CytoSpec - an APPLICATION FOR HYPERSPECTRAL IMAGING



 

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Spectral Preprocessing

Calculation of Derivative Spectra
Normalization (Vector, Offset)
Cut
Interpolate
Smooth
ABS <--> TR Conversion
Subtraction
Dispersion Correction
Quality Test
Baseline Correction
Water Vapor Compensation
Noise Correction
Cosmic Spike Removal
Batch Preprocessing

Spatial Preprocessing

Crop
Interpolate/Binning
Filter Images
3D-FSD

Univariate Imaging

Chemical Imaging
Chemical Movie
Frequency 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

Tools

Display Spectra
Set Display Limits
Grid On/Off
Set Colors
Capture
Export Maps
Map Statistics
Display Large Maps
Define ROI
Display Colorbar
Swap Data Blocks
Rotate
Flip

File Information

Show History
Show Instrument Parameters
Show measurement Parameters
Show Additional Parameters
Edit Parameters
About
Using the Help Function

PULL DOWN MENU "TOOLS"

 

Tools Menu
 

Display Spectra


 
    This option can be used to manage the appearance of individual spectra, or groups of spectra. You can activate the 'display spectra' window by selecting the option 'display spectra' from the 'tools' pull down menu.
     
    Please note: In order to display more than only one spectrum, check the option 'add spectra' in the Display option window. Then, you can display spectra of your choice by clicking in the IR maps generated from original or processed spectra. The 'display spectra' window will show you all active spectra with the x- and y- pixel coordinates. To select/unselect spectra in the 'display spectra' window use the mouse and hold either key 'Shift' or 'Ctrl' pressed (standard windows behavior).
display spectra window Activate the context menu by selecting one or more spectra and a right mouse click.
 
set color: allows to set the color of a selected spectrum/selected spectra.
 
hide from display: hides spectra from the spectral panel. Spectra can be, however, reactivated afterwards.
 
remove from display: removes spectra permanently from the spectral panel.
 
cancel: check out what will happen ;-).
 

Set Display Limits

 
 
    A function that permits to enter display limits of the spectral panel. This window can be activated by choosing option 'set display limits' from the 'tools' pull down menu.
set display limits Please indicated the new settings for the x- (in wavenumbers) and/or y- (usually in absorbance units) axis. Wrong settings will produce an error message.

 

Select and Adapt Color Maps

 
 
    Select and adapt color maps to a given hyperspectral map.

 change colors
select colormap: allows selection of one of the following color maps: jet, hsv, hot, cool, bone, winter, summer, autumn, copper, prism, flag, lines, colorcube, i-jet, i-hsv, i-hot, ann (multicolor mode), blue, red, green, yellow, black, cyan, and magenta (the latter are unicolor modes)
 
target map: please select whether you want to apply changes to the surface map reassembled from original or processed data.
 
interpolation: when this check box is activated, hyperspectral maps are interpolated. Otherwise, the maps are textured (see illustration below).
 
color range compression: permits to increase/decrease the offset and the contrast of the color map. The effects of the respective sliders are illustrated in the image below.
 
scale manually: permits to modify manually the color map by entering the minimal and maximal z-values into the appropriate edit boxes. When this check box is checked the functions 'set standard', 'invert', and the sliders 'offset' and 'contrast' (color range compression) are deactivated.
 
set standard: sets the offset and the contrast of the colormaps back to default values.
 
invert: this immediately inverts the colormaps.
 
draw: applies the changes to the hyperspectral map.
 
cancel: closes the application


     
    Illustration of the effect of the check box 'interpolation':
     
     
     this is a textured map        this is a interpolated map
     


     
    Illustration of the effects of changing the sliders 'offset' and 'contrast':
    (example of the colormap 'jet')
     
     
     change colors
     


     
    The colormap ann (artificial neural network): This colormap is particularly useful to generate maps on the basis of classification methods producing crisp class membership values, such as:
     
      HCA imaging - images re-assembled on the basis of hierarchical clustering
      KMC imaging - images re-assembled on the basis of k-means clustering
      Synthon imaging - images re-assembling on the basis of Synthon's NeuroDeveloper(TM) neural network software
      ANN imaging - images re-assembled on the basis of the Stuttgart Neural Network Simulator (SNNS)
       
    The colormap ann can be individually modified by editing a simple text file 'color.txt'. This file is located in CytoSpec's root directory, usually in C:\program files\CytoSpec\CytoSpec and is read by CytoSpec upon its initialization. When editing this file, please use only color names given at http://www.w3.org/TR/2003/WD-css3-color-20030214/ chapter 4.3. SVG color keywords. Please check for case sensitivity and spaces!
     
    An example of the content of the file color.txt is given here: color.txt
     
    The settings of the colormap ann define also the following color sequences:
     
    1. color options of the 'set color' function available from the context menu of the Display Spectra function.
    2. selectable colors available from the listbox 'color of spectra' of the Display Options window.
    3. the color sequence is furthermore used to display cluster average spectra of the functions KMC , FCM and HCA imaging (button 'spectra' --> button 'plot averages').

Grid On/Off

 
 
    This option is available from the tools pull down menu and has effect on the spectral plot window, only. The grid ON/OFF function may be useful when the spectral window is exported via the Capture --> Spectral Plot function.
     

Capture


 
    Capturing maps can be started from the 'capture' option of the 'tools' menu. You can either save the image maps to your hard drive (as bitmaps, map produced on the basis of original, or processed data, spectral window), or alternatively capture the entire program window to the clipboard.
     
      Saving images as bitmaps: Images reassembled on the basis of original spectral data (tools --> capture --> upper image ) and of processed spectra (tools --> capture --> lower image ) can be captured. When the corresponding option was selected, it is asked to type in a path and a file name. In order to store the spectral plot you have to select the 'capture --> spectral plot' option of the 'tools' pull down menu. The option Grid ON/OFF activates or deactivates a grid of the spectral plot (tools menu) The standard resolution used to capture the bitmaps is 300 dots per inch (dpi). Files are stored in a standard windows bitmap (.bmp) data format.
       
      Capturing program window: Along with storing images or spectra you may also want to take a screenshot of the program window. By choosing the 'capture' --> 'window' option of the 'tools' pull down menu and selecting the resolution (72, 150, 200, or 300 dpi) the entire CytoSpec program window is copied to the clipboard.
 
 
 capture images
 
 

Export Maps

 
 
    This function can be used to export the z-data of hyperspectral maps. The z-data are stored in standard ASCII-text files. To export the data you have to select first the option 'export maps --> upper plot (or lower plot)' from the 'tools' pull down menu. Then, in a standard windows dialog box you will be asked for path and file name of the data file to be stored.
     
    Data are stored in files of the following structure (example of a map of M x N pixel spectra, [xdim x ydim]):
     
 
1
2
3
4
5
6
7
8
9
10
.
M

1
0.2
0.4
0.5
0.7
0.8
0.9
0.7
0.4
0.2
0.6
.
0.6
2
0.1
0.7
0.4
0.2
0.4
0.9
0.7
0.4
0.8
0.2
.
0.5
3
0.2
0.4
0.5
0.7
0.8
0.9
0.7
0.4
0.2
0.6
.
0.3
4
0.1
0.7
0.4
0.2
0.4
0.9
0.7
0.4
0.8
0.2
.
0.1
.
.
.
.
.
.
.
.
.
.
.
.
.
N
0.1
0.7
0.4
0.2
0.4
0.9
0.7
0.4
0.8
0.2
.
0.9

 
    The ASCII-files are now available for import into other programs such as Excel, Origin or Matlab. Please note that the standard extension of the ASCII data files will be '*.dat'.
     

Map Statistics

 
 
    This function can be used to visualize the frequency distribution (histogram) of the actual z-data used to compose a given univariate (i.e. chemical) or multivariate hyperspectral image. Examples of univariate imaging parameters are intensity values, ratios, or band positions. In cases where the function 'map statistics' was applied to multivariate images the frequency distribution of cluster membership values, ANN activations, spectral distances, etc. is given. The option 'map statistics' is available from the 'tools' pull down menu. The frequency distribution of hyperspectral image data can be obtained either from original (upper right image), or any type of processed data (lower right image).  
     
      # of pixels: displays the total number of pixels of the hyperspectral map.
       
      # of bad pixels: displays the number of pixel spectra that had failed one of the Quality Tests.
       
      mean: displays the mean value of the data used for imaging.
       
      median: shows the median of the image data.
       
      std: the standard deviation.
       
 
 
 map statistics
 
 

Display Large Maps


 
    The function 'display large maps' is available from the 'tools' pull down menu but also from the context menus of hyperspectral maps (click by the right mouse button). When this option is chosen, a new window will appear showing the maps in the true spatial aspect ratio.
     
      The following information can be obtained from the 'large maps':
       
        1. the pixel position of the cursor,
        2. (x,y) spatial position of the cursor (obtained from the parameters SZX and SZY)
        3. the z-value (absorbance, transmittance, Raman intensity etc.) found at the current cursor location is given.
         
      Further options:
       
        1. the map can be stored as a bitmap by selecting 'capture to bitmap' ('tools' pull down menu).
        2. a colormap is available by selecting 'display colorbar' ('tools' pull down menu).
        3. the window can be deleted (chose 'exit' from the 'file' pull down menu).
        4. one can define Regions of Interest (ROI)
        5. individual pixel spectra can be replaced by an average of their neighbor spectra, see 'replace spectra' of the 'tools' pull down menu

 
 window display large maps

 

Define Region of Interest (ROI)


 
    The 'define region of interest (ROI)' function is available from the 'tools' pull down menu but also from context menus of hyperspectral maps (click right mouse button). When this option is chosen, a new window Large Map will appear that shows the map in the real spatial aspect ratio. Furthermore, an additional window 'define ROI' pops up which permits to define up to three different regions of interest in one hyperspectral map.
     
    window 'define region of interest'
      listbox ROI #: Up to three different regions of interest can be defined. Switching between active ROIs can be achieved by selecting the appropriate option from this listbox.
       
      edit fields 1: - 15: Please enter the (x,y) coordinates of ROI boundary points (in pixel coordinates) in the respective fields. Alternatively, you can click into the 'large map' - the pointer coordinates will be transferred automatically.
       
      calculate average spectrum: a tool that permits to calculate/display and store average spectra from all active regions of interest. Works in exactly the same way as the option 'spectra' described in the HCA imaging and KMC imaging functions.
       
      Mann-Whitney test: not yet implemented
       
      t-test: not yet implemented
       
      checkbox outside modus: this option permits to switch between the in- and outside modus of the ROI definition procedure.
       
      checkbox add ROI point: fields that permit to define additional ROI boundary points are added.
       
      checkbox delete ROI point: ROI points are deleted.
       
      checkbox delete ROI: all ROI point definitions made so far are deleted.
       
      display ROI causes to draw the region of interest in the window 'large map'
       
      cancel the routine is aborted

     
    When a region of interest has been marked within the hyperspectral map, the option 'apply ROI --> preproc data' from the pull down menu of the large window becomes activated (see screenshot below). The function 'apply ROI --> preproc data' creates a new set of preprocessed spectra from the data block of original spectra by transferring only spectra located within the actual ROI area. Spectra from areas outside are omitted and filled by NaN-values (Not a Number). Consequently, spectra originating from non-ROI areas are excluded from all further image processings and appear in any hyperspectral map generated on the basis of preprocessed data as black pixels. Thus, the 'apply ROI --> preproc data' function works similar to a manual Quality Test .
     
 define region of interest

 

Display Colorbar


 
    This function is available from the 'tools' pull down menu and displays a colorbar of the active map. It use the active colormap which is available from the Set Color function of the 'tools' pull down menu. Colorbars can be obtained for all types of maps, including Large Maps) and maps produced on the basis of crisp class membership values such as
     
      HCA maps - images re-assembled on the basis of hierarchical clustering
      KMC maps - images re-assembled on the basis of k-means clustering
      Synthon maps - images re-assembling on the basis of Synthon's NeuroDeveloper(TM) neural network software
      ANN maps - images re-assembled on the basis of the Stuttgart Neural Network Simulator (SNNS)


 
Example of a colorbar for a KMC map. Note that in the example below the active colormap is of type ann. Although only five clusters are displayed, the colorbar will always show the complete colormap which consists here of 27 different colors. Note furthermore, that the sequence of colors is defined by the numbering of colors in the text file 'color.txt' (can be found in the root directory of CytoSpec, usually C:\program files\CytoSpec\CytoSpec). For details, see ann Colormap Four examples of the colorbars of the types jet (top left), hsv, colorcube and hot (clockwise direction).

 
colorbar for the colormap 'ann' four different colorbars
    Colorbars can be captured in the bitmap format. A context menu (right mouse click) offers capturing with, and without labels, respectively.

 

Swap Data Blocks


 
    Overwrites the original data block by preprocessed data. This function is rarely required; however, the test for thickness of the Quality Test (which can be performed exclusively on original data) may require offset corrected spectra. As original data are lost it is highly recommended to store the data before performing the 'swap data block' function. If the block of preprocessed data is empty CytoSpec returns an error message. To avoid overwriting of the original data as a result of typing error, CytoSpec asks for confirmation (see window below).
     
     warning message (swap data blocks)
     

Rotate & Flip


 
    rotate hyperspectral data sets by an arbitrary angle
     
    Data blocks AND images are manipulated such that the spatial dimensions are changed (i.e. swapping the x- and y-dimensions) while the spectral dimension remains unaffected.
     
    Rotate function can be used to rotate the data arrays by 90 degrees clockwise/counterclockwise, or by 180 degrees, respectively.
     
    The Flip function permits the flip the spectral hypercube along the x-axis ('flip horizontally'), or alternatively along the y-axis ('flip vertically')
     

     

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