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Petrographic Image Capture and Archiving Tool (PICAT):User Guide

Introduction

This system was designed to digitally photograph Petrographic Thin Section samples, capturing the entire slide in an efficient manner in both cross-polarized and single (plane)-polarized states. Microscopes are commonly used for imaging thin sections, but they do not have a field of view wide enough to image the entire specimen. A whole specimen view is needed to provide a map (or guide) showing the relationship of the entire sample to specifically captured higher-detailed regions. The most common method of obtaining a full specimen image has been with the use of a modified flat bed or film scanner. Whereas these methods have been successful in some instances, they are cumbersome, slow, and tedious when the entire workflow process is considered.
The PICAT (Petrographic Image Capture and Archival Tool) provides an easy and versatile imaging process that captures a publication-quality image (8 x 10 inches at 300 DPI) within seconds rather than minutes. When coupled with a workflow-optimized software package, the time, effort, and training needed to capture thin section image data is significantly reduced. The live image displayed on a computer monitor instantly shows errors in exposure, focus, color balance, and cropping. The operator is confident the image is correct before rendering the sample to digital state.

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Available on request from the photographers, this is a Cannon-supplied utility that provides drivers and a software interface for tethering a camera to a computer. Note that this must be installed from original Cannon CDs, as the updates available on the Internet require that the software already be installed.
This utility allows full control and settings of the camera, though typically only the photographers will be involved in the more advanced and esoteric settings. This software is what defines the capture location of images (what directory they will be written to) and in our current configuration creates the date-based subdirectories as well.

Adobe Bridge

This is installed by default when Adobe PhotoShop is installed. This software is not required for the standard workflow and essentially serves as a branching point for those who wish to edit software directly in Photoshop or some other software before upload.

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The software is the only application that logs data to the TSIMAGE analysis. TSIMAGE analysis is defined as follows:

When deploying, the only setting that needs to be changed is the publish location and default server.

Standard Operation

The following sections describe the standard procedure for imaging and cataloging a thin section aboard the JOIDES Resolution. Notations are made where alternate workflows may be substituted, but such workflows are not described in this document. Standard operation includes

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1. Start the computer and navigate to the Windows desktop.
2. Ensure that the power strip under the monitor and the light power source are turned on.

1. Remove the lens cap from the camera.

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1. Select the type of specimen holder (for instructions on changing to the X/Y stage holder see Hardware > Specimen Holders > Installing the X/Y Style Holder).
2. Load the thin section slide into the recessed portion of the tray. Slide the tray in and out as needed.

1. 
   

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   Two polarization filter holders, one above the tray and one under it, are coupled by a magnetic linkage. The entire assembly can be rotated out of the way as needed. The filters can be rotated independently or together (the former by turning the polarizing \[bottom\] filter while preventing the filter holder from rotating, the latter by turning the white linkage knob).

   
   

1. Start the EOS capture software.

1. After startup click on the Live Image Preview button

1. A window shows exactly what the thin section image will look like.

1. If you are using the 65 mm macro lens, adjust the Macro (a zoom effect) setting on the side of the camera as desired.

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1. Adjust the filters at this point as follows:
   • Single-polarization mode: move the entire top filter assembly arm to the left (out of the optical view path).
   • Cross-polarization mode:
     1. Ensure that both filter arms are engaged (in the optical path).
     2. Turn the bottom polarizer while viewing the display on the monitor until a dark-field is achieved.
     3. Turn the friction wheel at the top filter plate to rotate both of the filters to view the effects and adjust the image as preferred.
   • As a matter of good practice check the dark-field and thus the cross-polarized state before the image is captured.
   • Refocus the image when switching polarization states, as the diffraction of light of the Analyzer filter and its subsequent removal affects the light path and focus.
   • If the camera is in auto-mode and is calculating the exposure properly, no further adjustment is needed.
   • If the camera is in manual mode, adjust the combination of aperture, shutter speed, and or ISO settings for the desired effect.
2. When the image on screen is deemed acceptable press the capture image button in the cannon EOS software (the large circle).

1. A preview window displays the captured image.

1. The preview window can be ignored/closed without affecting anything. If Adobe Bridge is already loaded, its icon will flash in the taskbar (burnt-orange square with the letters "Br"). If Bridge is not already loaded, it will open automatically after a few moments.
2. No action needs to be taken in Bridge at this point. Close/minimize Bridge at any time. The camera automatically creates and saves the JPEG and RAW files.

Processing and Uploading the Image

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1. Start the IODP Image Capture software and login using LIMS username and password.

1. After software log-in, a list displayed the upper left corner shows the images that were just taken (the JPG files specifically). Click on one of the images to select it for processing.

1. Next, associate this image with a sample:
   • Click on the Browse button.

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     Select a site and hole to select a sample (default type = Thin Section \[TS\]).

     
     

   • Select a sample from the list and go back to the main window (close/minimize/ignore sample browser window; it will open back to same location).

1. Once a sample has been selected, the sample text_id field populates and a new label is generated in the top right that indicates the new filename, based on the sample selected. If multiple pictures were taken of the same sample, the filename is appended with _2, _3, _4, etc., based on the number of previous images taken and processed. Fill out the rest of the values based on the conditions when the image was taken.

1. Click Upload to open a window indicating the upload status. When the upload process is finished another dialog box will appear indicating that the process is complete

1. Once uploaded, the selected image is removed from the pending uploads list and loaded into LIMS. Continue processing additional images.
2. After upload, the images are moved to the archive folder (at the same level as the capture folder). Under the archive folder are 3 subfolders:

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1. Rotate the camera height adjustment wheel to give at least 12 inches of clearance between the camera lens and the top filter assembly.

1. Lift the top filter assembly upward until it disengages from the stage plate under it. Keep the unit oriented in the normal position so filter parts do not fall out.

1. Slide the specimen holder out and begin loosening the bolts holding in the slide rails on the right side. Remove the bottom two bolts and loosen the tip bolt.

1. Rotate the right rail out of the way

1. Remove the X/Y stage from the box and prepare to install it.

1. Note the holes in the stage plate. These are what the X/Y stage will attach to.

1. Place the X/Y stage in position and attach it with screws threaded into the holes.

1. Once the stage is located, place a slide in it and use the X and Y adjustment knobs to set the final position.

Filter Module and Friction Wheel

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