CytoSpec - an APPLICATION FOR HYPERSPECTRAL IMAGING

Introduction/Preface
Installation, System Requirements
Ordering CytoSpec, License, Disclaimer
CytoSpec for LINUX
What's New in CytoSpec 2.00.07
Download a Free Demo Version (Time-limited)
 How to Produce Pseudo-Color Images?
Main Window - Basic Concepts
CytoSpec Keyboard Shortcuts
Data Organization
Working With Spectra - Basic Concepts
Studies for Which CytoSpec Has Been Used

 
File Pulldown Menu
 
Load
Save
Save Matlab
Import ASCII
Import Binary
Export
Delete
Clear
Plot
Customize
Batch Multiple Files
Exit
 
Spectral Preprocessing
 
Calculation of Derivative Spectra
Node Attenuation
Normalization
Cut Spectra
Interpolate Spectra
Smooth Spectra
ABS ↔ TR Conversion
Subtraction
Spectral Quality Tests
Baseline Correction
Water Vapor Correction
Noise Reduction
Cosmic Spike Removal
Fourier Self-Deconvolution
Batch Preprocessing
 Spatial Preprocessing
 
Crop
Interpolate/Binning
Replace NaNs
Filter Images
Edge Preserving Denoising
3D-FSD
 
Univariate Imaging
 
Chemical Imaging
Chemical Movie
Frequency Imaging
FWHM Imaging
 
Multivariate Imaging
 
HCA Imaging
KMC Imaging
FCM Cluster Imaging
PCA Imaging
VCA Imaging
n-findr Imaging
ANN Imaging
Synthon Imaging
Imaging with Distance Values
MCR-ALS imaging
Create Composite Images
HCA of Chemical Images
Tools
 
Display Spectra
Set Display Limits
Grid On/Off
Adapt Colormaps
Capture Images
Export Image Data
Image Statistics
Display Large Images
2D-COS
Define ROI
Display Colorbar
Swap Data Blocks
Rotate HSI
Flip HSI
 
File Information
 
Show History
Show Instrument Parameters
Show Measurement Parameters
Show Additional Parameters
Edit Parameters
About
Using the Help Function
 
Glossary
 

Menu Bar 'File Info'


File Info Menu

Help is available for the following functions of the 'File Info' and 'Help' menu bars:
show history
show instrument/measurement/additional parameters
edit parameters
about CytoSpec
help

 

Show Data Block History


Show data block history: The history of data manipulations is stored within the spectral multifile. In order to view this information select ' File info → show history' and select the data block of interest.
 
The information includes:
 
1.  data source, time and data of import (block of original data).
2.  time and date of data block creation (data block of preprocessed, derivative, or deconvolution spectra)
3.  parameters of preprocessing (derivatives, cut, smooth, interpolate, baseline correction, quality test, etc.)
 
Additional information is available from the log-file.
 
show data block history
Screenshot of the dialog box 'Show Data Block History' (3D-FSD of original data stored in datablock of deconvolution data, block #4)

 

Show Parameters


Displays parameter of the following data parameter blocks:
 
1.  Instrument parameters
2.  Measurement parameters
3.  Additional data acquisition parameters

 
Detailed information on the data parameters is available in the following chapter of this help manual. Additionally, the data parameters can be modified using the function Edit Parameters of the 'File Info' menu bar.
 

Edit Parameters and HSI Metadata


This option can be used to change and modify parameters and metadata of the currently active HSI data file. The 'Edit parameters' window is available by selecting the option 'Edit parameters' from the 'File info' menu bar.
 
edit HSI parameters
Screenshot of the 'edit HSI parameters' dialog box. Please note that the parameters LWN, UWN, WVS and NOD
define the spectral vector and thus represent internal program-wide variables that can have variety of effects
when changes are made. The same applies, in principle, to XDI and YDI which denote the number of pixel
spectra in x-, and y-direction of the given HSI (see below) for details.

 
 
Overview on the instrument, measurement and additional parameters, or metadata used by CytoSpec:
 
Instrument parameters: Measurement parameters: Additional data acquisition parameters:
 
INS - instrument type LWN - starting wavenumber TOS - type of spectra
MAN - instrument manufacturer UWN - ending wavenumber NOS - number of scans
SRC - source setting WVS - wavenumber step XDI - number of pixel in x-direction
BSP - beamsplitter setting NOD - number of spectral data points YDI - number of pixel in y-direction
FIL - type of optical filter DAT - date of measurement NSP - number of spectra
DET - type of detector TIM - time of measurement SZX - area size in x dimension (µm)
VEL - scanner velocity PHC - phase correction mode SZY - area size in y dimension (µm)
LAS - laser wavenumber PHR - phase resolution SAM - sample name
AQM - acquisition mode PIP - phase interferogram points SAF - sample form
SNG - signal gain ZFF - zero filling factor OPN - operator name
    RES - nominal resolution AS1 - additional sample information 1
    APO - apodization function AS2 - additional sample information 2
    APT - aperture size (µm) AS3 - additional sample information 3
    STY - step in y-dimension (µm)    
    STX - step in x-dimension (µm)    

 
Parameters highlighted by red color should be carefully modified since these parameters are used by the CytoSpec software. Modification of these parameters may cause malfunctioning.
 
Changes of the parameters highlighted by red color are tracked and checked when leaving the 'edit HSI parameter' window. In case of errors or data inconsistencies an error messages will be displayed (see error message to the right). The CytoSpec program also makes suggestions of how to change incorrect HSI parameters (see command window below). 		wrong parameters - error message
Error message: wrong parameters

 
command line window: suggestion for changing parameters
Command line window with suggestions to change the incorrect HSI parameters XDI or YDI

 

About


This function shows, among other information, the CytoSpec program version number and the license info.
 
Window displaying the License information ('About')
Screenshot of the dialog box 'About' with the CytoSpec software version and license information

 

Help - Description


This function displays the CytoSpec online help. To obtain the most recent version of the CytoSpec online help go to the CytoSpec web pages at
 
https://www.cytospec.com

 

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