SHIL Quick Start Guide
Introduction
The SHIL (Section Half Image Logger) creates high-resolution images, both line scans of sections (predominantly from the archive half) and 360° images of hard rock pieces.
Note: Do not look directly at the lights, or touch the copper poles. The Light source is extremely bright, and the copper can be very hot; both can cause physical harm.
Getting Started

1. Open MUT and login using ship credentials. For more information see the "Uploading Data to LIMS" section below.
2. Double clikc the IMS icon on the desktop (Figure 1). IMS initialize's the instrument and checks the movement of the track. Once initialized, the logger is ready to measure a section. For hard-rock 360° images, please see below.

Figure 1. SHIL Desktop Icon
Making a Measurement
Note: If you see any change in image quality, please contact the PP or Imagining technician.

1. For sediment cores: using either a metal scraper or glass slide scrape the surface of the core. Scrape sections from top to bottom, ensuring that the section surface is clean and flush to the section liner.
2. Place section in the core tray. Make sure the section is oriented blue endcap us, and is flush against the red benchmark (Figure 2).

Note: If a Whole-round sample (predominantly IW's) has been taken from the end of section (indicated by a yellow end cap), a foam spacer needs to be placed behind the section half. Whole-round samples are predominantly 5 or 10cm in length; the foam spacer MUST match the given length of the sample taken.

1. Adjust the section so that it is parallel to the benchmark
2. Make sure the white, grey, and black standard, as well as the ruler is clean and mud free
3. Click START. The Section Information screen is displayed (Figure 3).

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Figure 3. SHIL Section Information window

1. Place the cursor in the SCAN field and scan the section label. SAMPLE ID and LIMS ID automatically fills. These ID tags contain information on expedition, site, hole, core, section number and length.

Additional entry field options are the LIMS and MANUAL tags.

1. Select the appropriate values from Image Type, Wet/Dry and Condition located on the far left. Values chosen will be dependent on material scanned. Once set, values will remain as default.

Image Type:

• Section Imaging: Used for section halfs, predominantly sediment cores
• 360 Imaging: Used for hard-rock pieces

Note: Selecting 360 Imaging, intializes Imaging Control, allowing a user to select the angle of rotation. For more information see section below.
Wet/Dry:

• Soft Sediment: Used for sediment cores
• Dry-Hard Rock: Used for dry Hard-rock pieces
• Wet-Hard Rock: Used for wet Hard-rock pieces
• Not applicable: ??

Condition:

• Pristine: Used for cores which have just been split
• Sampled-Altered: Used for cores which have either been sampled, or altered in anyway.

Note: Natural alteration within the core material, does not qualify as a Sampled-Altered condition.


Note: To scan a Working section half, open the MANUAL tab. Click the Section Half drop box and Select W (Figure 4). To return to scanning Archive halfs, the Section Half value will have to be reset. Open the MANUAL tab, click the Section Half drop box and re-select A. 
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SECTION HALF IMAGE LOGGER (SHIL)

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Author:

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E. Fisher

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Reviewer(s):

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W. Mills, TOP Team Tethys

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Editor(s):

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Management Approval (Name, Title, Date):

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W. Mills (Lab Officer)

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Audience:

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Scientists, Technicians

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Previous Versions:

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1/22/2014, 8/15/2013

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Current version:

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V375 | V371T | July 2017

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Revised:

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T. Cobb, L. Crowder, C. Peng

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Domain:

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System:

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Section Half Image Logger

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Keywords:

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Image, Section Half

INTRODUCTION

This guide is designed to help the scientists use the Section Half Image Logger (SHIL) to image core sections, upload the image data to LIMS, and retrieve image data from LIMS. The SHIL takes digital images of the flat face of a split section or the surface of whole round hard rock cores using a line scan camera.
***Please have a technician give you an overview before using this instrument***
*PLEASE DO NOT TOUCH THE CAMERA or LEAN ON THE TRACK*

Section Half Imaging Procedure

Preparing the Section

• Optional: Once cores are split, use a spatula or glass slide to clean the surface of the core to remove any smearing caused by splitting. (It is up to the scientist to determine if this needs to be done.)
• Dab not wipe off excess moisture/mud and make sure ruler is clean!
• Place the section half on the holder with the BLUE end cap against the RED stop at the forward end.
• Rotate the section so that the surface is level with the ruler and perpendicular to the axis of the camera lens. Often the sample will have warped, so make sure the other end is level also. Be aware of badly uneven surfaces. If the sample is raised too high, it will push above what the light is covering making the raised part of the sample appear as a shadow. 

Start Imaging Application

Click the IMS-SHIL icon on the desktop (Figure 1) and wait for the program to Initialize. The process will include initializing the camera and moving the track into the "Home" position.

Image RemovedFigure 1. SHIL Desktop Icon

Click the START button on the main SHIL user interface (Figure 2). 

Image RemovedFigure 2. Main SHIL User Interface Window

Enter Sample Information

The Sample Information screen (Figure 3) will appear. 

Image RemovedFigure 3. SHIL Section Information window

Make sure that you have set the images attributes in the panel on the left side:

• Image Type: Select Section Imaging for split cores or 360 Imaging for whole round cores. When you select 360 Imaging, the 360 Imaging control will become available where you will select the angle of rotation. See 360° Imaging Section.
• Wet / Dry: This is for the hard rock folks who like to take images of the outer surface either Wet or Dry (set accordingly). For everything else, just select Soft Sediment or Not Applicable.
• Condition: Select Pristine for cores just split or select Sampled-Altered if you have sampled and/or otherwise mucked around with the core.

Once you set these values they will default to the previous values until changed.

Scan section (half) barcode label, make sure cursor is in the SCAN box.

No scanner or label? Select the tab marked LIMS and select you section's ID from the list boxes or use the MANUAL tab and enter the values by hand (not recommended).

Confirm Label, LIMS and physical length are within 2 cm of each other. If not, ask WHY?
Maybe there was some section expansion, whole round sample taken, or a mistake??

By default the instrument is set for imaging the archive half and will not allow you to scan a working label. If you want to take a picture of a working half you need to go to the MANUAL tab and select W (working) into the Section Half label (Figure 4). Once you have selected W (working), you will not be able to scan an archive half; in order to do that you need to go back into the MANUAL tab and re-select A (archive). 

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Figure 4. SHIL MANUAL Section Information window
If a whole round sample was taken (IW or MBIO), place whole round spacer where this sample was taken.

1. Click

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1. TAKE A PICTURE (Figure 5)

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Image AddedImage Removed
Figure 5. TAKE A PICTURE button
During the imaging process the Image DAQ screen

1. The imaging assembly moves to the bottom of section. A line scan image, will be acquired (Figure 6)

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Image RemovedFigure 6. Image DAQ window

The window at the top shows the current image frame and the construction of the full image, and the graph at the bottom displays the RGB data taken from a stripe down the middle of the image.

If the DROP LINES indicator is lit (orange), notify the technical staff.  The Acquisition Error indicator usually lights just at the end of the image and that’s OK but if it lights before then, we have a problem.  Again, notify the technical staff.

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Figure 6. Line scan of section
Note: If the Dropped Lines (located in the far left corner) indicator is orange, contact the PP or Imaging technician.
10) After the scan is complete, the Image Crop window is displayed.
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Figure 7. Image CROP window 

1. Check the position of the

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1. Green crop lines

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1. , using the Show Top of Image and

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1. Show Bottom of Image buttons.

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1. The cropped image should include the full section length and the additional foam spacer (if applicable). The ruler or red benchmark should NOT be included within the image.
2. Click Crop Image.
3. Click Save Image to save or Discard Image to delete.

Note: If the VCD (Visual Core Description) auto print is enabled, an image of the section half will be automatically printed. If you would like more information on this feature, see the Core Description technician.

1. All instrument data are stored in C:\DATA\IN.
2. Data is automatically uploaded to the LIMS database, and is available to view on LORE and LIVE. If data is not instantly visible, please contact the PP or Imaging technician.
3. Upon upload, data is moved to C:\DATA\Archive. If upload is unsuccessful, data is automatically moved to C:\DATA\Error. Please contact the PP or Imaging technician is this occurs.

Uploading Data to LIMS (COPY FROM SHMSL)

360° Imaging

1. Remove the section half scanning tray, and replace it with the Whole-round (WR) assembly.

Note: The WR assembly

When happy with the crop box location, click/touch CROP Image (Figure 8). The display will change to show the cropped image and the Save Image button (Figure 9) will be enabled. 

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Figure 8. Crop Image button

Click Save Image and you are finished! Image files are stored in 'C:\Data\in', and the Section Information window will be displayed to repeat the process for the next section.

 Image RemovedFigure 9. Save Image button

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If the VCD auto print is enabled (Figure 10), a sheet with the current image will be automatically print. Core Describers can use this sheet as a base for their descriptions.

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Figure 10. Set VCDS Parameters window

 Uploading Image To Lims

To upload the images into the database MegaUploadaTron must be running in background. If not already started do the following:

1. On the desktop, click the MUT icon (Figure 11).
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Figure 11. MUT icon

2. The following window (Figure 12) will appear:

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3. Check Automatic Upload in the lower right hand corner and then click the minimize window and MUT will run in background. The uploaded data will be moved from 'C:\Data\in' to 'C:\Data\archive'

Retrieving and Viewing Images from LIMS

1. LORE
   1. Go to LORE Reports at http://web.ship.iodp.tamu.edu/LORE/ .
   2. Under Select Report, choose Images > Core Section (LSIMG).
   3. Under Hierarchy Search, specify Expedition, Site, Hole, Core and Section image(s) to retrieve.
   4. Click View Data or Batch download linked files and specify if you want the uncropped or cropped .jpg image.
2. LIVE
   1. Open LIVE at http://web.ship.iodp.tamu.edu/LIVE/ .
   2. Click Template to choose the viewing options for the available templates.
   3. Click Exp, Site and Hole to view a drop-down list of available holes, and select a hole.
   4. Select the appropriate template (e.g. PP_LSIMG_SHMSL) , and then click View Data to view SHIL images in the LSIMG column.
   5. Click on any section in the Recovery column to zoom in on the SHIL image.
3. LSIMG QAQC
   1. Open LSIMG QAQC at http://ship.iodp.tamu.edu/QAQC/
   2. Click Exp, Site, Hole, Core to select the appropriate images
   3. Click View Report to generate the report
   4. A list will populate with any errors showing the exact section

Whole Round 360° Imaging Instructions

The SHIL also can be used to image the external surface of whole round hard rock cores in order to assemble a 360° composite image of the whole round. Using the custom whole round scanning tray, the whole round core surface is imaged four times at the 0°, 90°, 180°, and 270° orientation from the splitting line. The Imaging Specialist will download the images and assemble a composite image from the four scans and upload the composite separately.

Sample Preparation

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has 0°, 90°, 180°, and 270° markings

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, which will click and lock

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in place for each respective orientation.

1. Place the whole-rock section (in a split liner section with the whole round core ) on the tray auxillary rack below the SHIL and align the top with the 0cm on the ruler on the tray.
2. Remove the 0° aluminum strip and one from either side , in addition to two side pieces, from the scanning tray. Move Place the dry, oriented pieces into the scanning tray keeping their offsets as close as possible and align the splitting line with the 0° orientation (Figure 13).
3. Replace the non-zero aluminum strip strips and rotate the tray so that the 0° position is up, facing the camera.
4. Loading of the scanning tray can also be done elsewhere, such as the splitting room, and the tray carried over to the SHIL.

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  Figure 13. Alignment blocks position for whole round imaging

Enter Sample Information

1. Click START and the SHIL Section Information screen (Figure 3) will appear.
2. Scan the section barcode from the endcap.
3. Select the 360 Imaging type and the default quadrant will be 0°. Select Dry-Hard Rock. Click TAKE A PICTURE.
4. When the scan is finished, the image cropping window will open. Crop the image along the core liner and save it.
5. The whole round rotation window will open and the rotation angle will default to the next quadrant, in this case, 90°.
6. Replace the aluminum strip and rotate the tray to the next position, remove the aluminum strip facing up. Ensure that the rotation angle setting in the window is that same as on the tray. Click TAKE A PICTURE.
7. Continue the cropping, rotating and scanning process until all quadrants are complete. Once the images are uploaded to the database, the Imaging Specialist will create the 360 composite image and upload it to the database. If an image needs to be discarded, the software returns to the main screen and the user will need to start over, however, the user can select which quadrant to start on.

Archive Versions

1. Follow steps 5- 13 from the Making a Measurement section above.
2. Repeat this process for each orientation: 0°, 90°, 180°, and 270°. The Imaging Specialist will download the images and assemble a composite image from the four scans and upload the composite separately.

Image Added   Figure 13. Alignment blocks position for whole round imaging