Petrographic Image Capture and Archiving Tool (PICAT):User Guide
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Author:
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W. Crawford, C. Bennight
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Reviewer(s):
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J. Beck
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Management Approval (Name, Title, Date):
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D.J. Houpt
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Audience:
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Scientists
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Origination date:
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08/24/10
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Current version:
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DRAFT (1) 09/06/10
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Revised:
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V1.1 | 1/6/2014 (IODP-II)
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Domain:
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Imaging
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System:
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Keywords:
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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.
Apparatus and Materials
Hardware
The PICAT thin section imager consists of the following hardware:
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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.
Apparatus and Materials
Hardware
The PICAT thin section imager consists of the following hardware:
- Kaiser Camera Stand and Photo Table
- System-V RGB Light with OSRAM HLX 12V 100W Bulb
- Canon EOS 5D Mark II Camera
- Lenses
- Canon MP-E 65 mm 1x–5x Macro Lens
- Cannon EP 100 mm IS Macro Lens
- B&W 95 mm Diameter Linear Polarizing Glass Filter Element (2)
- Custom Filter Module with Friction Wheel
- Specimen Holders
- HP LP3065 Wide Gamut 30 inch LCD Monitor
- HP xw4400 PC Workstation
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The software is the only application that logs data to the TSIMAGE analysis. TSIMAGE analysis is defined as follows:
Name | Order | Alias | Reportable | Optional | Description |
camera | 1 | Camera | T | T | Camera used to take the image |
iso | 2 | ISO Speed | T | T | ISO Speed (sensitivity) of camera |
aperture | 3 | Aperture | T | T | Aperture of camera (f-stop) |
shutter_speed | 4 | Shutter Speed | T | T | Shutter Speed |
focal_length | 5 | Focal Length | T | T | Focal length of lens |
date_taken | 6 | Date Taken | T | T | Date the photo was taken (from EXIF) |
macro | 7 | Macro Setting | T | T | Reduction in field of view due to macro lens setting |
polarization | 8 | Polarization | T | T | Polarization setting (none, cross, single) |
polarizationangle | 9 | Polarization Angle (cross-pol) | T | T | Polarization Angle (for cross-pol only) |
jpeg_filename | 10 | Jpeg Filename | F | T | Filename of closeup image |
jpeg_asman_id | 11 | Thin Section Image | T | T | Asman id of thin section image |
raw_asman_id | 12 | Raw Image | T | T | Camera RAW image file |
raw_filename | 13 | Raw Image Filename | F | T | Raw image original filename |
comments | 14 | Comments | T | T | Comments |
When deploying, the only setting that needs to be changed is the publish location and default server.
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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).
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3. Two polarization filter holders, one above the tray and one under it, are coupled by a magnetic linkage. The entire assembly can assembly can be rotated out of the way as needed. The filters can be rotated independently or together (the former by turning the polarizing the polarizing [bottom] filter while preventing the filter holder from rotating, the latter by turning the white linkage knob).
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11. The preview window can be ignored/closed without affecting anything. If Adobe Bridge is already loaded, its icon will flash in the 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 saves the 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. Under the Settings menu, select the Thin Section Mode.
Here you can also select the folders Image Capture will look for the images taken.
2. After software log-in, a the 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.
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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 the 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 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 appear In the comments field, enter the description from the Thin Section Request form and the name of the requestor (e.g. "Fossiliferous limestone. Jane Doe.")
5. 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
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6. Once uploaded, the selected image is removed from the pending uploads list and loaded into LIMS. Continue processing additional 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 3 3 subfolders:
- JPEG
- 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.
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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 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 so filter 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 two bolts and two bolts and loosen the tip bolt.
4. Rotate the right rail out of the way
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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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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 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.
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.
Accessories
The light source for the PICAT is a color head from Kaiser. It has to be run with one of the transformers from Kaiser. A halogen bulb is situated inside the color head, that might burn out (see specs of the bulb below). Open the head box where the black cooling grid is screwed in with 2 screws, pull out the bulb and replace it.
Website for replacement parts: https://kaiserfotous.com/products/dark-room/
Color Head for Enlarger | Transformer with Voltage Stabilization | Transformer |
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| CATALOG #: 204544 | CATALOG #: 204451 | CATALOG #: 204453 |
Equipped with dichroic interference filters, calibrated in desitometric units up to 180. The dials are indirectly illuminated. Continuously adjustable, illuminated density aperature up to 60 densitometric densities (= two aperature settings). Best possible light distribution due to special diffusor plate. Requires transformer 204451 or 204453 to operate. Items Include: | Output power: 100 W Dimensions: approx. 120 x 80 x 140 mm (4.7 x 3.1 x 5.5 in.) Available for 230 V, 240 V, and 120 V Fuse: 1,6 AT (230/240 V) / 2,5 AT (120 V) 4451: Transformer with starting-current limitation and electronic voltage stabilization. For compensation of voltage deviations (for constant color temperature). Input: 230 V, + 10%, -15%, 50 Hz Output: 11,5 V ± 1%, 50 Hz | Output power: 100 W Dimensions: approx. 120 x 80 x 140 mm (4.7 x 3.1 x 5.5 in.) Available for 230 V, 240 V, and 120 V Fuse: 1,6 AT (230/240 V) / 2,5 AT (120 V) 4453: without voltage stabilization Input: 230 V, 50 Hz Output: 12 V, 50 Hz |
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LIMS Component Table
| ANALYSIS | TABLE | NAME | ABOUT TEXT |
| TSIMAGE | SAMPLE | Exp | Exp: expedition number |
| TSIMAGE | SAMPLE | Site | Site: site number |
| TSIMAGE | SAMPLE | Hole | Hole: hole number |
| TSIMAGE | SAMPLE | Core | Core: core number |
| TSIMAGE | SAMPLE | Type | Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X). |
| TSIMAGE | SAMPLE | Sect | Sect: section number |
| TSIMAGE | SAMPLE | A/W | A/W: archive (A) or working (W) section half. |
| TSIMAGE | SAMPLE | text_id | Text_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples. |
| TSIMAGE | SAMPLE | sample_number | Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table. |
| TSIMAGE | SAMPLE | label_id | Label identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples. |
| TSIMAGE | SAMPLE | sample_name | Sample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter. |
| TSIMAGE | SAMPLE | x_sample_state | Sample state: Single-character identifier always set to "W" for samples; standards can vary. |
| TSIMAGE | SAMPLE | x_project | Project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| TSIMAGE | SAMPLE | x_capt_loc | Captured location: "captured location," this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| TSIMAGE | SAMPLE | location | Location: location that sample was taken; this field is usually null and is unnecessary because any sample captured on the JR has a sample_number ending in 1, and GCR ending in 2 |
| TSIMAGE | SAMPLE | x_sampling_tool | Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula) |
| TSIMAGE | SAMPLE | changed_by | Changed by: username of account used to make a change to a sample record |
| TSIMAGE | SAMPLE | changed_on | Changed on: date/time stamp for change made to a sample record |
| TSIMAGE | SAMPLE | sample_type | Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ) |
| TSIMAGE | SAMPLE | x_offset | Offset (m): top offset of sample from top of parent sample, expressed in meters. |
| TSIMAGE | SAMPLE | x_offset_cm | Offset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm) |
| TSIMAGE | SAMPLE | x_bottom_offset_cm | Bottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm) |
| TSIMAGE | SAMPLE | x_diameter | Diameter (cm): diameter of sample, usually applied only to CORE, SECT, SHLF, and WRND samples; however this field is null on both Exp. 390 and 393, so it is no longer populated by Sample Master |
| TSIMAGE | SAMPLE | x_orig_len | Original length (m): field for the original length of a sample; not always (or reliably) populated |
| TSIMAGE | SAMPLE | x_length | Length (m): field for the length of a sample [as entered upon creation] |
| TSIMAGE | SAMPLE | x_length_cm | Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm). |
| TSIMAGE | SAMPLE | status | Status: single-character code for the current status of a sample (e.g., active, canceled) |
| TSIMAGE | SAMPLE | old_status | Old status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample |
| TSIMAGE | SAMPLE | original_sample | Original sample: field tying a sample below the CORE level to its parent HOLE sample |
| TSIMAGE | SAMPLE | parent_sample | Parent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR) |
| TSIMAGE | SAMPLE | standard | Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T) |
| TSIMAGE | SAMPLE | login_by | Login by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created]) |
| TSIMAGE | SAMPLE | login_date | Login date: creation date of the sample |
| TSIMAGE | SAMPLE | legacy | Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition |
| TSIMAGE | TEST | test changed_on | TEST changed on: date/time stamp for a change to a test record. |
| TSIMAGE | TEST | test status | TEST status: single-character code for the current status of a test (e.g., active, in process, canceled) |
| TSIMAGE | TEST | test old_status | TEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test |
| TSIMAGE | TEST | test test_number | TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table. |
| TSIMAGE | TEST | test date_received | TEST date received: date/time stamp for the creation of the test record. |
| TSIMAGE | TEST | test instrument | TEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input) |
| TSIMAGE | TEST | test analysis | TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table) |
| TSIMAGE | TEST | test x_project | TEST project: similar in scope to the expedition number, the difference being that the project is the current cruise, whereas expedition could refer to material/results obtained on previous cruises |
| TSIMAGE | TEST | test sample_number | TEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table |
| TSIMAGE | CALCULATED | Top depth CSF-A (m) | Top depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| TSIMAGE | CALCULATED | Bottom depth CSF-A (m) | Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole. |
| TSIMAGE | CALCULATED | Top depth CSF-B (m) | Top depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| TSIMAGE | CALCULATED | Bottom depth CSF-B (m) | Bottom depth [other] (m): position of observation expressed relative to the top of the hole. The location is presented in a scale selected by the science party or the report user. |
| TSIMAGE | RESULT | aperture | RESULT aperture: f-stop of the camera for this image (e.g., f/8) |
| TSIMAGE | RESULT | camera | RESULT camera: make and model number of the camera |
| TSIMAGE | RESULT | date_taken | RESULT date taken: date/time stamp the image was captured |
| TSIMAGE | RESULT | focal_length | RESULT focal length (mm): focal length of the camera |
| TSIMAGE | RESULT | iso | RESULT iso setting: ISO setting of the camera (e.g., ISO-4000) |
| TSIMAGE | RESULT | jpeg_asman_id | RESULT JPG image ASMAN_ID: serial number of the ASMAN link for the JPG/JPEG image |
| TSIMAGE | RESULT | jpeg_filename | RESULT JPG image filename: file name of the JPG/JPEG image |
| TSIMAGE | RESULT | macro | RESULT macro lens setting: multiplier from 1x to 5x if the macro lens is used (always 1x if standard lens) |
| TSIMAGE | RESULT | polarization | RESULT polarization: indicator for no polarization, single polarization, or cross polarization |
| TSIMAGE | RESULT | polarizationangle | RESULT polarization angle (deg.): angle of polarization (if measured; usually null) |
| TSIMAGE | RESULT | raw_asman_id | RESULT raw file ASMAN_ID: serial number of the ASMAN link for the raw (camera format) uploader file |
| TSIMAGE | RESULT | raw_filename | RESULT raw filename: file name for the raw (camera format) uploader file |
| TSIMAGE | RESULT | shutter_speed | RESULT shutter speed (s): shutter speed, usually expressed in a fraction of a second (e.g., 1/640 sec.) |
| TSIMAGE | SAMPLE | sample description | SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments" |
| TSIMAGE | TEST | test test_comment | TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments" |
| TSIMAGE | RESULT | result comments | RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments" |