Petrographic Image Capture and Archiving Tool (PICAT):User Guide
Author: | W. Crawford, C. Bennight |
Reviewer(s): | J. Beck |
Management Approval (Name, Title, Date): | D.J. Houpt |
Audience: | Scientists |
Origination date: | 08/24/10 |
Current version: | DRAFT (1) 09/06/10 |
Revised: | V1.1 | 1/6/2014 (IODP-II) |
Domain: | Imaging |
System: |
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Keywords: |
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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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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
- Starting up the system
- Acquiring an image
- Processing and uploading an image
- Shutting down the instrument
Starting up the system
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.
3. Remove the lens cap from the camera.
Acquiring an Image
1. Select the type of specimen holder (for instructions on changing to the X/Y stage holder see Hardware > Specimen Holders
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> 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.
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3. Two polarization filter holders,
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one
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above
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the
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tray
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and
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one
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under
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it,
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are
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coupled
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by
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a
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magnetic
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linkage.
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The
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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).
4. Start the EOS capture software.
5. After startup click on the Live Image Preview button
6. A window shows exactly what the thin section image will look like.
7. If you are using the 65 mm macro lens, adjust the Macro (a zoom effect) setting on the side of the camera as desired.
The lens in this camera has a fixed focal point; to bring the image into focus, adjust the distance of the camera from the sample using the hand crank attached to the camera arm.
8. 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:
- Ensure that both filter arms are engaged (in the optical path).
- Turn the bottom polarizer while viewing the display on the monitor until a dark-field is achieved.
- 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.
9. When the image on screen is deemed acceptable press the capture image button in the cannon EOS software (the large circle).
10. A preview window displays the captured image.
11. The preview window can be ignored/closed without affecting anything. If Adobe Bridge is already loaded, its icon will flash in
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the taskbar (burnt-orange square with the letters "Br"). If Bridge is not already loaded, it will open automatically after a few moments.
12. No action needs to be taken in Bridge at this point. Close/minimize Bridge at any time. The camera automatically creates and
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saves the JPEG and RAW files.
Processing and Uploading the Image
1. Start the IODP Image Capture software and login using LIMS username and password.
2. 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.
3. Next, associate this image with a sample:
- Click on the Browse button.
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select
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(default
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- 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).
4. Once a sample has been selected, the sample text_id field populates and a new label is generated in the top right that indicates
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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
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conditions when the image was taken.
5. Click Upload to open a window indicating the upload status. When the upload process is finished another dialog box will
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appear indicating that the process is complete
6. Once uploaded, the selected image is removed from the pending uploads list and loaded into LIMS. Continue processing
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additional images.
7. After upload, the images are moved to the archive folder (at the same level as the capture folder). Under the archive folder are
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3 subfolders:
- JPEG
Anchor _GoBack - TIFF (tiffs are not generally created in the standard workflow)
- RAW
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These folders contain a hierarchy in the form of \\{Expedition}\\{SiteHole}\filename.ext of all the files (essentially, images are organized by type, expedition, and site-hole when stored in the archive folder). These images do not need to be backed up (as they are already in LIMS/ASMAN) but can be selected by the photographers, etc., for alternate archiving if desired.
Note: These images may be deleted at any time, without notice, by the technicians or other scientists. They will continue to be available via LIMS. A local copy can be saved as well.
Shutting Down the Instrument
1. Shut down the Cannon EOS utility if it is still running.
2. Place the lens-cap back on the camera.
3. Turn off the light, but not the power strip. This is important to ensure the fan cools the light while it is still hot. The power strip
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can be shut down 15 min after light has been turned off.
Safety
- There are no outstanding safety issues associated with operation of this instrument
- When maintaining this instrument the technician should be aware of pinch hazards associated with the extremely strong magnets used in the magnetic filter coupling assembly.
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To install the X/Y specimen holder, the rail on the right side of the specimen stage (when facing the filter module) is modified by removing the three Allen screws that attach the rails to the specimen stage. Once the screws are removed, the rail can be swung back to the right and stored aft. Although it is not necessary to remove the rail entirely, you may do so if you wish. Detailed instructions follow.
1. Rotate the camera height adjustment wheel to give at least 12 inches of clearance between the camera lens and the top
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filter assembly.
2. Lift the top filter assembly upward until it disengages from the stage plate under it. Keep the unit oriented in the normal position
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so filter parts do not fall out.
3. Slide the specimen holder out and begin loosening the bolts holding in the slide rails on the right side. Remove the bottom
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two bolts and loosen the tip bolt.
4. Rotate the right rail out of the way
5. Remove the X/Y stage from the box and prepare to install it.
6. Note the holes in the stage plate. These are what the X/Y stage will attach to.
7. Place the X/Y stage in position and attach it with screws threaded into the holes.
8. 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
The filter module is simple and robustly built. Other than routine cleaning and maintenance, having to disassemble and reassemble should occur on only rare occasions.
The top filter plate is milled to countersink the friction wheel and bearings into the plate itself. The filter ring is machined so that the polarizing filter nestles within the filter holder ring. This configuration reduces the overall thickness of the assembly to allow maximum lens clearance. When using the Canon 5x magnification, the focus distance between the specimen and the lens barrel is 41 mm. The clearance between the surface of the Analyzing Filter (top polarizer) and the lens barrel is 5 mm! Care must always be taken when rotating the Analyzer Platform out of the light path. THE IMPACT OF THE PLATE AND THE LENS BARREL IS REAL POSSIBLITY; PLEASE BE AWARE. Because of countersink configuration of the top polarizer plate, the bottom and the top filter plates are not exchangeable.
The polarizing filter on the bottom filter plate and filter holder ring is installed so the polarizing filter ring can be reached by fingers and turned in relationship to the bottom filter holder ring. This is how the operator achieves the cross-polarized state. The top polarizing filter is recessed in the filter ring, and the bottom polarizing filter is placed (backwards or upside down) so that the body of the filter extends above the filter holder ring. This allows for manual adjustment of the polarization state. Note also that the bearings, friction wheel, and filter holder ring are surface-mounted because clearances for rotation were not factors in the design of the lower filter plate. Because of the countersunk nature of the components of the top filter ring, dust can accumulate over time. Periodic cleaning with canned air or a directed flow of clean compressed air will help to ensure free rotation and a friction-reduced operation.
Because both the lower and the upper filter plates rotate in and out of the light path, motion stops were designed into the mechanism. Detent balls are installed in the mounting block, and each filter plate has a semicircular track and indentions to hold the plates over the light source and 90° of left or clockwise rotation. The lower plate is held in position by a shaft collar around the tube that protrudes through the mounting block. This collar keeps the lower filter plate assembly from falling out of the mounting block.
A swing pathway was milled for the lower filter plate and assembly and a mounting shaft was installed in the very back. This is machined for the elevator block to receive the filter module. There is a detent ball on the elevator block and a receiver depression on the module. When these are aligned and tightened the filter module will be square fore and aft to the alignment of the column itself.
When reassembling this unit and adjusting the collar in place, squeeze the lower plate to the block, which in turn compresses the detent ball. Then snug the collar to the block and tighten. Attempt to rotate the lower filter out of the light path and note the amount of effort required to do so. Use your judgment in determining whether the rotation is too loose or too tight and adjust the pressure/collar as necessary.
All that is required is that the lower filter plate depression stops pull up to the detent ball. Conversely, the top filter plate shaft is placed inside the lower filter plate tube. Gravity holds this in place; therefore, the plate to detent ball adjustment is automatic and no adjustment is necessary. The machine fit between the top filter plate shaft and the bottom filter plate tube is 1/2000 inch.
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No major maintenance is necessary on the detent balls or plates other than slight lubrication with petroleum jelly along the track path to lessen the etching effect, which the chrome detent ball will have on the softer aluminum material of the filter plates.
Wipe the shaft with a silicone lubricant occasionally. Do not lubricate with a product that might gum the assembly, or the shaft and tube might have to be disassembled and cleaned.
The mounting block is milled from solid aluminum and is maintenance-free except for dusting and cleaning.
Although mounting of the camera can be done improperly, leading to alignment problems, the filter module is simply installed and tightened and its alignment is assured.
Clean the polarizing filters with the same care as cleaning a lens. Begin with the least aggressive technique, such as a camelhair brush, followed perhaps by lens cleaner and fluid. Never apply friction to the glass before brushing with a camelhair brush to remove grit or particles. Be aware of substances that may be abrasive to the filter surface.
Disassembly of the Filter Module
Note the following when working with or disassembling the filter module:
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The friction wheel provides traction and transmission for rotation and coordination of the two filters, due to the compression of the O-ring of the friction wheel to the surface of the filter-holding ring. The friction wheel also secures the shaft, which passes through the top filter stage, to which half of the magnet coupler is attached.
CAUTION: LOOSENING THE SET SCREWS WILL RELEASE THE MAGNET, WHICH CAN CAUSE SERVERE PINCHING DAMAGE TO HANDS AND/OR POSSIBLE DAMAGE TO THE COUPING ITSELF. THESE ARE VERY POWERFUL MAGNETS. PLEASE EXAMINE AND UNDERSTAND BEFORE ATTEMPTING DISSASEMBLY.
The filter-holding ring and the filter is held in place by press fit, and the filter is easily removed from the holding ring by gentle pressure with the fingers. It is best to wear cotton gloves when handling the filters; otherwise removal of fingerprints from the glass filter will be required later on. The filter-holding ring is easily removed from the three bearings that secure it to the top filter plate.
Note that reinstalling the filter-holding ring into the top filter plate requires compression of the friction wheel O-ring with the surface of the filter-holding ring. Push gently with the filter-holding ring held level and then push the ring vertically into location. Take care not to pinch the O-ring and subject it to damage during reassembly.
The magnetic coupling when installed has a sizable gap between the magnets (5/8 inch or 16 mm). The gap between the magnetic couplings is set by the total length of the assembly of the friction wheel-shaft-coupling assembly attached to the lower filter plate. This assembly and subsequent total length is set by a collar attached to the bottom of the shaft on the underside of the lower filter plate.
_IMPORTANT: THE LOWER MAGNETIC COUPLING MUST NOT EXTEND ABOVE THE SURFACE OF THE SPECIMEN STAGE PLATE. IF THIS OCCURS, THE FIXED SPECIMEN SLIDE CARRIER WILL BE OBSTRUCTED, PREVENTING CENTERING OF THE IMAGE UNDER THE CAMERA. THE LOWER MAGNETIC COUPLING SURFACE IS APPROXIMENTLY ¼ INCH BELOW THE TOP SURFACE OF THE SPECIMEN STAGE PLATE._
As stated earlier, the magnetic couplings are very powerful and exert a force in rotation equal to 5-inch-pounds. The 16 mm gap weakens that force in order ease the movement of the top and bottom filter stage plates in and out of the light path. This also serves to lessen the downward pull (top filter plate) and upward pull (bottom filter plate) that introduce a frictional force that is harmful to the free synchronous rotation of the filter holder rings.
The "take home message" here is: assembly of the magnetic couplings with too small a gap is bad. Assembly of the lower magnetic coupling above the surface of the specimen plate is bad.