Getting started

Turning ON the XSCAN

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 1). The top panel involves equipment running through the UPS, and the lower panel handles equipment connected to ship’s power. They should be turned on in the following order:

Lower Switches (connected to a UPS):

• X Ray Source & Camera: to turn on the main X-Ray source and the camera
• Patlite safety status lights
• cRIO and Excelsys power supply
• Power for the spare source’s safety light (Only needed when spare X-ray source is powered)

Upper Switches (connected to ship’s power):

• AFT A/C: to turn on the aft piezo air conditioner
• FWD A/C: to turn on the forward piezo air conditioner
• M-drive 23 and 34
• Cabinet light (Cab Light). Turns on overhead light inside the Xscan unit (optional)
• Power switch for the spare X-ray source (optional)

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

Figure 1: Switch board for powered subsystems

Launching the IMS X-Ray Imager application

The IMS XSCAN software can be launched from the desktop icon (Figure 2). 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 2: 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 3).  On start up the system will pause during initialization to ask the user to season the source, if the seasoning hasn't been preformed recently.

Figure 3: XSCAN IMS Main Window

The four buttons on the IMS-UI window provide access to utilities/editors via dropdown menus as shown in Figure 4.

Figure 4: IMS Control Panel Drop down Menus

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 4). The calibration utility window will open (Figure 5). 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 5: 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

Step 0: 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 6, A). Click the Grab button (Figure 6, 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 6, C-1). When it is done, the “DARK Measured” indicator becomes green (Figure 6, C-2).

Figure 6: 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). You can change the track speed which then updates the exposure settings (Figure 7, 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 7, B). A window will open (Figure 8). Enter the desired power settings (Figure 8, A), and click “Apply Values” (Figure 8, B).

Figure 7: Taking the White Image Calibration. Note the small WHITE Measured LED is lit in the lower right corner.

Figure 8: Modifying X-ray power settings

1. Turn on the X-rays by toggling the X-rays ON button (Figure 7, C-1). The source will ramp up to power.
2. Open the shutter (toggle the Shutter button, Figure 7, C-2), then again click the Grab toggle as you did for the dark image (Figure 7, D). The WHITE Measured LED will light up (Figure 7, E-2) when the grabs finish (Figure 7, E-1).

Once acquisition is completed (Figure 7, E-1), check the saturation value (Figure 7, F) and confirm that it is in the target range of 94-98%. If not, adjust the exposure values (Figure 7, A) and repeat.  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. When you are satisfied with everything then click the Accept Changes button (Figure 7, 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 section above). Once this step is complete, the user may begin imaging.

Positioning the section inside the XSCAN

Slide the bottom of the section fully into the bore of the logger (Figure 9). The top of a section should face the user. 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.

Proper insertion depth is attained by pushing with the base of the core extraction tool until the shoulder of the stop hits the side of the bore.

The tool can also be used to rotate the section half to be normal to the X-ray beam.

The fork end of the 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. 

Figure 9: Positioning a section inside the XSCAN

Entering Sample Information

Click START on the IMS main panel (Figure 4) to open the sample information window (Figure 10). This is where the user enters the imaging method and the sample ID for a section and initiates the measurement.

Figure 10: 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 10, 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: custom. The user can do multiple consecutive scans of a same section at evenly spaced desired angles but must crop the scanned images between each scan.
• 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.

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: 0-45-90-135. X-ray imaging of a full or partial section at 0, 45, 90 and 135 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 10, B).  Each provides a different method for entering the sample ID information (Figure 11).

• 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 11, 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 11, B).
• Manual: Manually enter the sample’s Text ID and Label ID values and a length (Figure 11, 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 the USE ME button to update and validate the entries and enable the SCAN button.

Figure 11: 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 10, 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 STARTon the IMS panel (Figure 4) to open the sample information window (Figure 10).
2. Insert the section in the XSCAN (Figure 9)
3. Enter the Sample ID Information and Imaging method as described above (Figure 11)
4. Select SCAN (Figure 10, D)

The track reverses ~0.8 cm from its home position, in order to accelerate to a constant speed for triggering and exposure during imaging.  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.

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 12).

Figure 12: 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 opening and scan again to get the 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 13). 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 13).

Figure 13. Utility window to process, crop and save an X-Ray image

Left panel (Figure 13, 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.

Middle panel: four tabs showing different images (Figure 13, B and Figure 14)

• 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 14: Raw and processed images, mask and calculated edges

Right panel: Options to process, crop and save (Figure 13, 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.

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.
• 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.

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 “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 choose between three process methods: (i) by full core profile (most commonly used and recommended method), (ii) by smoothing, (iii) by synthetic half profile, and (iv) by synthetic whole-round profile.

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 LUT (look-up table) curve on the right – a blue curve with an S-shape is preferred.

More details regarding the processing methods are found in the XSCAN User Guide.

Saving the images

When a user is satisfied with the crop area and the processed image, the user clicks “Crop”, and then “Save”. After saving the image, IMS will output 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 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 4).  The X-rays will ramp down and eventually turn off.

NOTE: During imaging, the user can use the software STOP/CANCEL button (Figure 12) 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 instantly stop X-rays and motion.

File Formats

IMS automatically outputs the raw and processed images.  Three images are saved: two are .jpg (corrected. cropped and processed images, respectively) and a raw .tif image.

Examples of Image 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

File location: C:\Data\In\SiteHole (e.g., U1999A for regular scans and CT-style scans will be found in a subfolder C:\Data\In\SiteHole\SiteHole-CT (e.g., U1999A-CT)

Calibration Data (Dark and White): C:\IMS-10\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

A text file with extension .XSCAN contains information regarding the settings used is automatically saved in the C:\Data\In folder.

This file contains the paths to each image file and the calibration file.  In order to successfully upload data, all 3 image files must be at path listed in the text file. The uploader, MegaUploadaTron, parses the information from the .XSCAN file and links the images.

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.