ribbon works together with the acquisition tab, which is for spectrometer
control and live data acquisition. Here you can connect to a variety
of spectrometer types, set acquisition parameters, acquisition and
measurement modes, execute x axis calibration and define live post-processing
All parameters and settings can be changed on the fly, even during
continuous acquisiton, and effects will be immediately visible.
New Acquisition view
Create a new
Acquisition view as the tab for spectral data acquisition from
spectrometers. It is possible to connect to several spectrometers
by creating several acquisition tabs. The acquired spectra can
be handled and processed in all ways just like "normal"
spectra by using all the normal functions available. The acquisition
tab behaves like a normal Spectra tab, with live data acquisition
The initial steps for data acquisition:
- have your spectrometer plugged into the computer
- select spectrometer device type from [Device Type] list
- connect with [Connect] button
- acquire a live spectrum with [Acquire] button
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. . .
Spectrometer & Acquisition control
As a first step,
always select the device type from the "Device type"
list. Currently, there are: Andor cams, OceanOptics and Stellarnet
spectrometer modules and USB webcams. The dropdown list below
shows the available devices to select from, if there are more
than one devices attached. Only after successful selction of a
device type does it make sense to actually connect to a device
with the [Connect] button. The connector image will change after
successful connection to a "plugged" state. The desired
exposure time can be set anytime (in milliseconds) and will apply
to the next spectrum acquisition.
To acquire live
spectra, use the "Acquire" button. This button shows a
"down" state only during acquisition, thus it is always
visible if there is an acquisition ongoing. Several acquisition
modes are possible:
- single shot: grab a single spectrum from the spectrometer, replace
the last spectrum in the plot
- continuous: continuing live update of acquired spectra, as fast
as exposure time and data transfer allow
- additive: grab a single spectrum from the spectrometer and add
it as a new spectrum to the plot
- burst: continuous spectra acquisition, adding them as new spectra
to the plot. Process will slow down with present spectra number
- loop: continuous spectra acquisition in preset time intervall
(use the entry field on the right). To be stopped by pressing [Acquire]
This gives access to multiple parameters at once and allows to save
them together as "Spectragryph acquisition settings" file
(*.sgas). This file can be loaded again and applied to the currently
The upper part give access to parameters that are common to all
devices, like exposure tome, loop time, acquisition mode and averaging.
On the right, there are the calibration coefficients and designated
axis types used for x axis calibration. This part is disabled for
spectrometers that have their calibration onboard. The lower part
of the window gives access to device-specific settings.
After entering or loading parameters, they can be put to use by
clicking the [Apply] button below, or changes can be ignored by
closing the window again with the [Close] button below.
- detector temperature
- readout mode with single track positions
- shutter open mode
shutter signal type
- opening/ closing time
- correct detector nonlinearity
- electrical dark correction
- strobe lamp trigger
- external trigger mode
- temperatur compensation
- show black pixels
- x timing resolution
USB webcam settings
access to webcam settings is provided by a MS Windows
dialogue, that may look different between OSes. Exposure time
is often not accessible. At least you can prevent clipping
by controlling "Brightness" parameter.
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measurement mode defines the y axis type of the measured live
spectrum, with one or more auxiliary spectra needed, depending
on the chosen mode. As auxiliary spectrum, there can be dark,
reference and Blank spectrum, while each of those can be set,
removed and viewed anytime. As soon as these are assigned, they
are kept behind the scenes for further use. To update any of them,
set them again with a newly measured live spectrum. The dark and
the Blank spectrum type are optional, so their use has to be activated
by clicking onto the respective button. Reference spectrum is
mandatory for each y axis type except intensity, so it is used
automatically, when necessary.
How to measure
the auxiliary spectra:
- dark spectrum: light source off, shutter closed, so that
no light falls onto the detector, measurement mode: intensity
- reference spectrum: light source on, full light (100%
level) falling onto the detector, measurement mode: intensity
- blank spectrum: with blank sample present (like pure
solvent or buffer in sample container), with the final measurement
Each one should be measured again after changing exposure time.
Reference should be measured again after any changes in the excitation
Here are the
calculations that happen for the measurement modes, starting with
the initially acquired raw spectrum:
Live = Raw - Dark
Live = (Raw - Dark) / (Reference
- Dark) -
Live = (Raw - Dark) / (Reference
- Dark) -
Live = - log10 ( (Raw - Dark)
/ (Reference - Dark) )
Dark and Blank
are used optionally and therefore can be acitvated/deactivated,
while reference is mandatory, therefore transmittance/ reflectance/
absorbance can't be measured without a previously measured reference
spectrum. Not all combinations might make sense for all spectroscopy
types, you have to know what suits you best. For example, while
it might be well advised to subtract both a dark and a blank spectrum
in intensity mode for measuring fluorescence intensity, this would
make no sense for an absorbance measurement. There, you would
subtract the Blank spectrum in absorbance mode. And so on...
"averaging" is checked, the defined number of raw spectra
gets averaged, before being shown as live spectrum.
For devices that don't have their calibration on board and give
out pixels as x axis data values, an x axis calibration has to be
executed. For this, first a light source or sample with known peak
positions is measured. Then the measured positions get mapped onto
the known positions with polynomial regression. The polynomial coefficients
are then ready for use, until the calibration gets invalidated by
changes in optical setup or whatever. It is possible to calibrate
- absorbance: by using a sample with known peaks, like a
Holmium or Didymium filter. Target: wavelength scale
- fluorescence: by using a light source with known emission
peaks, like a pen lamp source (Hg, Hg/Ar, Xe, Ne). Target: wavelength
- Raman shift: by using a sample with known Raman lines,
as described in ASTM E1840 standard guide. Target: Raman shift scale
an appropriate spectrum, open the calibration dialog from the
"calibr. x axis" button's drop down menu. In the upper
field, select the spectrum to be used. Change the peak finding
threshold, if necessary. Select the desired x axis type after
calibration on the right side. Below are the fields for the calibration
coefficients, that result from the calibration process.
In the table below, the x axis positions of the found peaks from
the selected spectrum are displayed. You can either enter the
known positions into the "desired position" column manually,
or select from a number of precompiled positions that are shown
as dropdown list. The content of this dropdown list depends on
the calibration source chosen above. Only the "custom"
option allows to manually enter position values. Check the values
to be used during calculation.
Finally, select the polynomial order for the regression calculation
and press the "Calculate" button. The calculated calibration
coefficients will show up in the respective fields above. To keep
the coefficients and the set target x axis type, use the "Apply"
The peak data for the selectable calibration sources is in a file
called "calibration_lines.csv" in the program folder,
this file's content can be changed to adapt or enhance the range
of available calibration peak data.
Turn the calibration-induced
axis transformation on/off with the "calibr. x axis"
button. This can be done on the fly while measuring.
HINT: To better find the peaks to be used during calibration,
you might turn on "Peak labels" before starting the
The calibration coefficients are saved and loaded together with
other settings from the "Settings" dialogue.
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All the parameters
and settings described above affect the acquired raw data before
being shown in the plot. Therefore, they get active with the next
acquired spectrum. The post-processing options however affect
the displayed live spectrum, so the differences while turning
them on and off are directly visible.
has a dropdown menu to access it's settings. It is wise to inspect
the currently set parameters before activating the respective
option. Activation just happens by clicking the button down, another
click will deactivate again. It is possible to use any function
in any combination, from only one to all six of them, as there
- cut off spectrum part
- remove spikes
- advanced baselining
- advanced smoothing
- Raman transformation (as alternative to directly transforming
pixels to Raman by calibration)
- calculate derivative
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