CytoSpec - Biomedical Applications of Vibrational Spectroscopy - Hyperspectral Imaging

A

about
absorbance ↔ transmission spectra
add mode
additional parameters
Agilent *.dat file import
ANN imaging (Synthon)
ANN imaging (SNNS)
ANN colormap (color.txt)
AQM - acquisition mode
artificial neural networks (ANN)
AS1 - additional sample information 1
AS2 - additional sample information 2
AS3 - additional sample information 3
aspect ratio (display large maps)
ASCII, export
ASCII, import
asym. least squares, baseline correction
APO - apodization function
APT - aperture size
auto scale
automated preprocessing
average factor (export)
average data (export)
average linkage (HCA imaging)

B

baseline correction
basic concepts (main window)
batch preprocessing
batch multiple files
binning (spatial domain)
Bruker OPUS file import
BSP - beamsplitter setting

C

capture
cbt-file (batch preprocessing)
centroid method (HCA imaging)
change colors
chemical imaging
city block distances (HCA imaging)
class assignment (export)
clear
cluster analysis (HCA imaging)
color
colorbar
color range compression
colormap
color.txt file (change ann colormap)
compensation (water vapor)
complete linkage (HCA imaging)
composite image (from context menus)
composite image (multivariate imaging)
compress (memory option)
conversion of ABS ↔ TR spectra
convolution data
cosmic spike removal
criterion (quality test)
crop (spatial domain)
customize
cut (spectral domain)
cut (spatial domain)

D

data blocks
data block history
DAT - date of Measurements
data organization
data reduction

data selection for multivar. imaging
dead pixels
deconvolution (3D-FSD)
deconvolution data
deconvolution factor (DF)
define ROI
delete data blocks
delete class assignment
dendro (button: HCA imaging)
denoising, edge preserving
derivative
derivative order
derivatives (frequency maps)
DET - type of detector
Digilab (now Agilent) *.dat file import
dispersion correction
disclaimer
display colorbar
display large maps
display multiple spectra
display spectra
distance matrix (HCA maps)
double column ASCII data import
download demo version
draw (change colors)
D-values (HCA imaging)

E

edit colormap
edit parameters
edge preserving denoising (EPD)
Euclidean distances (HCA imaging)
Euclidean squared distances (HCA imaging)
exit
export spectra
export maps
external spectrum, subtraction by

F

factor of interpolation
feature selection (export)
FIL - type of optical filter
file (pull down menu)
file info (pull down menu)
flip
fnm file (batch multiple files)
FSD, spatial preproc.
FSD, spectral preproc.
frequency imaging
FPA detector
Fourier self-deconvolution
fuzzy C-means (FCM) imaging
FWHM imaging

G

ga_ors (export)
gamma factor (3D-FSD)
Galactic Grams/32 *.spc file import
grid on/off
group average (HCA imaging)

H

hardware requirements
HCA imaging
help
hierarchical clustering (HCA imaging)
history.log
hot keys

I, J

icons
image (button: HCA imaging)
imaging, ANN
imaging, chemical
images, composite (manually)
images, composite (multivariate)
imaging, FCM
imaging, frequency
imaging, FWHM
imaging with distance values
imaging, HCA
imaging, KMC
imaging, MCR-ALS

imaging, n-findr
imaging, PCA
imaging, Synthon
imaging, VCA
import ASCII
import binary
increment filename (import ASCII)
increment extension (import ASCII)
INS - instrument type
instrument parameters
intermediate (memory option)
internal data organization
internal spectrum, subtraction by
interpolate (spectral domain)
interpolate (spatial domains)
interpolation (set color)
interpolation factor (frequency imaging)
installation
invert colormaps

K

k-factors (3D-FSD)
k-means cluster (KMC) imaging)
Kramers-Kronig transform (KKT)

L

LAS - laser wavenumber
large maps
LDA (export)
load
load ASCII
license
license.pdf
lines to skip (load ASCII)
log file
LWN - lower wavenumber limit

M

macro

main window (basic concepts)
MAN - instrument manufacturer
Matlab data format (save)
map statistics
maxima (frequency maps)
MCR-ALS imaging
measurement parameters
median algorithm (HCA imaging)
min-max normalization
memory options
methods A-H (chemical imaging)
minima (frequency maps)
move mode
multivariate imaging
multivariate imaging, data selection
multivariate imaging, dialog box spectra

N

n-findr imaging
NaN, replace NaNs
NeuroDeveloper interface
Neural networks (Synthon)

Nicolet (now Thermo) *.map file import
noise (quality test)
noise reduction (PCA based)
noise reduction factor (NRF)
NOD - number of data points
NOS - number of scans
normalization
normalized Euclidean distances (HCA imaging)
normalize scores (PCA imaging)
number of spectral regions (multivariate imaging)
number of clusters (HCA imaging)

O

obtain peak positions from derivatives
offset correction
OPN - operator Name
ordering the program
original data

P

PCA imaging
PCA based noise reduction
peak pick (frequency maps)
Perkin-Elmer *.fsm file import
PHC - phase correction mode
Photothermal *.ptir file import
PHR - phase resolution
PIP - phase interferogram points
preface
preprocessing
preprocessed data
plot (file menu)

Q

quality tests

R

ratio (chemical imaging)
readme
region of interest (ROI)
replace spectra
replace NaN spectra
report window
RES - nominal resolution
rotate

S

sample thickness
save
save Matlab
SAM - sample name

SAF - sample form
Savitzky-Golay (smooth)
Savitzky-Golay (derivative)
Savitzky-Golay baseline correction
scale manually (set color)
set color
select colormap
set standard (colormap)
set path
set display limits
settings
shortcuts
show class assignment
search maxima/minima
(frequency maps)
show class assignment
show manipulations
show parameters
show mode
signal-noise-ratio (S/N)
single column ASCII data import
single linkage (HCA imaging)
smooth
smoothing points (derivative)
smoothing points (interpolate)
SNG - signal gain
SNNS (export)
SNNS result file (ANN imaging)
software requirements
source block
spatial preprocessing
spectral preprocessing
spectra (dialog box, multivariate imaging)
spectral regions (multivariate statistics)
spectral region for peak search (frequency maps)
speed (memory options)

SRC - source setting
statistics of a map
STX - step in x dimension
STY - step in y dimension
subtraction, spectral
swap data blocks
Synthon imaging (ANN)
system requirements
SZX - area size in x dimension
SZY - area size in x dimension

T

target data block
Thermo-Nicolet *.map file import
thickness (quality test)
threshold, activations (ANN imaging)
threshold, mult. activations (ANN imaging)
TIM - time of Measurement
test for additional bands
test for sample thickness
test for S/N
test for water vapor
tools (pull down menu)
TOOLDIAG
TOS - type of spectra
transmission ↔ absorbance spectra
true aspect ratio (display large maps)
two-dimensional correlation spectroscopy

U

univariate imaging (menu bar)
use log file (export)
use spectral windows (export)
UWN - upper wavenumber limit

V

Varian (now Agilent) *.dat file import
VCA imaging
vector normalization
VEL - scanner velocity

W

Ward's algorithm (HCA imaging)
water vapor compensation
wavenumber table (export)
WITec data file import
WVS - wavenumber step

X

XDI - number of pixel in x-direction
xyz-1 ASCII data import
xyz-2 ASCII data import

Y

YDI - number of pixel in y-direction

Z

ZFF - zero filling factor
zoom mode

CytoSpec - an APPLICATION FOR HYPERSPECTRAL IMAGING

A - E

F - J

K - O

P - U

V - Z

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