May 21, 2026
Hands-On Operational Protocol of Hyperspectral Scanner Specim PFD-CL-65-V10E Operated by ChemaDAQ
Forked from a private protocol
- Petra Zahajská1,2,
- Hanyu Xu1,2,
- Stan Schouten1,2,
- Noé Schmidhauser3,2,
- Martin Grosjean3,2
- 1Institute of Geological Sciences;
- 2Oeschger Centre for Climate Change Research;
- 3Institute of Geography
Protocol Citation: Petra Zahajská, Hanyu Xu, Stan Schouten, Noé Schmidhauser, Martin Grosjean 2026. Hands-On Operational Protocol of Hyperspectral Scanner Specim PFD-CL-65-V10E Operated by ChemaDAQ. protocols.io https://dx.doi.org/10.17504/protocols.io.36wgqxze3lk5/v1
Manuscript citation:
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
This protocol is actively used and validated in routine scanning workflows.
Created: April 20, 2026
Last Modified: May 21, 2026
Protocol Integer ID: 315390
Keywords: operational protocol of hyperspectral scanner specim pfd, hyperspectral scanner specim pfd, hyperspectral scanner, v10e hyperspectral scanner, acquiring hyperspectral imaging, hyperspectral imaging, specim pfd, scan configuration, chemadaq this protocol, resolution sediment core, scanner preparation, including scanner preparation, complete acquisition procedure
Disclaimer
This protocol is intended for research purposes only. Laboratory safety regulations and local instrument operation guidelines must be followed at all times.
Abstract
This protocol provides a hands-on operational workflow for acquiring hyperspectral imaging (HSI) data using the Specim PFD-CL-65-V10E hyperspectral scanner operated through ChemaDAQ. It is designed for high-resolution sediment core scanning and outlines the complete acquisition procedure, including scanner preparation, calibration, scan configuration, white reference acquisition, data handling, and system shutdown.
Scanner Overview
This section provides a general overview of the scanner system.
Scanning Preparation
Turn on the scanner by pressing the buttons in sequence, slowly from MAIN POWER to VNIR POWER.
Remove the cap from the camera lens. Use a mirror to check the halogen lights.
Note: There should be 23 lights on each side.
Start ChemaDAQ on the computer.
Place the sediment core with a smoothed and cleaned surface into the tray. Adjust the core so that the surface is level and aligned within a single focal plane. If the surface is tilted along the liner, use paper to raise part of the core as needed. An uneven or misaligned surface will reduce image quality.
Note: Red or white tape indicates the top of the core, and black tape indicates the bottom. Always smooth the sediment surface from bottom to top. If the core contains excess water and visible surface reflections are present, allow it to dry for 30 minutes to 1 day, depending on the material and moisture content. Cover any white or reflective areas (e.g., liner or foam) with black matte tape or black paper to minimize unwanted reflections.
Adjust the scale bar to the same height as the core surface and ensure it is level.
Use a spirit level if needed.
Adjust the scale bar so that it is positioned close to the sediment liner.
Set the focus table to the same height as the scale bar and record the height shown on the side.
IMPORTANT: Remove the wheel (circled in white) from the table to prevent the tray from getting stuck.
Prepare the core label (first drawer) and place it on the focus table.
Open the Camera Calibration Tool. Enter Table Position, Field of View, Exposure Time, Frame Rate, and Core Length. The tool will automatically calculate the calibration result and generate the scan information.
Note: Select the calibration candidate that works best for the sample.
Adjust the camera height using Arrow 1 or Arrow 2 from the calibration result.
Note: A wheel located at the top rear can be used to move the camera up or down.
Scanning Settings
In the Cube Maker module, complete the required fields as follows:
- Current directory: Enter the path where the data will be stored. Create a dedicated folder if needed.
- File Name: Enter the file name. The core name is commonly used, as it is unique for each core.
- Operator: Enter your initials.
- Sample type: Enter sediment, the default for most samples.
In the Sensor/Camera Controls module, complete the required fields as follows:
- Spectral/Spatial Binning: Set to 2.
- Frame Rate: Set according to the selected operating value.
- Exposure: Set according to the selected exposure setting.
Note: After each adjustment, a red indicator appears, denoting that the changes are not yet applied. Click "Set" to apply them.
Dark sediments use an exposure of 120–150 ms; brighter, more minerogenic sediments use 80–100 ms. Before scanning, check the exposure by previewing and inspecting the Spectral View. Values should be within 1000–3000 on the y-axis. If below, increase exposure; otherwise decrease.
In the sisuMOTION module, complete the required fields as follows:
Note: Please do not change any other parameters.
How to focus the camera?
- In the sisuMOTION Motion panel, press "Focus" to move the tray and position the focusing table bars beneath the camera. To focus directly on the core surface, press "Preview" instead.
- In the ColorView and Spatial View modules, observe the stripe patterns. Adjust the camera lens by rotating the focus ring until the stripes appear as sharp as possible and the "tooth" in the Spatial View appears as square as possible.
- Once finished, press "Eject" and wait until the tray returns to the starting position.
Note: If the stripes are barely visible in the ColorView module, reduce the exposure to 30 ms to improve visibility. Ensure that the exposure is reset to the selected scanning value before starting the scan.
Place the white reference (second drawer) on the designated tray. Ensure that the surface is free of dust and debris. If necessary, clean it using a soft brush or a Kimtech wipe with acetone.
To initiate the scan, switch off all lights in the room. Press "Capture" in the sisuMotion module, then promptly turn off the computer screen and exit the room.
Set the door label to "Scanning in Progress."
Note: There must be absolutely no other light sources in the room. No phones, smart watches, or any other devices. The halogen lamps must be the only light source.
Check the estimated scan time in the Camera Calibration Tool, or remotely connect to the Specim PC and confirm that "Recording Complete" is shown in the bottom status bar.
White Reference Scan
After completing the scan, perform an additional scan of the white reference. Proceed as follows:
- In the Cube Maker module, append "_WR" as a suffix to the file name.
- Set the exposure time in the Description field to 30 ms.
- In the Sensor/Camera Controls module, set the exposure time to 30 ms and click "Set".
- Turn off all lights, press "Capture", and immediately turn off the computer screen.
- Stop the scan when the progress bar displays "Acquiring data for the target."
- A Workflow message will appear. Click "OK". The white reference scan is complete.
Shutting of Scanner
- Attach the cap securely to the camera lens.
- Remove the core, clean the workspace, and remove the core label from the focus table.
- Close the ChemaDAQ.
- Copy the data to the server (Specim02) and, if possible, remove it from the D: drive.
- Switch off the scanner from right to left, pausing a few seconds between each button.
- Turn off the lights, leave the room, close the door, and set the sign to "Access Granted".