I. Introduction

This guide describes the standard operating procedures for the X-Ray imager (XSCAN) located in the Core Lab. The system is capable of collecting linescan X-radiographs on whole round and section half cores. Furthermore, the source and detector can be rotated around the core material for linescans with different view angles.  A specific region of interest (ROI) on a core section can be imaged separately using the ROI feature.

Theory of Operation

Users should review the X-Ray Methods and Theory Powerpoint from B. LeVay, 2019 for background on X-Ray radiograph acquisition before operating the system.

Hardware

The IODP X-Ray scanner is composed of a 210W, 160 kV, 1.3 mA constant potential X-Ray source and a linescan detector. The source is a Spellman XRBD 160PN210 Monoblock X-Ray generator with a 0.5 mm focal spot. The beam fan angle is 90 x 12 degrees which is distanced approximately 36 cm from the source. The detector is a Hamamatsu C12300-321 composed of a CCD sensor with a ~22 cm field of view utilizing time-delayed integration (TDI) and a resolution of 48 microns per pixel.

Shielding

The shielding consists of several complimentary designs. The primary shield (Figure 1) houses the X-Ray source and detector. It is constructed of 3D-printed ABS plastic with hollow walls that are filled with Tungsten powder. The base of the primary shield (under the detector) is a solid piece of 1-cm thick Tungsten plate to block the primary X-Ray beam.  X-Ray scatter is shielded by 2mm lead equivalent leaded vinyl or leaded acrylic panels on the sides, ends, top and bottom of the logger (Figure 2). The leaded acrylic provides a view of the inside of the logger while it operates. The hatches that allow insertion of core material on either end of the logger are also shielded with solid Tungsten plates.

 Figure 1: Primary shield top and bottom halves, the latter shows the tungsten powder filling and solid tungsten plate used in the first design of the XSCAN.

Figure 2: Leaded acrylic and leaded vinyl shielding panels

Safety Systems

The XSCAN imager has multiple safety systems in place to ensure a user does not operate the system in a radiologically unsafe manner. Never attempt to operate the X-Ray source without the proper shielding in place! The safety subsystems include:

• X-rays ON amber lights on two corners (Figure 3)  Note an extra X-rays On amber light is mounted on the aft of the Xscan and indicates when the xrays are on for the spare source.
• Colored light status indicators (AKA Patlite tower) (Figure 5)
• Shutter position sensors
• Door electronic locks (Figure 6)
• X-ray source interlock
• Emergency Stop Switch (motion and X-ray abort) (Figure 7)
• X-rays auto-off after a user-selectable period

These components are wired into one fail safe system controlled by a National Instruments cRIO-9053 unit. 

Figure 3: X-Ray emitting lights (lit=ON) on two corners of the XSCAN

Failsafe Circuitry

In order to generate X-Rays, a series of safety switches and shutter positions must be verified to enable the generation of X-Rays.  Certain switches or sensors are operated electrically, others use pneumatics.

Figure 4 shows the failsafe circuit and the safety switches involved.  All switches must be verified before the software command to generate X-Rays will be performed.

Figure 4: Fail safe circuit schematic. 

Visual Indicators

A multi-color tower light mounted horizontally on the top corner of the logger acts as a visual indicator of the safety system and X-Ray status. It has four segments that reflect specific safety subsystems of the logger plus one for the measurement phase at the time (Figure 5).

• X-Ray source:
  • Amber: source is in use, X-Rays are emitted
  • Green: source is ON, but there is no X-ray emission
  • Light OFF: source is OFF
• Shutter light indicator:
  • Amber: shutter is open
  • Green: shutter is closed – safe to open doors
  • Light OFF: shutter is disabled
• Door light indicators:
  • Amber: doors are latched and/or unsafe to open
  • Green: doors are unlatched, safe to open
• IMS measurement operations status colors:
  • Purple – initialized
  • Green – idle
  • Blue – translational move of the camera
  • Sky blue – rotational move of the camera
  • Amber – image in progress
  • Off – IMS software is not open

Figure 5: Multi-section Patlite tower mounted horizontally at the top of the logger. These lights act as visual indicators of measurement operations, door(s), and X-Ray status.

The Table 1 below illustrates the status combinations:

Table 1. Different Patlite status indicator combinations

Door Switches

Electronically-controlled safety locks have been installed on both the forward and aft doors.  If either of these doors are open at the beginning of imaging, calibration or seasoning the c-RIO will disallow the process and warn the user about it. There are also indicator lights on the door lock electronics (Figure 6).  Note that a lit red indicator means that the door is unlocked and can be opened.  These switches are always energized and therefore are usually warm to the touch, but this is not an issue.

Figure 6: Electronic safety lock on the logger door

Emergency Stop Switch

There are two main Emergency Stop switches installed on the XSCAN, one for each source.

• Main (in use) source (S/N: 135769488-A00001)

An emergency stop (e-stop) switch is located on the port  side of the XSCAN along the top rail (Figure 7).  When activated, i.e., the user hits the button, the e-stop switch cuts two circuits.  One circuit runs straight to the source power supply and one circuit runs through the cRIO with the safety circuit. The e-stop switch opens the interlock on the XRB and the X rays go OFF. It also kills the MDrive and will immediately stop all motion.

Figure 7: X-ray logger Emergency Shut Off Switch. 

• Spare source (S/N: 132614727-A00001)

The emergency stop for the spare source is located near the spare source on aft end, starboard side near the bottom of the XSCAN.  This switch cuts the power circuit to the spare source when pressed.

Figure 8: Emergency Shut Off Switch of the spare source

Thermal Management

The detector (camera) on the XSCAN logger can run warm when it is on. Additionally, the X-Ray source adds heat while producing X-rays: due to the low efficiency of the X-ray tube, most of the power it uses will be expended as heat. Optimally the camera should be operated at temperatures less than 40°C.  The IMS software continuously monitors the camera and X-ray source temperatures and displays them on the main acquisition screen (Figure 9).  Cooling modifications such as two air conditioners on the cabinet portion of the logger and directed fans on the camera itself help to keep things cool during operations.    If the camera temperature exceeds 40°C, the temperature diagram (Figure 9) will flash. The user must stop using the instrument to allow the camera to cool down before resuming scanning.  Note the AC units are connected to a drain and container that must be emptied periodically.

Figure 9: IMS temperature monitor sub-window for the source and the camera

• Source temperature: A graphical temperature display is provided to monitor the temperature of the X-ray source. The source is usually at room temperature or below 30°C.
• Camera temperature: A graphical temperature display is provided to monitor the temperature of the camera. The manufacturer recommends that the camera temperature should not exceed 40°C.

II. Procedures

Getting Started

Turning ON the XSCAN

The cRIO switch is always on, unless troubleshooting the instrument requires the cRIO to be reset. All other switches are off when the XSCAN is off.

If the XSCAN is completely shut down, a series of switches must be activated for the instrument to operate properly. The switches are located on two surge protector panels below the shielded cabinet (Figure 10). The top panel involves equipment running through ship’s power, and the lower panel handles equipment connected to a UPS. They should be turned on in the following order:

Lower Switches (connected to a UPS):

• cRIO and Excelsys power supply
• X Ray Source & Camera: to turn on the main X-Ray source and the camera
• Patlite safety status lights

Upper Switches (connected to ship’s power):

• M-drive 23 and 34
• Power switch for the spare X-ray source (optional)
• Power for the spare source’s safety light
• AFT A/C*: to turn on the aft piezo air conditioner
• FWD A/C*: to turn on the forward piezo air conditioner
• Cab lite = Cabinet light: to turn on the cabinet light (optional)

*Only one A/C is required to be on in most situations. If the lab is warmer or if the XSCAN seems to be heating up, the second unit can be turned on.

Note: The computer and its monitors are plugged directly into the UPS. The computer must be powered down via Windows or the computer’s power button.

Figure 10: Switch board 

Launching the IMS X-Ray Imager application

The IMS XSCAN software can be launched from the desktop icon (Figure 11). Before launching the IMS software, make sure that all Patlite sectors (except the one for IMS) are green. If IMS is launched before the instrument is fully on, it may generate communication issues between the IMS software and the cRIO safety system.

Figure 11: XSCAN Desktop Icon

At launch, the program begins the following initialization process:

• Testing instrument communications (camera, X-ray source)
• Homing the rotational actuator
• Homing the linear actuator
• Verify connectivity with the c-RIO safety system

After successful initialization, the main IMS-XSCAN window will appear (Figure 12).

If the computer has been restarted, the software will typically give a W-axis error when first opened.  Close IMS and reopen the program and this error will clear itself.

Figure 12: XSCAN IMS Main Window

A Quick Introduction to the IMS Program Structure

IMS is a modular program. Individual modules are as follows:

• INST plug-in: code for each of the instruments (source and detector)
• MOTION plug-in: code for the motion control system
• DAQ Engine: code that organizes INST and MOTION plug-ins into a track system

The XSCAN system, specifically, is built with one INST module (I_PI_Hama), one MOTION module (M_PI_M-Drive), and one DAQ Engine module (DAQ_PI_XSCAN).

The IMS Main User Interface (IMS-UI) calls these modules, instructs them to initialize, and provides a user interface to their functionality.

Each module manages a configuration file that opens the IMS program at the same state it was when previously closed and provides utilities for the user to edit or modify the configuration data and calibration routines.

The four buttons on the IMS-UI window provide access to utilities/editors via dropdown menus as shown in Figure 13.

Figure 13: IMS Control Panel Drop down Menus

Initial Instrument Setup

XSCAN Configuration

Configuration values should be set during initial setup and by the technician or scientist(s). There should be no need to change these values unless the configuration file is corrupted or the hardware setup is changed. The logger will provide some default values automatically if the configuration file is missing or unreadable at startup.

XSCAN Instrument General Setup

To open the XSCAN instrument setup window (Figure 14), select Instruments > Camera: General Setup from the IMS panel menu (Figure 13).  This window displays information about the source and camera hardware, primarily for metadata recording. The Table 2 below gives a description of the different settings. These settings are hard coded and cannot be changed by the user.

Table 2. XSCAN camera parameters

The shutter should be enabled and the air pressure should be selected for safety reasons: both buttons should be YES (Figure 14).

The user can set the time limit for the X-ray Auto off, i.e., the number of minutes when the X-rays will automatically be ramped down after the instrument is in the idle state with no action from the user. It is recommended to set a time of 15 min.

Click Accept to save the changes and write them to the configuration file.  Click Cancel to revert to previous values.

Figure 14: XSCAN Parameters Window 

X-Ray Power Settings

Prior to collecting X-Ray radiographs on whole rounds or section halves in the XSCAN, the user must set the imaging X-ray power (voltage and current). These are set during the calibration process. 

• kV: X-ray tube voltage.  Maximum voltage for the source is 160 kV, minimum voltage is 35 kV. Lowering the voltage while maintaining the number of X-rays penetrating the core (longer exposure or higher current) will increase image contrast. 
• mA: X-ray tube current.  The maximum allowable current is 2.1 mA. Maximum power for the source is 210 watts.  Therefore, the source is either voltage limited or current limited as seen in Table 3 below.  Increasing the current will increase contrast if voltage is kept constant.

Table 3. X-ray source power ranges

Detector Calibration

Detector calibration should be done at the beginning of the expedition or whenever the power settings are changed.  It is a quick and easy process to do.

To calibrate the detector, select Instruments> Camera: Calibrate from the main IMS menu (Figure 13). The calibration utility window will open (Figure 15). The purpose of this utility is to collect White and Dark images that will be used to perform offset and gain corrections for all images acquired with the camera at given power settings. 

Figure 15: Detector Calibration user interface window.  From this utility a user takes the Dark and White correction measurements after setting the track speed, which dictates the camera’s exposure.

Calibrating the Detector

Make sure the bore is empty and clean before starting a calibration.

Step 1: Dark Image Correction

The DARK image is normally made with the X-rays off to capture the electrical background noise of the detector (Figure 16, A). 

To capture the dark image:

1. Click the Grab button (Figure 16, B) to take twenty Dark grabs, numbered 0 to 19. The “Current Grab Stacked” sub window will display the resulting dark grabs with its characteristic striping (Figure 16, C-1). When it is done, the “DARK Measured” indicator becomes green (Figure 16, C-2).

Figure 16: Taking the Dark correction image. Note the small DARK Measured LED is lit in the lower right corner.

Step 2: White Image Calibration

The WHITE image is taken with the X-rays on and the shutter open.  We simulate motion by using the exposure of the camera since everything is stationary (this detector has no internal shutter). Changing the track speed will also update the exposure settings (Figure 17, A). The number of scans is automatically calculated from the chosen speed and exposure.

The WHITE image is used for the gain correction after the offset correction from the dark image is completed. 

To capture the WHITE image:

1. Click “Update X-Ray” (Figure 17, B). A window will open (Figure 18).
2. Enter the desired power settings (Figure 18, A), and click “Apply Values” (Figure 18, B).

Figure 17: Taking the White Image Calibration. Note the small WHITE Measured LED is lit in the lower right corner.

Figure 18: Modifying X-ray power settings

2. Turn on the X-rays by toggling the X-rays ON button (Figure 17, C-1). The source will ramp up to power (Figure 19).

3. Open the shutter (toggle the Shutter button, Figure 17, C-2)

4. Click the Grab button (Figure 17, D). The WHITE Measured LED will light up (Figure 17, E-2) when the grabs finish.  The “Current Grab Stacked” sub window will display the resulting white grabs with its characteristic white to grey pattern (Figure 17, E-1).  The grey outside edges are the tube.

Figure 19: X-Rays ramping up for white calibration

5. Once acquisition is completed, check the saturation value (Figure 17, F) and confirm that saturation percentage is in the target range of 94-98%.  To get more exposure within the image, the saturation values can be higher (100%).  This will clip the data, but can produce a better image in denser materials. Adjust the exposure values (Figure 17, A) and repeat until user is satisfied. 

6. Adjust the position of the blue left-hand mask bar if needed; this will be rare. XSCAN uses masking to eliminate the bore walls from our images. By default the mask width is set to 1600 pixels.

7. When you are satisfied with everything then click the Accept Changes button (Figure 17, G).  This saves the calibration information to memory and to the configuration file.

Starting Measurements

Prior to imaging cores, especially at the start of an expedition, the user must perform a detector white-dark calibration at the chosen power settings (see Detector Calibration). Once this step is complete, the user may begin imaging.

Entering Sample Information

To take images, the user selects the Start button on the IMS main panel (Figure 13) to open the sample information window (Figure 20). This is where the user enters the imaging method and the sample ID for a section and initiates the measurement.

Figure 20: Section Information Window (default display)

Imaging Method

It is possible to measure either section halves or whole round sections. Select “SHLF-A” or “SHLF-W” in the Section Type box for sections halves, and “SECT” for WRND measurements. The selection will determine which imaging method presets are active. The available presets for the selected sample type on the left are highlighted/activated in light grey. The preset selected for the scan is highlighted in green (Figure 20, A).  Note that this selection will affect how the sample id information is parsed and displayed when the user scans or selects a sample from LIMS.

Definition of the presets:

• For Archive and Working halves

-Section half: only: Basic X-ray imaging of a full or partial section (angle is 0 degrees, camera is perpendicular to the section’s split surface)

-Section half: thickness: X-ray imaging of a full or partial section at 0 and 90 degrees to estimate the thickness of a section half.

-Section half: CT: the user can do multiple consecutive scans of a section at different evenly spaced angles without cropping the image between scans. It is possible to do CT-like imaging at angles from 0 to 180 degrees, with an angle step as low as 1 degree.

-Section half: custom: The user can do multiple consecutive scans of a section at evenly spaced angles.  The user must crop the scanned imaged between each scan.

• For Whole Round sections

-Whole Round: only: Basic X-ray imaging of a full or partial section (angle is 0 degrees)

-Whole Round: 0-90: X-ray imaging of a full or partial section at 0 and 90 degrees.

-Whole Round: CT: the user can do multiple consecutive scans of a same section at different angles evenly spaced without cropping the image between scans. It is possible to do CT-like imaging at angles from 0 to 180 degrees, with an angle step as low as 1 degree.

-Whole Round: custom: The user can do multiple consecutive scans of a same section at evenly spaced desired angles and crops the scanned imaged between scans.

Sample Entry Tabs

There are three tabs available on the sample information screen (Figure 20, B).  Each provides a different method for entering the sample ID information (Figure 21).

• Scanner: Scan the IODP barcode to enter the sample’s Text ID and Label ID values, using either a barcode gun or the barcode camera by the loading door (Figure 21, A).
• LIMS: Select expedition, site, hole, core, and section values from a series of list boxes that are populated with data from the LIMS database (Figure 21, B).
• Manual: Manually enter the sample’s Text ID and Label ID values and a length (Figure 21, C). The name fields will accept any name, but that does not guarantee the data will upload. The user must be careful to enter the name properly.  If the name is incorrect files will be created, but it may not upload properly. The Text ID information must match an actual section in order for the data to upload. Click USE ME to update and validate the entries and enable the SCAN button.

Figure 21: Sample Information Window – A. Scanner (barcode gun or barcode camera) entry, B. LIMS entry, and C. Manual Entry

Scanned Interval Length

It is possible to scan either a full section or a portion of it.

The user can select the desired scan length by clicking on the ROI/FULL SECTION button on the right (Figure 20, C). Select full section to scan a section over its entire length (i.e., LIMS length). A user can scan a specific region of interest (ROI), by selecting the ROI option and setting the measurement interval in centimeters (start and end) to scan.

Positioning sections inside the XSCAN

Section position is important within the XSCAN unit. The unit is intended to only image sections up to 150 cm long.  

Sections are loaded into the XSCAN by sliding the section into the aft door, bottom of the section first (Figure 22a). The top of a section should face the user, this is typically a blue end cap and where the label for the section will be. If imaging section halves, ensure that the surface of the core is level, i.e., horizontal while inserting the section. If imaging whole round sections, ensure that the double lines are facing up. This ensures that the XSCAN rotation angle matches that of the IODP orientation frame.

To position the section properly in the XSCAN imager, use the double ended core extraction tool (Figure 22a). Use the round flat end to push the section into the acrylic tube until the round stop contacts the outside edge of the XSCAN unit. The user must also be careful not to push sections to quickly into the XSCAN or they may slide further along the track than intended. The forked end of the extraction tool can also be used to rotate the section half to be normal to the X-ray beam if the section twists while being loaded.

Imaging sections longer than 150 cm

Sections longer than 150 cm require multiple images and adjustments to the sample positioning to capture the entire section. The user must first position the section as they would for sections under 150 cm and take an image.  After the first image, the user must pull the section back until the top of the section is flush with the end of the acrylic tube and take a second image. 

Retrieving Sections from inside the XSCAN

The fork end of the double ended extraction tool is used to retrieve sections.  Insert the fork until you feel it touch the end of the section.  A brisk short motion will pop the tines of the fork over the end cap and allow you to pull the section back towards you.  If repeated attempts are not successful, rotate the fork 180° and try again. When retrieving section halves, the fork often needs to be rotated from horizontal to properly connect the tines to the end cap.  

Short sections can be easily loaded into the XSCAN unit, but can be difficult to retrieve using the typical extraction tool. It can also be difficult to retrieve cores with extender caps. The user may use the U-shaped extractor tool to scoop under or over the top of a section and pull it out (Figure 22b).  A string tied to the section can also work well on small sections such as core catchers.  Loop the string around the top of the core, tighten the loop, and put the knot under the core so the weight is on the string. When pulling the core out, gently pull the string. If none of these methods work, the user may push the section out from the forward end of the XSCAN.

Figure 22a: Positioning a section inside the XSCAN

Figure 22b: Using the U-shaped extractor

Entering Sample Information

Click START on the IMS main panel (Figure 13) to open the sample information window (Figure 23). This is where the user enters the imaging method and the sample ID for a section and initiates the measurement.

Figure 23: Section Information Window (default display)

Imaging Method

It is possible to measure either section halves or whole round sections. Select “SHLF-A” or “SHLF-W” in the Section Type box for sections halves, and “SECTION” for WRND measurements. The available presets for the selected sample type on the left are highlighted/activated in light grey. The preset selected for the scan is highlighted in green (Figure 23, A).

Definition of the presets:

• For Archive and Working halves

-Section half: only: Basic X-ray imaging of a full or partial section (angle is 0 degrees, camera is perpendicular to the section’s split surface)

-Section half: thickness: X-ray imaging of a full or partial section at 0 and 90 degrees to estimate the thickness of a section half.

- Section half: CT: the user can do multiple consecutive scans of a same section at different evenly spaced angles without cropping the image between scans. It is possible to do CT-like imaging at angles from 0 to 180 degrees, with an angle step as low as 1 degree.

- Section half: custom. The user can do multiple consecutive scans of a same section at evenly spaced desired angles and crops the scanned imaged between scans.

• For Whole Round sections

- Whole Round: only. Basic X-ray imaging of a full or partial section (angle is 0 degrees)

-Whole Round: 0-90. X-ray imaging of a full or partial section at 0 and 90 degrees.

- Whole Round: CT. the user can do multiple consecutive scans of a same section at different angles evenly spaced without cropping the image between scans. It is possible to do CT-like imaging at angles from 0 to 180 degrees, with an angle step as low as 1 degree.

- Whole Round: custom. The user can do multiple consecutive scans of a same section at evenly spaced desired angles and crops the scanned imaged between scans.

Sample Entry Tabs

There are three tabs available on the sample information screen (Figure 23, B).  Each provides a different method for entering the sample ID information (Figure 24).

• Scanner: Scan the IODP barcode to enter the sample’s Text ID and Label ID values, using either a barcode gun or the barcode camera by the loading door (Figure 24).
• LIMS: Select expedition, site, hole, core, and section values from a series of list boxes that are populated with data from the LIMS database (Figure 24, B).
• Manual: Manually enter the sample’s Text ID and Label ID values and a length (Figure 24,C). The name fields will accept any name, but that does not guarantee the data will upload. The user must be careful to enter the name properly.  If the name is incorrect files will be created, but it may not upload properly. The Text ID information must match an actual section in order for the data to upload. Click USE ME to update and validate the entries and enable the SCAN button.

Figure 24: Sample Information Window – A. Scanner (barcode gun or barcode camera) entry, B. LIMS entry, and C. Manual Entry

Scanned Interval Length

It is possible to scan either a full section or a portion of a section using the ROI feature.

The user can select the desired scan length by clicking on the ROI/FULL SECTION button on the right (Figure 23, C). Full section will be used to scan a section over its entire length (i.e., LIMS length). ROI, which stands for Region of Interest, will be selected to set an interval (top/start and bottom/end) to scan.

Taking X-Ray Images

1. Select START on the IMS panel (Figure 13) to open the sample information window (Figure 23).
2. Insert the section in the XSCAN (Figure 22)
3. Enter the Sample ID Information and Imaging method as described above (Figure 24)
4. Select SCAN (Figure 23, D)

The track reverses 0.5 cm from its home position.  For the first scan after launching IMS the X-ray source will ramp up and a window with the X-ray source status will appear (Figure 25).

Figure 25: Status window displays the progress of the X-ray source ramping up to the requested kV and mA settings.

Once the mA and kV are stable, the window will close, the shutter will open, and image acquisition will begin.  The user may abort at any time by clicking the STOP/CANCEL button (Figure 26).

Figure 26: Stop/cancel button during image acquisition.

The system will scan down the section until it reaches the end of the section or 150.0 cm*, whichever is greatest, at which time the shutter will close and the scanner will return to the home position. Then the loading door will unlock in preparation for removing and replacing the core for the next scan. Note that the X-ray source is still ON.

*Note: Logger design decisions dictated that the maximum length of core that can be imaged on this logger is 150.5 cm, to minimize the overall size of the instrument.  If it is imperative that every centimeter of a section that is longer that this be imaged, the user must pull the section out until the end cap is flush with the end of the bore and scan again to get the very bottom imaged.  The images can be spliced together manually later if a single composite core image is desired.

Cropping and Processing an X-Ray image

When the imaging is complete, the image will flip around the +z downcore axis in the background to mimic the SHIL image. The user must then process and crop the image (Figure 27). Note that processing and cropping is not performed by the user when the imaging is done in CT mode.

Processing an X-ray image involves three steps:

1. Cropping the image to eliminate non core-material elements, e.g. core liner and white areas at the edges of the image
2. Selecting a method and degree of image manipulation to enhance features
3. Saving the image which produces its file for uploading to the database

The IMAGE Process & Crop window can be separated into 3 areas: on the left the X-ray histograms of the image acquisition, in the middle, the raw and processed images, and on the right the different options for processing and cropping (Figure 27).

Figure 27: Utility window to crop, process and save an X-Ray image

Left panel (Figure 27, A):

• Original Histogram: This histogram represents the X-Ray penetration for a section with the X-Ray counts (Y-axis) as a function of the number of X-ray transmitted (X-axis).
• DIFF Histogram: This is the DIFFERENCE histogram. Each column of pixel values is averaged down the entire length of the image, and this average value is then subtracted from each pixel down the same column of the raw image, continued for every pixel column across the image. The yellow line indicates the Maximum or mean value of the resulting histogram depending on user selection.
• Processed Histogram: this displays the effects of the user-selected level of histogram expansion on the slider to the right. Adjust the slider while observing both the changes to the processed histogram and the image itself in the Processed tab in the center of the screen. 

When you are satisfied with the quality of the image then click the Save Image button.

Details are provided in the Processing the image section below.

Middle panel: four tabs showing different images (Figure 27, B and Figure 28)

• Raw tab: This is the raw, dark and white corrected image after flip.
• Processed tab: This is the resulting image after the processing performed by the user.
• Mask tab: this is the mask of the image where all scanned material is shown in white.
• Edges tab: Profile of the section edges detected using weighted intensities.

The green box represents the crop area and can be adjusted by the user using the settings on the right.

Figure 28: Raw and processed images, mask and calculated edges

Right panel: Options to process, crop and save (Figure 26, C)

The red asterisks are important options to consider for a good, processed crop. IMS will automatically process the raw image based on the parameters set by the user. In this window, the user can choose an appropriate imaging process, crop, and save the images.

It the user is not happy with the image, the user can redo the imaging by clicking Discard Image. A pop-up window will ask confirmation to the user.

Selecting the crop area

To select a good crop area, the user can:

• Adjust the Mask Threshold by moving the red line up/down within the graph. The shape of this curve is effectively an across-core profile of a WRND or section half. Thinner areas on the edges produce brighter pixels with higher values while the thick centers are darker.  Many images will have “shoulders” that represent the core liner.  We recommend keeping the threshold below these shoulders.
• It is equally important to select a good across-core profile through the section, as the default profile is the first one imaged by the camera. To find a good across-core profile, one might slide the Profile Line Position slide bar.
• Choose the Crop Width by sliding the cursor: this defines the width of the green box in pixel. Recommended setting is between 1600 (default) and 1700 px.

The full image can be seen by sliding the bar on the right and by using the arrows for the top and bottom of the section. That way, the user can make sure that the full section is comprised within the green crop box. If the user does not want to verify the processed image or wants to save time in the cropping, it is possible to halt processing by ticking the Suspend Process box.

When a crop is good, the crop status appears as “GOOD CROP”. If the crop is not good, the status appears as “TOO SHORT”, and the Crop button will become unavailable. The user must check the crop area and correct as necessary. If the crop area is good and the message is still there, the user needs to check the box Override Crop Restrictions to enable the Crop button.

If there is a void or missing part at the top of the scanned section, the user can force the crop area to be tight to the top of the section liner (endcap) by ticking the Lock to top box, so that the zero cm offset of the virtual ruler starts at the endcap and not at the top of the section material. Similarly, the user can force the crop area to be tight to the bottom of the liner by ticking the Lock to bottom box.

The user can choose to save the mask parameters for the next images by ticking the Save Mask box.

The Un-crop & Init ROI button is used to set the green box back to its original position. This can be repeated until the user is happy with the selected crop area.

Processing the image

The user can either choose to process the image after acquisition or not. If the user wants to process the image and save it, the user has to tick the Save Process Image box (i.e., yes). If the box is not ticked (i.e., no), only the raw image (.tif) will be saved and uploaded to LIMS.

For processing an image, the user can choose between four process methods: (i) by full core profile (most commonly used and recommended method), (ii) by smoothing, (iii) by synthetic half profile (not fully ready at the time of X399), and (iv) by synthetic whole-round profile (not fully ready at the time of X399).

Other processing options

• Histogram expansion: The expansion of the processed histogram (displayed on the bottom left of the window) is adjusted by sliding the cursor on the bar between 1 for a sharp (narrow) histogram and 9 for a smooth (wide) histogram. This feature changes the shape of the processed on the right – a blue curve with an S-shape is preferred.

More details about the processing methodology are found in the Appendix.

Saving the images

When a user is satisfied with the crop area and if the case, the processed image, the user clicks “Crop”, and then “Save Image”. "Save Image" is not available until cropping is made. After saving and processing the image, IMS will output three images: a processed image with virtual ruler and label (file name_P.jpg), a processed cropped image (file name_C.jpg) without ruler and label, and a white-dark corrected raw TIF image with embedded metadata (file name_R.tif) to the C:\DATA\IN folder sorted by site and hole. If the user has chosen to save the raw image only without processing, only the .tif image (file name_R.tif) will be uploaded to LIMS.

If sample information was added manually the images will appear in C:\DATA\IN\OTHER.

Turning the X-Rays OFF

For safety and to save the X-ray source from emitting when not in use, the user can turn off the X-ray source from the IMS main menu by sending the CAMERA: X-ray | Ramp Down command to the source, via the Instruments menu on the IMS main window (Figure 13).  The X-rays will ramp down and eventually turn off.

Figure 29: X-ray status window (ramp down)

NOTE: During imaging, the user can use the software STOP/CANCEL button (Figure 26) to end the imaging process and ramp down the source. 

In case of emergency, the X-Ray source can be immediately turn off by selecting Instruments >  CAMERA: Off now ! If the software is unresponsive, then activate the hardware abort button to stop X-rays and motion (Figure 7).

X-Ray Auto Off

When the XSCAN is not in use for a certain time, the X-ray source will automatically shutdown after a time chosen by the user. Three options are available: 5, 10 or 15 min of inactivity. This can be selected in Instruments > CAMERA: General Setup (Figure 14).

ABORT a measurement sequence

At any time during a measurement (imaging, calibration, or seasoning), the user can stop/abort the sequence by using either IMS or the emergency hardware abort button.

The hard Abort button (Emergency Switch) is located on the front panel of the XSCAN (Figure 7). If it is used, the X-Rays will automatically shut down. During imaging, the camera will stop moving, the imaging will end, and the user will need to start imaging the section from the beginning. 

After releasing the hard Emergency Switch button, it is not necessary to restart IMS. Starting a new scan or any other work will reset the error and move the camera to the Load/Home position.  

Seasoning

Seasoning is to ensure a longer life for the X-Ray tube. The X-Ray sources, both main and spare, must be seasoned every week with the recommended daily seasoning type (1 to 7 days). Seasoning procedure can be activated in the IMS main menu Instruments > Camera: Season Tube. Please fill in the Confluence logsheet /wiki/spaces/LN/pages/7338164275 for a record of the seasoning conducted.

More details about the Seasoning is found in the Appendix below.

III. Uploading Data to LIMS

File Formats and File Saving

A text file with extension .XSCAN contains information regarding the settings used is generated and automatically saved in the C:\DATA\IN folder.

This file contains the paths to each image file (one or three paths) and the calibration file (Figure 30).

Figure 30: Path directories for images and calibration file to be uploaded to LIMS

IMS automatically outputs the raw (one image) with, if the case, the two processed images. One or three images are saved: the two processed are .jpg (corrected, cropped and processed images, respectively) and a raw .tif image.

Examples of file names:

Raw file name (.tif):

385-U1545A-3H-4-A_SHLF10354871_0000_deg_20230124132738_R.tif

Cropped file name (.jpg):

385-U1545A-3H-4-A_SHLF10354871_0000_deg_20230110125632_C.jpg

Processed file name:

385-U1545A-3H-4-A_SHLF10354871_0000_deg_20230130154107_P.jpg

Image File location: C:\DATA\IN\SiteHole (e.g., C:\Data\In\U1601A) for regular scans. Scans performed at different view angles are found in C:\DATA\IN\SiteHole\Section Rotary (e.g., C:\DATA\IN\U1385F\2X-1 Rotary). CT-style scans are found in C:\DATA\IN\SiteHole\SiteHole CT (e.g., C:\DATA\IN\U1601A\U1601A CT)

Calibration Data (Dark and White): C:\IMS\CONFIG_XSCAN\I_PI_HAMA.ini 

Note: this calibration data is also contained in every MUT load file.

A unique time stamp is appended to each image.

File Uploading to LIMS

Open the MUT2 application (Figure 30) and select "X-Ray Imaging" as analysis.

Figure 31: MUT2 application icon

Load files are text files with the extension .XSCAN. In order to successfully upload data, all image and configuration files must be at path listed in the text file. The uploader, MegaUploadaTron2, parses the information from the .XSCAN file and links the images. They are used by the MUT2 application to load acquired data and images into LIMS. Correct files appear with a green tick on MUT2 (Figure 32) and MUT2 will process them and then move them to the C:\DATA\archive folder.

Figure 32: Uploading files to LIMS with MUT2

The files uploaded by LIMS are found in C:\DATA\IN as Exp-SiteHole-Core-Section-Type-Timestamp.XSCAN (e.g., 399-U1601A-6R-1-W_20230421043105.XSCAN). 

Any file that fails to upload is moved to the C:\DATA\error folder.

All XSCAN line scan images are saved as a single set of files and once uploaded can be found in the LORE report under Images > X-ray Images (XSCAN).  CT images are not uploaded to the database at this time.  Any CT images collected need to be transferred to Data1.

IMPORTANT NOTE: When the images are uploaded to LIMS AND saved on Data1, make sure to delete at the end of the expedition all the images acquired during the expedition from the XSCAN workstation. Keeping big images on this computer will cause a full memory and prevent future image saving.

Displaying the images with LIVE

XSCAN images can be viewed in LIVE templates as thumbnails. A couple of points need to be kept in mind:

• For section with a WRND sample taken at the bottom, i.e., section with a yellow end cap, the user must select the "ROI" feature of IMS in the Sample Information Window and set the top and bottom offset of the section scanned. For instance, a section curated at 150 cm (LIMS length) with a WRND sample taken at the bottom (for instance a 5 cm long IW sample) must be entered in the Sample Information Window with "ROI-Custom", start at 0 cm and end at 145 cm. The XSCAN image will then match the SHIL image. Failure to do so will result in a stretched thumbnail image in LIVE (Figure 33). That happens when the default feature "full section" is selected in the Sample Information Window. This can be fixed by editing the .XSCAN file by changing the bottom offset and changing the position specified line to TRUE.

Figure 33. Display of XSCAN image in LIVE for section with a WRND taken at the bottom - "full section" on the left and "ROI" on the right

•  If there are several images taken for one section (for instance, full core and ROI), the last image taken (i.e., the last image uploaded by MUT) will be displayed in LIVE. This is because whenever a second (or more) image is uploaded for a sample, the new image is set with the "display flag" set to true, and all others have it set to false. The display flag controls what will be shown in LIVE and some other apps. LIME can be used to set the display flag to one of the older images. Scientists must ask a technician to change the display flag in LIME.

In LIME (Figure 34), select Test > Edit Display Image. Enter the TEXT ID in the box and select XSCAN - X-Ray images for the analysis. Select the section and click Display. In the pop-up window, all images taken for the selected section will be listed. Select the image to be shown in LIVE (based on the Test number) and click Update. In LIVE, refresh the page to display the desired image.

Figure 34. How to modify a display flag in LIME

IV. Appendix

A.1. Health, Safety and Environment

Safety

• Keep extraneous items and body parts away from the moving platform, belt, and motor.
• The scanner has a well-marked emergency stop button to halt the system if needed.
• Don't insert your hand between the source and the detector, and near the spare source when seasoning is ongoing.
• Do not attempt to work on the system while a measurement is in progress.
• Do not lean over the scanner.
• Do not stack anything inside the scanner.
• This analytical system does not require personal protective equipment.

XSCAN Safety Systems and Logic

• Power will be keyed locked
• Primary Beam will be shuttered (failsafe)
• Access Hatches will be latched during operations
• Maintenance access panels will be interlocked

• Shutter will close on loss of power, interlocks are open or emergency stop engaged
• Shutter can be open only when access hatches are closed and latched
• Hatches will be unlocked when shutter is closed

Pollution Prevention

This procedure does not generate heat or gases and requires no containment equipment.

A.2. Maintenance

Seasoning

After initial installation and/or after periods of idle time (idle time is defined as X-ray production unused), the manufacturer of the X-ray source used in the XSCAN recommends warm-up schedules to ensure proper operation for the X-ray Tube. Disregarding this may cause irreversible damage to the X-ray tube and/or decrease its life expectancy.

{from Spellman website} Typically seasoning is done after initial installation and after periods of idle time. This would include a profile for daily seasoning and longer profiles for increased idle time. The seasoning procedure carefully raises the tube current and voltage to reduce any residual gas in the X-ray tube before the tube is operated at full output. Seasoning also minimizes un-even distribution of potential/electric field on the tube glass. Following the recommended seasoning schedule will help prolong the life of the X-ray tube and prevent tube arcing that can potentially cause irreversible damage to the X-ray tube.

The X-Ray sources, both main and spare, must be seasoned every week with the recommended daily seasoning type (1 to 7 days). Seasoning procedure can be activated in the IMS main menu Instruments > Camera: Season Tube. Please fill in the Confluence logsheet /wiki/spaces/LN/pages/7338164275 for a record of the seasoning conducted.

Alternatively, the IMS software, when launched, will tell the user to proceed to seasoning whenever necessary by showing the window on Figure A1.

Figure A1. IMS asking to perform the required weekly seasoning

X-Ray source can be seasoned in 5 different ways, whether it is a new tube installed (Figure A2) or based on the idle time (Figure A3).

Figure A2. Seasoning window when a new tube is installed.

Figure A3. Seasoning type based on idle time (from short to long break in time)

When a user clicks on “Use selected and Start”, the X-Ray tube seasoning window appears (Figure A4), the X-Rays ramp up, and the seasoning starts. The season table on the left is set with default values for the selected seasoning method. The seasoning can be stopped anytime by the user by clicking on “Stop seasoning” or “Abort”.

Figure A4. X-Ray tube seasoning window with the season table of the weekly seasoning.

IMPORTANT: The seasoning is done for the main tube (in use) AND the spare tube.

To season the spare tube, turn on the switches for the spare source (Figure A5). Go to Instrument > Camera: Season Spare Tube to start the seasoning.

Figure A5. Switches to turn on to season the spare X-Ray source

X-Ray Source Status

The Spellman X-ray source status and usage, for both main and spare sources, can be checked by using Monoblock X software provided by the vendor. This is a user-friendly GUI which indicates usage hours, faults, temperature, and allows seasoning (independently of IMS) amongst other features. The user is referred to the MonoblockX Manual for more information (MonoblockX_Manual_RevB.pdf).

Make sure that IMS is closed to allow the sources to communicate with MonoblockX. Open Monoblock X (Figure A6) and accept the terms of use.

Figure A6. HR GUI MonoblockX software icon

In the Options tab, check that the serial settings are the same as in Figure A7.  Click Connect to communicate with the Spellman XRB source. Change the communication port according to the source you want to check.

Figure A7. Serial settings for the XRB sources

Once the communication is established (Figure A8), verify the source status in the Main tab and the number of hours in high voltage (HV on time) (Figure A9).  Please report this information on the Confluence logsheet /wiki/spaces/LN/pages/7338164275 for a record of the source usage.

Figure A8. Connection with the source established - no faults detected

Figure A9. High Voltage on Time displaying the total number of hours of use of the source

Cleaning tube

The bore inside the XSCAN needs to be cleaned when it is dirty. To remove the tube, the Working Half rack needs to be emptied so that the bore can be removed from this side. High pressure water (catwalk) is recommended to clean the inside. While doing that, a second bore can be put in place to keep running the measurement. Spare bores are available in the Upper Tween (above the gas bottles).

B1. Troubleshooting

• Computer memory full

Images generated by the XSCAN are huge. A .tif image is usually around 180 MB. It is very likely that during the course of an exposition where the XSCAN is intensively used that the computer will reach its capacity to save images. It is very important that the user checks regularly if the image files are correct. When the computer reaches its full memory capacity, the images will be saved with a size of 0 kb !!! There is no warning from IMS.  If the Xscan unit begins to stall on the way back to home, check the computer memory.  If the computer is full the communications are interrupted and the track will freeze.

To avoid such a thing to happen, the user must ask a technician to save the files on Data1 in order to be able to delete those files from the computer.

• Seasoning of the spare tube does not start

If the seasoning of the spare tube does not start, with the main source on, turn off the spare source, but not the main source. Close IMS. Leave the main source on, turn on the spare source, and re-open IMS. This should allow you to do the seasoning of the spare tube.

• IMS frozes during X-Ray Auto off

It is very likely that this happens when a scan is about to start and the X-ray Auto-off is ongoing. Two contradictory commands may have been sent at the same time: one telling the source to ramp down, one telling it to ramp up. IMS needs to be killed and restarted. XSCAN switches must be turn off and on again to clear any potential residual error.

X-Ray Auto-Off frozen window

B2. NI Communication Ports

The figures B2.1 and B2.2 below show the NI Max settings for the XSCAN to communicate with MonoblockX software and in case of communication loss.

Figure B2.1. NI Max settings for the main source

Figure B2.2. NI Max settings for the spare source

C1. Motion Control Setup

Motion control should be set during initial setup and further changes should not be necessary. Motion control setup can be accessed by selecting Motion > Setup from the IMS panel menu (Figure C1). The M-Drive Motion Setup control panel will open (Figure C1).

Figure C1. Motion Setup Menu from the IMS panel menu

The user may select between four setup panels from this window.

• • • Motor and Track Options
    • Fixed Positions
    • Limit and Home Switches
    • Motion Profiles

Motor and Track Options Menu

Once these values have been properly set, they should not change. This panel is only for initial setup.

Make sure to use the values shown for the XSCAN (Figure C2).

The relationship between motor revolutions and linear motion of the track is defined in this window and is critical to both safe and accurate operation. User should be familiar with the M-Drive motor system prior to adjusting these settings.

• X-axis (Figure C2A)
  • Select Axis: Select X for translational motion of the camera.
  • Encoder Pulses/rev: Defined by the manufacturer of the M-Drive as 2048.
  • Screw Pitch: Set to 4.0 (the ratio of 2048 steps per revolution and chain displacement (cm) as a function of the drive gears diameter).
  • Gear Ratio: Set to 2.0.
  • Direction: Clockwise rotation moves the tray in a positive direction (from home to end of track).

• W-axis (Figure C2B)
  • Select Axis: Select W-axis for the rotational system of the XSCAN
  • Encoder Pulses/rev: Defined by the manufacturer of the M-Drive as 2048.
  • Screw Pitch: Set to 125
  • Gear Ratio: Set to 2.0.
  • Direction: Counter clockwise rotation moves the tray in a positive direction (from home to end of track).

Click Accept to save the values or Cancel to return to previous values.

Figure C2. XSCAN Motor and Track Options Setup Window for (A) the X-axis and (B) the W-axis

Fixed Positions Menu

Once these values have been properly set, they should not change. This panel is only for initial setup.

In this window the user may define fixed track locations used by IMS motion control. For the XSCAN, make sure to use these values unless there has been a physical change to the system (Figure C3).

• X-axis (Figure C3A)
  • Select Axis: Select X for translational motion of the camera.
  • Max Section Length: Maximum length of section that can be placed in the track. This value is set to 150 cm.
  • Allowable Track Move: Distance in cm between the limit switches. Currently the value is set at 0 cm.
  • Load and Unload positions: For the XSCAN, these values are set to 0. This will always bring the tray back to the sample load end after a measurement sequence.
  • Top-of-SectionSwitch?: OFF
  • Top-of-Section Switch Offset: 0
  • Push Past: 0
  • Fast Past: 0
  • Run Out Switch?: OFF

• W-axis (Figure C3B)
  • Select Axis: Select W-axis for the rotational system of the XSCAN
  • Load and Unload positions: For the XSCAN, these values are set to 0.

Note, these values along with the detector position set in the Camera: General Setup under instruments must be accurate for proper motion control. Take care in setting these values.

Figure C3. XSCAN Fixed Positions Window for (A) the X-axis and (B) the W-axis

Limit and Home Switches Window

Once these values have been properly set, they should not change. This panel is only for initial setup.

This panel is used to define the orientation of the track system, limit switches, and the home switch (Figure C4). The MDrive can be used with either a dedicated Home switch or a limit switch as a home switch. In the case of the XSCAN track we use a home switch.

• X-axis (Figure C4A)
  • Select Axis: Select X for translational motion of the camera.
  • Select Track and Home Geometry:For the XSCAN, select CCW look @ CW Edge

• W-axis (Figure C4B)
  • Select Axis: Select W-axis for the rotational system of the XSCAN
  • Select Track and Home Geometry:For the XSCAN, select CW look @ CCW Edge

Figure C4. XSCAN Limit and Home Switches Window for (A) the X-axis and (B) the W-axis

Motion Profiles

The motion profiles window can be used to adjust the speed, acceleration and deceleration profiles used by the track for various types of movements. In the case of the XSCAN, the motion profile is hard coded for both the X- and W-axis for safety reasons. It is NOT possible to adjust these values (Table 4).

• DAQ Move: This profile controls moves between measurement positions. 
• Limit Seek: This profile finds the limit switch location. 
• Home Final: This profile finds the final location of the home switch. 
• Load/Unload: This profile is used for moving the actuator for general movements and moving out of the XSCAN to the final position prior to ending a measurement.

Table 4. Motion profile values for the X- and W- axes of the XSCAN

C.2. MDrive Motion Utility and Widget

The MDrive Motion Utility window (Figure C5), accessible in Motion>Utility, allows the user to move and rotate the camera as needed/necessary.

Figure C5. MDrive Motion Utility Window

The Motion Widget window (Figure C6), accessible in Motion>Motion Widget, is a simpler interface and allows the user to move and rotate the camera as needed/necessary.

Figure C6. Motion Widget Window

V. Credits

All improvements to the Quick Start Guides and User Guides are a communal effort, with honorable mention to the group of LOs, ALOs, and technicians who have helped.

VI. LIMS Component Table

VII. Archived Versions

This User Guide is the first of its kind.