Agilent Instrument User Guide


user guide has an orientation to the instrument and step-by-step workflows for different measurement modes

Instrument Orientation

FPA Detector and Liquid Nitrogen

The FPA (Imaging) detector is cryogenically cooled for operation with liquid nitrogen. A single detector fill will last for approximately 8 hours. It is very important not to allow the detector to warm up while it is powered on, and especially during data collection. The detector should not be refilled during data collection, so you will need to plan your experiments accordingly.

Liquid nitrogen filling is handled by a Norhof auto-filler, so you do not need to be present at the beamline to refill the detector. The auto-filler operates on a 4 hour refill cycle. It is possible to trigger an early detector fill to accommodate your experimental schedule.

At the end of your beamtime, beamline staff will direct you how to leave the detector / auto-filler. If in doubt, keep the auto-filler running.

Spectrometer and Microscope


Microscope controls

Manual and software controls exist for most microscope functions.


Stage position

Stage focus

Condenser focus

Transmission / Reflection

Sample illumination

Aperture controls

Objective Selection

Optics / Accessories

The Cary microscope is equipped with both 15X and 25X magnification objectives, as well as a 4X visible-only objective for sample viewing. There are internal zoom optics available which further increase the magnification by a factor of 5 at the cost of signal intensity at the detector. See the Capabilities section of the Agilent page for more details.

The 15X objective can be configured with a Ge ATR imaging crystal.

The main compartment of the Cary spectrometer can be configured for bulk spectroscopy using standard transmission mounts, a single-bounce Ge ATR or a multi-sample autosampler in both the Mid- and Near-IR.


Resolutions Pro is the primary software for instrument control and data acquisition.

The Agilent Wizard software assists with stage control, sample orientation and experiment planning.

Experimental Parameters


You may also find the Wizard helpful for experiment planning.

Experimental Setup

These steps should be completed for you by beamline staff, however you should confirm the flap positions and detector cooling before starting your work. If you are remote, you can only confirm that the auto-filler is running.

  1. Start the Norhof liquid nitrogen auto-filler to cool the FPA using the "Fill FPA" desktop link.
  2. Open microscope input flap between FTIR and microscope.
  3. Ensure there is a light path through the main FTIR compartment to the internal DTGS detector and that the compartment flaps are open. Any of the following configurations will work for imaging measurements:
    1. Pike MIRacle ATR accessory
    2. Multisample wheel (wheel removed)
    3. Empty compartment (with purge cover)
  4. For transmission mode, confirm that the installed condenser matches the desired magnification
  5. Turn on the detector

Resolutions Pro Method Settings

Experimental settings are controlled through the Resolutions Pro Imaging Method Editor.

Settings specific to your experiment can be saved to a custom method in the Users folder. After saving a new method, you should close and re-open the Imaging Method Editor window.

Check the following settings are correct for your measurements: 

Page Setting Description Remote Control
Microscope Configuration Visible Objective Objective used to collect Visible images ❌ Must reflect objective in use
IR Objective Objective used to collect IR hyperspectral images ❌ Must reflect objective in use
Mode Optical configuration, can be Transmission / Reflection / ATR ✅ Changes microscope between Transmission / Reflection optical paths
High Magnification Enable HiMag IR optics Magnification is 5x objective in use ✅ Adds / removes internal 5X optics from IR optical path
Common Settings Number of scans Number of co-added scans Background is commonly set to match sample
Resolution Spectral resolution desired Determines time to collect a single scan
Scan type Y-axis output of calculated spectra (Absorbance/Reflectance)
Scan range Energy range to store in calculated output Maximum range (FPA) is 3925 - 850 cm<sup>-1</sup>, recommended 3900 -- 900 cm<sup>-1</sup>
Advanced Settings: Collect Speed Interferometer mirror velocity Set to 2.5 kHz for 128x128 FPA
Interferogram Sampling Interval Data sampling interval Set to 4 for 128x128 FPA
Number of Pixels Aggregated Spatial averaging (binning) during collection Influences S/N and file size, but not collection time
Advanced Settings: Spectrometer Configuration IR Source Set to "Rear: MIR Source"
Beam splitter Set to "KBr" ❌ Must reflect installed beam splitter
Aperture Set to "Open" for FPA Imaging
Beam Attenuator Throughput Set to "100%" for FPA Imaging

Agilent Wizard setup

The Agilent Wizard assists with sample location and experiment planning. At a minimum, you should ensure the objective setting on the Helper tab matches the infrared objective you plan to use.

Important note: The Agilent Wizard assists with experiment setup and planning, but does not affect the data acquisition step. All data acquisition is controlled through Resolutions Pro.

Mounted Sample Overview Images

You can take 4X visible overview images of your sample(s) to assist with navigation when the purge shield is on. This will be done for you by beamline staff if you are operating remotely.

  1. Mount sample(s) on plate, and mount on microscope
  2. Create a Project folder in the F:\ drive if not already done, using the User Services Online format (F:\35G12345~Rosendahl\)
  3. In the Agilent Wizard Samples tab, enter User name, Project, and Sample Name of first sample
  4. Open Imaging Method Editor in Resolutions Pro:
    1. Select Method "FPA Imaging/4X Overview.clm"
    2. Visible Image: find focus
    3. With joystick, mark corners for visible mosaic and Capture
    4. View "Captured visible image"
      1. Click somewhere on the image to make a single red (IR grid) rectangle
      2. Using Windows Explorer, copy the 4X VisMosaicCollectImages_Thumbnail.bmp from VisMosaicCollectImages to Project folder
  5. In the Agilent Wizard Helper:
    1. Click "Add Visible Image"
    2. Check ROI Microscope setting is correct
  6. Repeat steps 3-5 for each additional mounted sample
    1. In Wizard Samples tab: Click "Add new Sample" and update sample name
  7. Close Resolutions Pro Imaging Editor window when finished adding overview images

Workflow: Transmission Imaging

  1. Load method file
    In Resolutions Pro Imaging Method Editor, select your method file from the "Users" folder.
  2. Find Centerburst
    Press the "Find Centerburst" button. This will check operation of the interferometer and determine the current centerburst position.
    - Note this uses an internal detector and can be performed regardless of sample position in the microscope.
  3. Focus Sample
    - Sample position / focus can be controlled using the joystick or the Agilent Wizard Stage Control and Focus Control tabs.
    - You may need to adjust the sub-stage condenser to get a bright, even illumination.
    - It is common practice to find the focus in reflection and then switch to transmission.
  4. Mark Sample Region of Interest
    - Using the joystick / Stage Control buttons, navigate around your desired measurement area.
    - At each position you wish to include in the measurement, press "Add ROI point" in the Agilent Wizard Helper tab.
    - The selected ROI points will appear with estimated IR grid locations.
  5. Locate clean background / reference position
    - Using the joystick / Stage Control buttons, locate a position on your sample substrate which is clean from particles or contamination.
    - Note that the IR field of view is larger than the visible camera.
  6. Non-Uniformity Correction Calibration
    - Open Resolutions Pro Imaging Method Editor "Live FPA" window
    - Check that the FPA is at the operating temperature ( <80 K)
    - Select "Show Raw Data"
    - Adjust the sub-stage condenser to increase the signal while maintaining uniform illumination (if you are operating remotely, this step must be done for you by beamline staff)
    - Adjust the vertical slider bar (integration time) so that the displayed signal is not greater than 70% of the full height. The 70% line is between the "Frame Rate" and "Frame Period" text lines.
    - Click "Calibrate" to perform the correction. The results of the correction will appear.
    - You may wish to make a note of the integration time and resulting LowFlux/HighFlux values.
    - Using the Stage Control, move the stage 100 μm in X or Y and check the live image for deviations which indicate contamination on your reference position. If observed, move to a new spot and repeat the calibration procedure. Otherwise, return to the position where the current calibration was measured.
  7. Measure background
    - Click "Background" to start the background / reference measurement
    - When the "Save as" dialog appears, navigate to the appropriate file location and then enter the background file name.
    Tip: If you are going to collect a mosaic, create a folder with your sample name and put the background file inside it. You can then use this folder as the mosaic save location and keep the background and sample files together. Make sure you give the background a distinct name, i.e. "..._bkg" or similar.
    - Check the resulting IR image for appropriate signal levels or undesired material.
    - If you see a circular speckle pattern in the background image, you have too much light on the detector. You should repeat the calibration and lower the integration time slider one step.
    Tip: Do not re-use background file names.
  8. Visible sample image
    - Open Resolutions Pro Imaging Method Editor "Visible Image" tab.
    - Select "Enable" in the "Visible Mosaic" section
    - In the Agilent Wizard Helper tab, press the orange "Go ❶" button. The stage will move to the corner of your sample region of interest
    - Press Imaging Method Editor "Set Corner 1" button
    - Press the Agilent Wizard Helper "Go ❷" button. The stage will move to the opposite corner of your sample region
    - Press Imaging Method Editor "Set Corner 2" button
    - Click Imaging Method Editor "Capture" to start visible mosaic collection.
    - Open "Captured visible image" tab to monitor collection and view the full mosaic.
  9. Define IR measurement area
    - In the Resolutions Pro Imaging Method Editor "Captured visible image" tab.
    - Click and drag to define the desired measurement area. The locations to be measured will be drawn as red boxes.
    - If the mosaic area is incorrect, select a new area
    Tip: the mosaic area always snaps to the top-left corner of the box drawn
    - If you wish, you can temporarily store this visible image in the Agilent Wizard Helper tab with the "Add Visible Image" button
  10. Start sample scan
    - With the correct region identified, press "Scan"
    - When the next dialog appears, navigate to your Project folder on the F:\ drive and
    (single tile) Enter a file name in the Save as dialog
        (mosaic) Select the folder you created when collecting the background or click Make New Folder and create a folder
    - At the end of the data collection, Resolutions Pro calculates the
    Fourier transform of the raw data. For a large mosaic, this can take
    20-30 minutes, during which time the software will not provide any
    Tip: For single FPA tile measurements, the visible image is not saved with
    the IR data. Use the shortcut on the desktop ("VisCaptureBitmap.bmp -
    Shortcut") to open the visible bitmap and save a copy using "File / Make
    a Copy..." to the folder with the matching IR data.