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• Camera
  • 3CCD (charge-coupled device) line scan camera: JAI model CV107CL
  • Macro lens: AF micro Nikkor 60 mm (1:2.8)
• Light system
  • High-current line lights: Advanced Illumination model LL068
  • Power supply: 24 V/6 A
  • Current source: model CS420-0103 constant (modified)
• Linear encoder: Newall 2 µm/72 in. model SHG-TT
• Motor system
  • Motors: Galil model BLM-N23-50-100
  • PCI controller card: model DMC-1846
  • Motor amplifier: model AMP-19520
  • Breakout board: ICB-90044-M 44-pin
  • Power supply: CPS 56V/12A
  • Connectors for motor extension cords: AMP 4-pin connectors (172167-1 male, 172159-1 female)
• Robot modules: NSK 2-meter model XY-HRS200-F06246
• PC Workstation
  • NI frame grabber card model PCIe-1429
  • NI camera link I/O extension board

Software

data are collected using the Operates with LabVIEW 10.0 application.

Maintenance

Before taking images make sure the lights and camera are calibrated properly. See section Light Array Setup and Camera Calibration for instructions on procedures.

Instrument Settings

Image Capture Motion Setup

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General Camera Setup

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General Camera Setup fixed Settings

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Sample Preparation & Imaging

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If the surface of the archive half is not even rough use a flat spatula to provide a "clean" surface for imaging to better reveal layering and structures. Sediment cores should be imaged as soon as possible after splitting and scraping are completed to minimize color change through oxidation and drying.

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Rock pieces should be dry and individually rotated such that the split face is approximately perpendicular to the axis of the camera. The lights and lens aperture are configured to give consistent illumination and focus to effectively image rubble bins.
For 360 Imaging of hard rock cores refer to Appendix X, the section 360 Imaging of Hard Rock.

Loading Section

1. Pick up section half and place in the track loading area with the blue end cap forward against the color block. Make sure the section the section is pushed all the way against the block so the end cap is lined up with 0cm on the ruler.
2. Bring the endcap for the section to the SHIL workstation for entering sample information.
3. If the section has a whole round sample taken, denoted by a yellow bottom endcap, place a  split styrofoam spacer at the end of the section. Cut the styrofoam to same length of the sample taken and write letters on the styrofoam to indicate the type of the sample taken. For example a 5cm Interstitial Water whole round sample taken. A 5cm styrofoam spacer with 'IW' written on it would be placed at the bottom. Once a spacer has been made it can be used over the course of the expedition for applicable section halves.

Launch IMS Application

First 1. First open the IMS Application 'SHIL' on the desktop.(Figure X)

IMS will open and test communication with the  instruments, reads configuration files, and homes the instrument . After successful initialization the main IMS

2. At launch, the program begins an initialization process:

• Testing instrument communications
• Reloading configuration values
• Homing the pusher arm of the motion control system.

3. After successful initialization, two Two windows will appear: The ' IMS Control Panel on the left and the measurement window along the top of the screen. FIGURE (XX)

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• Decimate Interval: The interval that sets the recorded offset along the length of the core. This value can be set between 1 - 2.9 cm

• Stripe Width: Centered in the middle of the core, this determines the width across the core that will be used to calculate RGB data. This is typically set to 2cm. While the value can be changed higher or lower it is commonly at 2 cm. The advantage is this width provides enough material to not exaggerate small disturbances but rather provides RGB data representative of the bulk lithology.
• Mean or Midpoint: Can choose how RGB is calculated for the interval. Interval mean calculates the mean RGB values over the interval. Interval Midpoint uses the RGB value at the center of the interval. This is typically set to Interval Mean.

Adjust RGB Settings

1.Go to Instruments > General Setup

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2. Adjust values in the 'RGB Data' setting controls. The 'General' and 'Dropped Lines Warning Threshold' should not need to be adjusted. If something needs to be altered talk to the programmers and ALOs.

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3. Click 'Accept' to save values. If select 'Cancel' the values will revert back to prior settings and the window will close. 

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Camera Speed

Camera Speed is calculated during the calibration procedure. The camera speed set must be lower than the speed determined by the calibration or else the camera will start 'dropping lines'. Dropped lines means the camera is moving too quickly to calculate the RGB and offsets at the bottom of the core will return values of '0'.

Adjust Camera Speed

1.Go to DAQ > Image Capture Setup

Start A Measurement

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1. Image Type: 'Section Imaging' or '360 Imaging'. For instructions on the 360 imaging refer to XXXXXX
2. Wet/Dry: Indicates the type of the material being imaged
3. Condition: 'Pristine' or 'Sampled/Altered'. Sampled/altered could include imaging the working half or a highly disturbed section. Most instances should be pristine.
4. 360 Imaging: This area is grayed out unless '360 Imaging' Image Type is selected. For instructions on the 360 imaging refer to XXXXXX

2. The Image Scan Setup window appears. There are four settings in this window:

• Speed: This is the speed in cm/sec the camera moves while measuring the section. This speed must be set lower than the speed determined by the Camera Calibration.
• Acceleration: The rate in cm/sec the camera ramps up to when not measuring a section.
• Deccelaration: The rate in cm/sec the camera will slow down when not measuring a section
• Start Position: This is the position the imaging begins. Note it will be a negative number. The top of the core starts at 0cm in order to image the standard gray-scale card in front of the core, that location will be negative

Start A Measurement

1.Click the green Start Button in the IMS Control panel.

2. The SHIL Section Information Window will pop up (FIGURE XX).

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3. The area on the left has four fields to define the condition of the sample measurement:

1. 1. Image Type: 'Section Imaging' or '360 Imaging'. For instructions on the 360 imaging refer to XXXXXX
   2. Wet/Dry: Indicates the type of the material being image
   3. Condition: 'Pristine' or 'Sampled/Altered'. Sampled/altered could include imaging the working half or a highly disturbed section. Most instances should be pristine.
   4. 360 Imaging: This area is grayed out unless '360 Imaging' Image Type is selected. For instructions on the 360 imaging refer to XXXXXX

        Select the conditions appropriate for the section half.

4. There are three ways to enter sample information into IMS:

• Barcode (most common): Put cursor in the 'Scan' box. Use the bar-code scanner to scan the label on the end-cap. The sample information will parse into the 'Sample ID', 'LIMS ID', and Length fields.
• LIMS Entry: Select the 'LIMS' tab at the top of the window. Navigate through the hierarchy to select the correct, expedition, site, hole, core, and section. Length information will automatically populate when the section is selected. 
• Manual Entry: Select the 'Manual' tab at the top of the window. Click in the box and manually type sample information into the box.

5. Click Take a Picture. The lights will turn on and start moving down the length of the core. In the IMS interface the sample information will go away revealing the measurement windows. The image and RGB data is displayed and updates as the measurement progresses. 

6. When the measurement is complete, the camera lights will turn off and move back to the home position on the track.

7. The Image Crop window pops up. An image should be cropped to include all material and the inner edge of the end-cap. RGB data will exclude data outside of the Crop area. The green box is the IMS estimation of the crop area. Click and drag the green lines to adjust the cropped area  at the top,  bottom, and sides of the image. Tools in this window include:

• Show Bottom of Image: Takes image down to illustrate the bottom of the image and crop box.
• Show Top of Image: Brings image up to show the top of the image and crop box.
• Crop Image: Crops the image to show only image inside of the green box.                   
• Uncrop Image: Will undo a crop and allow user to re-adjust the green crop box.
• Save Image: Saves the image, RGB data, and writes the upload files
• Discard Image: Does not save the image or RGB data.

The Image crop restricts users to limit adjustments to 2cm or less. The message box will indicate if the crop has exceeded allowable limits and the 'WRND Info' message box indicates if and where any whole round samples were taken from the section. If the image needs to cropped by more than 2cm check the correct section/end cap is being uses, a styrofoam spacer is not missing, and the curated length. Cores can expand so if the curated length is incorrect, talk to the curator on shift to correct the length. Note this will also create a need for the curator to re-calcuate depth of the hole. If the error is in the curated length of the core a user can check the 'override crop restriction' button to crop the image and upload the data.

8. Click Crop Image when satisfied the green box will capture the entire image.

9. If satisfied with the image click Save Image. If the image needs to be re-imaged click 'Discard Image' and re-start the measuring process.

10. The 'Image Crop' window will go away and the 'Sample Information' window will appear again.

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Uploading data

Data Structure

Two files are uploaded to LORE via MegaUploadaTron (MUT):

1. .roi file : Contains callouts to the uncropped TIFF , uncropped JPEG, and cropped JPEG images. The images are linked files in LORE as Images > Core Closeup (LSIMG).
2. .RGB file : Contains the red, green, and blue values calculated for each offset. The information is in LORE under Physical Properties > RGB Channels (RGB).

The files are independent of eachother, both do not need to be present in order to upload, and often appear in MUT at different times.

MUT and .ini file

Be aware uploaded files have a callout for the .ini file. There is only one .ini file and the files will callout the .ini file currently present at the moment of uploading to LORE. If changes are made to settings that will alter the .ini and there are files piled up that have not uploaded to LORE, those files will upload the current .ini file, not the .ini file settings used for measurement. This implies files could have incorrect .ini files if rapid changes are made and users are not being careful.

How to Upload data

1. Open up MUT (FIG XX). Use LIMS Applications password to login.
2. Set 'Project' at the bottom of the screen to either the current expedition or '999' if performing tests.
3. Files with checkmarks in the right column will upload. A green arrow in the COLUMN XX indicates it is in process of upload. A purple question mark indicates the file is not recognized by MUT. This could be due to an incorrect sample name or only one file being in the 'IN' Folder.
4. Check 'Automatic Upload'. At the refresh interval the files will upload to LORE.
5. After files are successfully uploaded they move from 'data > in' to the 'data > archive' folder. When the files move they will not longer appear MUT. If a file was unable to upload it will move from 'data > in' to 'data > error' and two new buttons will appear in MUT saying 'Show Error' and 'Show Error Files'.

MUT Configuration

File Path

The file path MUT should look for files to upload is C: > data > IN. IMS writes upload files to C: > data > IN, so ensure the filepath is set correctly. Note the uploaded files are written directly into the 'IN' folder. Images are not directly uploaded and are written to C: > data > IN > Images

Active Analyses

In MUT the 'active analyses' should be set to Linescan Image, Processed RGB channels, and Whole-round Linescan. Linescan Image and Processed RGB Channels are for section half measurements. The Whole-Round Linescan Image is for 360 Imaging of hard rock cores. All three analyses should be set in the 'Active Uploaders' Column. Note it is ok for analyses to be in the 'Active Uploaders' even if MUT at that instrument host does not generate those files.

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Auxillary data Produced

The SHIL has the capability to produce two additional file types at the scientist's request:

1. Hi RES RGB
2. VCD-S

These files appear in separate folders in C: > data > in

Hi RES RGB: This file default is turned off and can be turned on in Instruments > General Setup (FIG XX). The Hi-Res RGB file reports a Red, Green, and Blue value for each line of pixels down the length of the core. 1cm is 200 lines of pixels so a 150cm core will yield approximately 30,000 lines of data depending on the exact crop length. The file is not currently uploaded to the database and is instead copied to data1 at the end of the expedition. The files can be put on the server for scientist access to a convenient, shared location such as UserVol

VCD-S: The SHIL can preserve a digital copy of the VCD-S that is printed out. If a scientist wants to keep a digital copy of the scratch sheet turn on the feature in "XXXXXXXX". Files are then written to C: data > in > VCD-S. These files are not uploaded to LORE and should be put in

        Select the conditions appropriate for the section half.

       4. There are three ways to enter sample information into IMS:

                  Barcode (most common): Put cursor in the 'Scan' box. Use the bar-code scanner to scan the label on the end-cap. The sample information will parse into the 'Sample ID', 'LIMS ID', and Length fields.

                  LIMS Entry: Select the 'LIMS' tab at the top of the window. Navigate through the hierarchy to select the correct, expedition, site, hole, core, and section. Length information will automatically populate when the section is selected. 

                  Manual Entry: Select the 'Manual' tab at the top of the window. Click in the box and manually type sample information into the box.

       5. Click 'Take a Picture'. The lights will turn on and start moving down the length of the core. In the IMS interface the sample information will go away revealing the measurement windows. The image and RGB data is displayed and updates as the measurement progresses. 

       6. When the measurement is complete, the camera lights will turn off and move back to the home position on the track.

       7. An 'Image Crop' window pops up. An image should be cropped to include all material and the inner edge of the end-cap. RGB data will exclude data outside of the Crop area. The green box is the IMS estimation of the crop area. Click and drag the green lines to adjust the cropped area  at the top,  bottom, and sides of the image. Tools in this window include:

                   Show Bottom of Image: Takes image down to illustrate the bottom of the image and crop box.

                   Show Top of Image: Brings image up to show the top of the image and crop box.

                   Crop Image: Crops the image to show only image inside of the green box.                   

                   Uncrop Image: Will undo a crop and allow user to re-adjust the green crop box.

         The Image crop restricts users to limit adjustments to 2cm or less. The message box will indicate if the crop has exceeded allowable limits and the 'WRND Info' message box indicates if and where any whole round samples were taken from the section. If the image needs to cropped by more than 2cm check the correct section/end cap is being uses, a styrofoam spacer is not missing, and the curated length. Cores can expand so if the curated length is incorrect, talk to the curator on shift to correct the length. Note this will also create a need for the curator to re-calcuate depth of the hole. If the error is in the curated length of the core a user can check the 'override crop restriction' button to crop the image and upload the data.

      8. Click 'Crop Image' when satisfied the green box will capture the entire image.

      9. If satisfied with the image click 'Save Image'. If the image needs to be re-imaged click 'Discard Image' and re-start the measuring process.

     10. The 'Image Crop' window will go away and the 'Sample Information' window will appear again.

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Data Structure

Two files are uploaded to LORE via MegaUploadaTron (MUT):

1. .roi file
2. .RGB file

.roi File: Contains callouts to the uncropped TIFF , uncropped JPEG, and cropped JPEg images. The images are linked files in LORE as Images > Core Closeup (LSIMG).

.RGB File: Contains the red, green, and blue values calculated for each offset. The information is in LORE under Physical Properties > RGB Channels (RGB).

The files are independent of eachother, both do not need to be present in order to upload, and often appear in MUT at different times.

MUT and .ini file

Be aware uploaded files have a callout for the .ini file. There is only one .ini file and the files will callout the .ini file currently present at the moment of uploading to LORE. If changes are made to settings that will alter the .ini and there are files piled up that have not uploaded to LORE, those files will upload the current .ini file, not the .ini file settings used for measurement. This implies files could have incorrect .ini files if rapid changes are made and users are not being careful.

How to Upload data

1. Open up MUT (FIG XX). Use LIMS Applications password to login.
2. Set 'Project' at the bottom of the screen to either the current expedition or '999' if performing tests.
3. Files with checkmarks in the right column will upload. A green arrow in the COLUMN XX indicates it is in process of upload. A purple question mark indicates the file is not recognized by MUT. This could be due to an incorrect sample name or only one file being in the 'IN' Folder.
4. Check 'Automatic Upload'. At the refresh interval the files will upload to LORE.
5. After files are successfully uploaded they move from 'data > in' to the 'data > archive' folder. When the files move they will not longer appear MUT. If a file was unable to upload it will move from 'data > in' to 'data > error' and two new buttons will appear in MUT saying 'Show Error' and 'Show Error Files'.

MUT Configuration

File Path

The file path MUT should look for files to upload is C: > data > IN. IMS writes upload files to C: > data > IN, so ensure the filepath is set correctly. Note the uploaded files are written directly into the 'IN' folder. The images are recorded

Active Analyses

In MUT the 'active analyses' should be set to Linescan Image, Processed RGB channels, and Whole-round Linescan. Linescan Image and Processed RGB Channels are for section half measurements. The Whole-Round Linescan Image is for 360 Imaging of hard rock cores. All three analyses should be set in the 'Active Uploaders' Column. Note it is ok for analyses to be in the 'Active Uploaders' even if MUT at that instrument host does not generate those files.

Image Removed

Auxillary data Produced

The SHIL has the capability to produce two additional file types at the scientist's request:

1. Hi RES RGB
2. VCD-S

These files appear in separate folders in C: > data > in

Hi RES RGB: This file default is turned off and can be turned on in Instruments > General Setup (FIG XX). The Hi-Res RGB file reports a Red, Green, and Blue value for each line of pixels down the length of the core. 1cm is 200 lines of pixels so a 150cm core will yield approximately 30,000 lines of data depending on the exact crop length. The file is not currently uploaded to the database and is instead copied to data1 at the end of the expedition. The files can be put on the server for scientist access to a convenient, shared location such as UserVolVCD-S: The SHIL can preserve a digital copy of the VCD-S that is printed out. If a scientist wants to keep a digital copy of the scratch sheet turn on the feature in "XXXXXXXX". Files are then written to C: data > in > VCD-S. These files are not uploaded to LORE and should be put in data1 at the end of the expedition. The files can be put on the server for scientist access to a convenient, shared location such as Uservol.Uservol.

360 Imaging Hard Rock

The SHIL 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. Oriented rock pieces are imaged after they have been binned and the structural scientist has marked the split lines on the pieces. 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

Maintenance

Instrument Preparation

Preparing the track system for imaging cores requires adjusting the position of the lights and barcode imager for optimal quality and calibrating the system by adjusting camera settings. The position of the lights and barcode imager, once set, should be stable throughout an expedition. The technical staff will calibrate the camera settings (SHIL: Camera Configuration AUG) and light array (SHIL: Light Array AUG) whenever the camera or light sources have been repositioned or changed.

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