load
save
save Matlab
import ASCII
import binary
export spectra
delete data blocks
clear
plot
options
batch multiple files
exit

Matlab

Internal Data Organization

• Minfo.Readme: The readme information ('File created by CytoSpec - software for hyperspectral imaging ... ')


• Minfo.Ver: Version information of the multispectral data file


• Minfo.File: A structure array with fields (char arrays) such as 'Minfo.File.INS', 'Minfo.File.MAN', Minfo.File.'SRC', etc.). These char arrays contain important data acquisition parameters and are required for all types of spectral analyses. A detailed description of these parameters can be found in the chapter Edit Parameters of the CytoSpec online manual.


• Minfo.Org: char array describing the manipulations performed with the data block of original spectra


• Minfo.Pre: char array describing the manipulations performed with the data block of preprocessed spectra


• Minfo.Der: char array describing the manipulations performed with the data block of derivative spectra


• Minfo.Dec: char array describing the manipulations performed with the data block of (de)convolution spectra

Import Single Column ASCII Data
Import Double Column ASCII Data
Import xyz-1 ASCII (option #1) Data
Import xyz-2 ASCII (option #2) Data
Import xyz-3 ASCII (option #3) Data

Agilent® (Digilab®)	Hyperspectral imaging data (*.dat) files acquired with the Resolutions Pro software from Agilent®, former Varian®, former Digilab®, or BioRad®) can be loaded in the native format. Please note that the *.dat and the *.bsp file (same file name!) must reside in the same directory.
Agilent® (Mosaic files)	CytoSpec's import filter for mosaic files acquired with Agilent's Resolutions Pro software. Please note that the *.dmt file and the complete series of mosaic tiles (*.dmd files) must reside in one directory. Please do not change files names. The root file name must not be modified!
AFMIR	AFMIR data files. Import filter for AFMIR data.
Alfasoft® (Grams 3D)	Galactic Grams32, now Alfasoft, hyperspectral Grams 3D multifiles (*.spc). No problems have been reported so far.
Bruker®	CytoSpec offers import of Bruker OPUS multifiles. The filter allows importing OPUS hyperspectral data files, including mapping and FPA data. Aug. 2019 (CytoSpec v. 2.00.06, Release 360b): Update of the Bruker OPUS import filter which supports now also importing 64-bit hyperspectral data files (so-called mosaic FPA data).
CytoSpec	The import filter for hyperspectral data in the CytoSpec data format.
Horiba Jobin-Yvon®	The import filter for Horiba Jobin-Yvon ASCII (xyz) data files. This filter requires conversion into an ASCII data format by the data acquisition software. Hyperspectral data can be also imported via Alfsasoft's® spc data format. This requires conversion of Raman hyperspectral images into the spc data format.
Kaiser®	Kaiser Raman Holospec data files. Import filter for Kaiser Raman Holospec data files. Requires conversion into an ASCII data format.
Matlab®	The import filter for hyperspectral images in a Matlab compatible data format. Details of this file format can be found in CytoSpec's online documentation for the Matlab file format.
NT-MDT®	NT-MDT data files. The CytoSpec import filter for NT-MDT multispectra (Matlab script files).
Photothermal®	The Photothermal ( Photothermal Spectroscopy Corp.) filter allows importing *.ptir files that may contain PTIR and/or Raman hyperspectral data. Spectral data are imported via the HDF5 format. The filter has been introduced with CytoSpec version 2.00.07 from Oct 2023.
PerkinElmer®	The filter allows loading hyperspectral data collected with PerkinElmer's SpectrumSpotlight IR data collection software. The filter allows import of *.fsm files. No problems reported so far. Note that *.sp files cannot be imported by this filter.
Renishaw® (WiRE 4.0)	Import filter for Renishaw WiRE *.wdf spectral hyperspectral data files. This filter has been introduced with CytoSpec version 2.00.02 and supports importing of WiRE 4.0 *.wdf mapping data files in Renishaw's native hyperspectral data file format.
Renishaw® (ASCII)	Import filter for Renishaw WiRE *.txt Raman data files (ASCII data format). Renishaw 3D data files can be also imported by CytoSpec via Alfasoft's® spc data data format. Requires conversion of Raman hyperspectral images into the spc data format. When loading spc data you may have to enter the values for xdim and ydim (number of pixel spectra in x- and y-direction). This information is sometimes not contained in the converted spc data files.
Thermo® (Nicolet)	Thermo Atlus (former Nicolet®) *.map data files. Updated (CytoSpec v. 2.00.01) import filter for Atlus version 7 mapping data files.
Thermo® (Thermo/Raman)	Import routine for Thermo/Raman data files acquired by OMNICxi Raman imaging software for the DXR3®xi Raman Imaging Microscope. 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's 64-bit toolbox (CytoSpec 64-bit stand-alone, or Matlab pcode toolbox). August 2023, Cytospec 2.00.07 (build 372): The Thermo/Raman import *.h5 filter has been updated.
WITec® pre-v.2.10	Import filter for WITec confocal Raman microspectrometer data produced by the WITec Project software 2.0x. Requires conversion into an ASCII data format. Assumes the presence of two separate ASCII text files in the same directory
WITec® v.2.10	Import filter for WITec confocal Raman microspectrometer data produced by the WITec Project software 2.10. Requires conversion into an ASCII, or spc data format. See this description for details).
WITec® Project Four	Import filter for WITec confocal Raman microspectrometer data produced by the WITec Project Four software. Requires conversion into a Matlab format. Project Four data files can be also imported via the ASCII, or spec format. In these cases refer to the description of the WITec®v.2.10 import filters (see above).

here

• 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.)
• csv format: spectra are stored as comma separated values in one ASCII file. The first column contains the spectral vector of wavelength, wavenumber, or Raman shift values.
• x,y-ASCII text files: simple export function for spectra export to applications software such as OPUS ( Bruker Optics), Grams/AI ( Alfasoft®), Microsoft Excel, or Origin ( OriginLab).
• JCAMP-dx: export of spectral data files into the JCAMP-dx data format.
• Galactic spc: spectra are exported as single files via the spc data format.
• Matlab mat: pixel spectra, their [x,y] pixel coordinates and other information is converted and copied for export in a Matlab structure array. The structure array can be stored in a Matlab data format.

export selection: Check this checkbox to export a selection of spectra. If unchecked complete hyperspectral images are exported. Details of how to select spectra for export are given below).   export all spectra: a complete 3D spectral data block will be exported. Note that this option is available only in combination with the options export plain ASCII' or 'export JCAMP-dx' data files. To export complete hyperspectral maps into a format compatible with SNNS, GA_ORS or TOOLDIAG select the 'use log file' option.   print wvn table: a file 'wvn_conversion_table.dat' is created. This file contains the wavenumber positions of the spectral features.   average data: to lower the computational efforts the data point spacing can be increased by averaging in the spectral domain. Please select an average factor.   average factor: this factor indicates the degree of reduction of the spectral resolution.   source block: please choose one of the four data blocks: original, pre-processed, derivative, or (de)convolution data.   feature selection: if activated, you can select between the options ANOVA, Kruskal-Wallis and COVAR. 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. Note that only the feature selection option ANOVA has been implemented yet.   use spectral windows: permits selecting distinct spectral windows.

number of spectral windows: please indicate the number of spectral windows.   use log file: a log file from a previous CytoSpec export session can be loaded. This function is required for creating external validation hyperspectral image image tests sets. When this option is chosen the settings for feature selection and spectral window selection of a previous CytoSpec export session are loaded and utilized. IMPORTANT: after loading the log file, the checkbox 'export all spectra' which is usually inactivated becomes activated. In this way it is possible to export complete hyperspectral images for external validation (classification) purposes to applications like the SNNS, or ga_ors.   export: press this button to open a standard Windows, or LINUX file browser. Choose an appropriate file name and the target directory.   cancel: aborts the export function

1. The context menu shown in the screenshot to the left can be obtained by a mouse click (right button).   2. To assign point spectra to class 1 choose 'class 1' → and 'add/start'. This activates the 'select spectra' mode. In this mode, the mouse cursor changes the appearance (arrow plus cross).   3. 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 indicated in the report (command line) window, see below.   4. To assign spectra to another class select 'class X' → and 'add/start'. Add then point spectra as it is described above.   5. If all spectra are selected, stop the selection mode by choosing 'selection mode off' from the context menu. CytoSpec returns to the standard mode 'show spectra' and the mouse pointer will regain its normal appearance. You can now call the 'export' function and export selected spectra.   Delete selections / delete class assignments: Deleting class assignments can be carried out either for a class of choice by selecting 'class X' → and 'delete' (see screenshot to the left); 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 select the 'class X' → and 'show' function. Alternatively, one can also use the 'show class assignments' function from the context menu. The screen output of the 'show class assignments' function is exemplary illustrated in a screenshot of the CytoSpec report window (see below).

• preprocessed data.
• derivative data.
• (de)convolution data.

here

• the memory management mode, or
• the way of how NaN values are handled when constructing pseudo-color images
• define the format of stored spectra files
• define whether spectra files to be stored are supplemented by standard deviation spectra
• a permanent program work directory

64-bit version of CytoSpec

1. 'speed' the fastest mode, but highly memory consuming. Recommended for hierarchical cluster analysis (HCA) with hyperspectral images containing up to 128 x 128 pixel spectra (32-bit version, 4 GB of RAM required). In this mode all spectral data are hold in memory with 8 byte precision as float64 values. The option is recommended also for HCA of larger hyperspectral data sets when using 64-bit versions of CytoSpec
2. 'intermediate' - relatively fast, but less memory consuming. Try this option when data sets are large and/or the amount of installed RAM is low. Spectral data are stored with 4 byte precision as float32 values on disk. Only the required data block will be stored in memory (RAM). When performing HCA, the distance matrix is stored in RAM.
3. 'compression' - this memory option has been removed with version 2.00.01 (see 64-bit version of CytoSpec for details).