by the ASCII import routine.
 
The double column ASCII import function expects files to be incremented by the file extension (e.g. spec.0, spec.1 ... spec.999). This permits to load 1000 double column ASCII spectra at the maximum.
 
After pressing the 'load' button, a standard file window will appear, in which you may browse the directory structure of your computer or network connections. Select the first ASCII data file of the map and press the 'load' button. A progress indicator shows you then the progress of loading the data files. If problems are encountered during loading of double column ASCII files, try first to import the data of the CytoSpecRootDir/Testdata/ASCII/xy/.. directory of the program CD before contacting CytoSpec. Once the ASCII data are loaded you can Store them in a binary file format.
 

 

 

This option permits to load ASCII data of a Raman mapping experiment written in one single multifile.
The example below shows the content of a xyz-ASCII file (4 x 4 spectra)
 

first column: x-coordinates
second column: y-coordinates
first line: wavenumber values of the spectra
second line: spectrum at the coordinates x(1) y(1)
separator is tab

		1641.69	1640.83	1639.98	1639.12	1638.27	1637.41	1636.56	1635.7	1634.84	. . .	702.739	701.726
1	4	0.1245	0.1242	0.1250	0.1263	0.1249	0.1262	0.1241	0.1254	0.1251	. . .	0.1244	0.1244
1	7	0.1233	0.1243	0.1247	0.1251	0.1275	0.1254	0.1249	0.1249	0.1237	. . .	0.1245	0.1256
1	10	0.1259	0.1220	0.1242	0.1239	0.1252	0.1225	0.1223	0.1242	0.1245	. . .	0.1279	0.1240
1	13	0.1243	0.1258	0.1254	0.1225	0.1256	0.1259	0.1261	0.1231	0.1252	. . .	0.1255	0.1258
3	4	0.1237	0.1218	0.1254	0.1235	0.1244	0.1256	0.1242	0.1247	0.1249	. . .	0.1240	0.1239
3	7	0.1243	0.1220	0.1254	0.1252	0.1247	0.1246	0.1249	0.1237	0.1234	. . .	0.1240	0.1264
3	10	0.1248	0.1255	0.1247	0.1211	0.1242	0.1247	0.1246	0.1241	0.1245	. . .	0.1232	0.1263
3	13	0.1225	0.1235	0.1239	0.1241	0.1237	0.1242	0.1250	0.1241	0.1241	. . .	0.1237	0.1248
5	4	0.1256	0.1239	0.1252	0.1249	0.1251	0.1254	0.1252	0.1252	0.1241	. . .	0.1232	0.1244
5	7	0.1236	0.1233	0.1250	0.1231	0.1240	0.1226	0.1234	0.1243	0.1235	. . .	0.1240	0.1252
5	10	0.1226	0.1246	0.1244	0.1258	0.1225	0.1233	0.1248	0.1237	0.1243	. . .	0.1255	0.1232
5	13	0.1251	0.1236	0.1247	0.1252	0.1247	0.1266	0.1243	0.1249	0.1248	. . .	0.1247	0.1266
7	4	0.1266	0.1238	0.1244	0.1252	0.1272	0.1238	0.1260	0.1252	0.1259	. . .	0.1229	0.1266
7	7	0.1278	0.1248	0.1269	0.1261	0.1246	0.1255	0.1238	0.1249	0.1250	. . .	0.1254	0.1257
7	10	0.1259	0.1237	0.1238	0.1239	0.1245	0.1243	0.1259	0.1246	0.1220	. . .	0.1252	0.1237
7	13	0.1233	0.1223	0.1247	0.1232	0.1245	0.1252	0.1241	0.1258	0.1250	. . .	0.1269	0.1247

 

After pressing the 'load' button, a standard file window will appear, in which you may browse the directory structure of your computer or network connections. Select the ASCII data file and press the 'load' button. If problems are encountered during loading, try first to import the example files in the directory CytoSpecRoot/Testdata/ASCII/xyz/ (xyz-1.txt - xyz-1d.txt).. before contacting CytoSpec. Once the ASCII data are loaded you can Store them in a binary file format.
 

 

The second option for importing XYZ-2 ASCII data of a mapping experiments.
The example below shows the content of a xyz-ASCII file. This file contains four columns:
 

first column: x-coordinates
second column: y-coordinates
third column: ordinate values (wavenumber or frequency positions)
second line: abscissa values (intensities)
separator is tab
 


6.97	-89.09	2000.61	12461
6.97	-89.09	1999.65	12585.6
6.97	-89.09	1998.69	12474.8
6.97	-89.09	1997.72	12543.1
6.97	-89.09	1996.76	12616.5
6.97	-89.09	1995.8	12464.2
6.97	-89.09	1994.83	12576.6
6.97	-89.09	1993.87	12432.1
6.97	-89.09	1992.9	12461.5
6.97	-89.09	1991.94	12672.3
6.97	-89.09	1990.98	12390.5
6.97	-89.09	1990.01	12241
6.97	-89.09	1989.05	12280.7
6.97	-89.09	1988.08	12216.7
6.97	-89.09	1987.12	12282.3
6.97	-89.09	1986.15	12171.8
6.97	-89.09	1985.19	12462.7
...	...	...	...
...	...	...	...
24.97	-71.09	114.925	727.855
24.97	-71.09	113.682	601.091
24.97	-71.09	112.438	468.337
24.97	-71.09	111.194	387.876
24.97	-71.09	109.95	257.204
24.97	-71.09	108.705	180.819
24.97	-71.09	107.461	156.686
24.97	-71.09	106.216	90.3816
24.97	-71.09	104.971	84.3432
24.97	-71.09	103.726	74.2909
24.97	-71.09	102.481	54.2039
24.97	-71.09	101.235	18.0652
24.97	-71.09	99.9897	26.0901


 
After pressing the 'load' button, a standard file window will appear, in which you may browse the directory structure of your computer or network connections. Select the ASCII data file and press the 'load' button. If problems are encountered during loading, try first to import the example files in the directory CytoSpecRoot/Testdata/ASCII/xyz/xyz-2.txt before contacting CytoSpec. Once the ASCII data are loaded you can Store them in a binary file format.
 

 

CytoSpec currently offers seven options of importing hyperspectral data files, among them a number files of a proprietary data format:
 

Matlab data files. Details of Matlab file format can be found in the online help for Saving Matlab Files.
 
Varian WinIR Pro multi files (*.dat, former Digilab) can be loaded in their native file format. Please note that the *.bsp file (same file name!) must reside in the same directory.
 
Perkin Elmer SpectrumSpotlight data files can be loaded without limitations. No problems reported so far.
 
Bruker The Bruker/OPUS import filter was updated with CytoSpec version 1.03.03 [Feb. 2008]. With this filter OPUS multifiles including older OS/2 OPUS versions and also HYPERION multi files can be imported. If multifiles are collected with the option 'Video Assisted Measurement' the parameters XDI and YDI (number of pixel in x- and y-direction, see Edit Parameters may be missing. In these cases they must be entered manually (see window below). Workaround: When acquiring data use the 'Automated stage control --> grid' option of the OPUS instrument software
 



 
Known limitations and restrictions:

If Bruker OS/2 mapping files are loaded, which are collected with OPUS versions earlier than 3.0 problems may occur when reading the parameter XDI and YDI. In order to import the data you may have to convert the spectra into an ASCII data format. Problems may also occur if the option 'calculate integral' (measurements --> special measurements --> mapping) is selected.

WITEC data format (after ASCII conversion): With CytoSpec version 1.2.03 WITEC Raman data are now allowed to import. Please note that CytoSpec assumes two ASCII files in the directory (Y_fname.txt and X_fname.txt)
 
Thermo (former Galactic's) Grams/32 multi files (*.spc) can be imported. No problems have been reported so far.
 
Thermo (former Nicolet) *.map files. Since CytoSpec version 1.1.04 built261b the import of OMNIC 6 multifiles is supported. OMNIC ver. 7 multifiles cannot be imported [updated February 2008].
 

Note that the import filters are in an experimental stage and include a few assumptions and guesses of internal file parameters.
Bug free operation of these filters cannot be guaranteed at this point! Import filters were tested using data of the CytoSpecRootDir/Testdata/bin directory on the program CD.
 
If you encounter problems when importing your data, send the data files and the version of the CytoSpec program you are using to CytoSpec.
 

 

 

This function permits exporting spectral data to other applications. Spectral data can be exported for re-classification (complete maps) or as a selection of spectra for teaching classification models. The routine offers furthermore an number of options for data reduction such as the selection of spectral windows and an average function working in the spectral domain. The export function offers furthermore specialized routines for automated feature selection such as ANOVA, COVAR, and PCA. Data can be exported in the format for the following applications:
 

• SNNS/JavaNNS: the Stuttgart Neural Network Simulator
 

• GA_ORS: Genetic Algorithm - Optimal Region Selection, a command line based UNIX/LINUX tool for analysis of IR, Raman and MRI data (optimization, feature selection).
 

• TOOLDIAG: TOOLDIAG is a command line based UNIX/LINUX tool for multivariate data analysis (classification, feature extraction, feature selection, etc.)
 

• Plain ASCII text files: simple export function for spectra export to applications software such as OPUS ( Bruker Optics), Grams/AI ( Thermo), Microsoft Excel, or Origin ( OriginLab).
 

• JCAMP-dx: export of spectral data files into the JCAMP-dx data format.
 

Options of the CytoSpec data export/feature selection routine:

export selection: if this check box is activated, only a selection of spectra will be exported (details of how to select spectra for export are given below).   export all spectra: a complete 3D spectral data block will be exported.   print wvn table: a file 'wvn_conversion_table.dat' is created. This file contains the wavenumber positions of the spectral features.   average data: to reduce the amount of data the spectra can be averaged. If checked, you also have to choose an average factor.   average factor: This factor indicates the grade of reduction of the spectral resolution.   source block: please choose one of the four data blocks: original, pre-processed, derivative, or 3D-FSD data).   feature selection: if activated, you can select between the options ANOVA, COVAR and PCA. Please indicate also the number of data points, that is the number of the best discriminative spectral features. According to the feature selection criterion only the best n features are exported.   use log file: you can import the settings of previous CytoSpec program sessions. This function may be useful to make current data compatible to the data of earlier evaluations (including spectral features).   use spectral windows: permits to restrict the spectral information on distinct spectral windows.   number of spectral windows: please indicate the number of spectral windows.   export: pressing this button opens the standard Windows file browser. Please choose an appropriate file name and the target directory.   cancel: the export function is canceled

Either the entire 3D spectral data set, or a selection of spectra can be exported. Spectra can be selected and assigned to defined classes in the following way:
 

1. The context menu which is shown in the screen shot below, can be obtained by a right mouse click over the hyperspectral maps.
 

2. Choose 'class 1' --> and 'add/start' if you want to assign spectra to class 1. Now, you are in the 'select spectra' mode. In this mode, the mouse cursor changes its appearance (arrow plus cross).
 

3. You can select now an unlimited number of spectra by left mouse clicks. Please note that spectra are not displayed in this mode. The spatial coordinates will be given in the command line window.
 

4. To assign spectra to another class select 'class X' --> and 'add/start'. Then add spectra by mouse clicks.
 

5. If all spectra are selected, stop the selection mode by choosing 'selection mode off' from the context menu. CytoSpec returns to the mode 'show spectra' and the mouse pointer will regain its normal appearance. You can now call the 'export' function and export selected spectra
 

 

Deleting class assignments: Deleting class assignments can be carried out for a class of your choice by the 'class X' --> and 'delete' function (see figure below); or for all classes by selecting 'delete class assignments' from the context menu.
 
Show class assignments: To display class assignments for an individual class of spectra you can select the 'class X' --> and 'show' function. Alternatively, you can use the 'show class assignments' function from the context menu. The screen output of the 'show class assignments' function is exemplary illustrated in a screen shot of the command line window.
 

Example of the screen output (command line window) of the 'show class assignments' function available from the context menu of hyperspectral maps.

 

 

This function helps you to organize the spectral data (save disk or memory space). Choose one of the following data blocks that can be deleted:
 

• preprocessed data.
• derivative data.
• 3D-FSD data.

 

 

This function permits to plot the gui into an eps (encapsulated postscript) file. These files are ready to import into vector graphic programs such as CorelDraw.
 
Alternatively, you can either Capture the spectral maps and store them in an bitmap format or save the zdata information (the data parameters used to generate the surface maps) in an ASCII format by using the Export function of the 'tools' menu. Furthermore, it is possible to produce a screen shot of the program window ('see function Capture')

 

 

Batch multiple files. With version 1.2.02 CytoSpec permits to automatically batch-process spectral multifiles. The 'batch multiple files' function is based on the Batch Preprocessing routine and requires a functional predefined macro file (*.cbt -CytoSpec batch)
Before starting the 'batch multiple files' routine it is strongly recommended to carefully check the 'batch preprocessing' function for errors.
 
Using the function 'batch multiple files':
 

First, it is required to create a text file which contains path and file name of the batch preprocessing file (first line) followed by paths and file names of the spectral multifiles to be processed (next lines). An example of the file content is given here . This file should have the extension '*.fnm'
 
The 'batch multiple file' function can be used to import and process multifiles of many origins. Supported data formats are Matlab (*.mat), Varian (former Digilab), Bruker OPUS, Thermo OMNIC (former Nicolet), Grams/32 (*.spc), PerkinElmer (*.fnm) and CytoSpec (*.spc).
 
Spectral data are processed as defined by the batch file order and are stored when finished in the respective file directory by using CytoSpec's own data format and the original file name + '_b.cyt'.
 
It is not possible to batch-process multivariate imaging functions such as agglomerative hierarchical clustering.
 

 

Exit: Closes all windows and performs a shutdown of the program. Data not stored are lost