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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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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

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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. 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            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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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 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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Color Head for Enlarger

Transformer with Voltage Stabilization

Transformer

CATALOG #: 204544CATALOG #: 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:
* Halogen cold light mirror lamp: 12 V, 100 W, 3400 K (204459)

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 HzOutput 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

LIMS Component Table

ANALYSISTABLENAMEABOUT TEXT
TSIMAGESAMPLEExpExp: expedition number
TSIMAGESAMPLESiteSite: site number
TSIMAGESAMPLEHoleHole: hole number
TSIMAGESAMPLECoreCore: core number
TSIMAGESAMPLETypeType: type indicates the coring tool used to recover the core (typical types are F, H, R, X).
TSIMAGESAMPLESectSect: section number
TSIMAGESAMPLEA/WA/W: archive (A) or working (W) section half.
TSIMAGESAMPLEtext_idText_ID: automatically generated database identifier for a sample, also carried on the printed labels. This identifier is guaranteed to be unique across all samples.
TSIMAGESAMPLEsample_numberSample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table.
TSIMAGESAMPLElabel_idLabel identifier: automatically generated, human readable name for a sample that is printed on labels. This name is not guaranteed unique across all samples.
TSIMAGESAMPLEsample_nameSample name: short name that may be specified for a sample. You can use an advanced filter to narrow your search by this parameter.
TSIMAGESAMPLEx_sample_stateSample state: Single-character identifier always set to "W" for samples; standards can vary.
TSIMAGESAMPLEx_projectProject: 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
TSIMAGESAMPLEx_capt_locCaptured 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
TSIMAGESAMPLElocationLocation: 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
TSIMAGESAMPLEx_sampling_toolSampling tool: sampling tool used to take the sample (e.g., syringe, spatula)
TSIMAGESAMPLEchanged_byChanged by: username of account used to make a change to a sample record
TSIMAGESAMPLEchanged_onChanged on: date/time stamp for change made to a sample record
TSIMAGESAMPLEsample_typeSample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ)
TSIMAGESAMPLEx_offsetOffset (m): top offset of sample from top of parent sample, expressed in meters.
TSIMAGESAMPLEx_offset_cmOffset (cm): top offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset, converted to cm)
TSIMAGESAMPLEx_bottom_offset_cmBottom offset (cm): bottom offset of sample from top of parent sample, expressed in centimeters. This is a calculated field (offset + length, converted to cm)
TSIMAGESAMPLEx_diameterDiameter (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
TSIMAGESAMPLEx_orig_lenOriginal length (m): field for the original length of a sample; not always (or reliably) populated
TSIMAGESAMPLEx_lengthLength (m): field for the length of a sample [as entered upon creation]
TSIMAGESAMPLEx_length_cmLength (cm): field for the length of a sample. This is a calculated field (length, converted to cm).
TSIMAGESAMPLEstatusStatus: single-character code for the current status of a sample (e.g., active, canceled)
TSIMAGESAMPLEold_statusOld status: single-character code for the previous status of a sample; used by the LIME program to restore a canceled sample
TSIMAGESAMPLEoriginal_sampleOriginal sample: field tying a sample below the CORE level to its parent HOLE sample
TSIMAGESAMPLEparent_sampleParent sample: the sample from which this sample was taken (e.g., for PWDR samples, this might be a SHLF or possibly another PWDR)
TSIMAGESAMPLEstandardStandard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T)
TSIMAGESAMPLElogin_byLogin by: username of account used to create the sample (can be the LIMS itself [e.g., SHLFs created when a SECT is created])
TSIMAGESAMPLElogin_dateLogin date: creation date of the sample
TSIMAGESAMPLElegacyLegacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition
TSIMAGETESTtest changed_onTEST changed on: date/time stamp for a change to a test record.
TSIMAGETESTtest statusTEST status: single-character code for the current status of a test (e.g., active, in process, canceled)
TSIMAGETESTtest old_statusTEST old status: single-character code for the previous status of a test; used by the LIME program to restore a canceled test
TSIMAGETESTtest test_numberTEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table.
TSIMAGETESTtest date_receivedTEST date received: date/time stamp for the creation of the test record.
TSIMAGETESTtest instrumentTEST instrument [instrument group]: field that describes the instrument group (most often this applies to loggers with multiple sensors); often obscure (e.g., user_input)
TSIMAGETESTtest analysisTEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table)
TSIMAGETESTtest x_projectTEST 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
TSIMAGETESTtest sample_numberTEST sample number: the sample_number of the sample to which this test record is attached; a foreign key to the SAMPLE table
TSIMAGECALCULATEDTop depth CSF-A (m)Top depth CSF-A (m): position of observation expressed relative to the top of the hole.
TSIMAGECALCULATEDBottom depth CSF-A (m)Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole.
TSIMAGECALCULATEDTop 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.
TSIMAGECALCULATEDBottom 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.
TSIMAGERESULTapertureRESULT aperture: f-stop of the camera for this image (e.g., f/8)
TSIMAGERESULTcameraRESULT camera: make and model number of the camera
TSIMAGERESULTdate_takenRESULT date taken: date/time stamp the image was captured
TSIMAGERESULTfocal_lengthRESULT focal length (mm): focal length of the camera
TSIMAGERESULTisoRESULT iso setting: ISO setting of the camera (e.g., ISO-4000)
TSIMAGERESULTjpeg_asman_idRESULT JPG image ASMAN_ID: serial number of the ASMAN link for the JPG/JPEG image
TSIMAGERESULTjpeg_filenameRESULT JPG image filename: file name of the JPG/JPEG image
TSIMAGERESULTmacroRESULT macro lens setting: multiplier from 1x to 5x if the macro lens is used (always 1x if standard lens)
TSIMAGERESULTpolarizationRESULT polarization: indicator for no polarization, single polarization, or cross polarization
TSIMAGERESULTpolarizationangleRESULT polarization angle (deg.): angle of polarization (if measured; usually null)
TSIMAGERESULTraw_asman_idRESULT raw file ASMAN_ID: serial number of the ASMAN link for the raw (camera format) uploader file
TSIMAGERESULTraw_filenameRESULT raw filename: file name for the raw (camera format) uploader file
TSIMAGERESULTshutter_speedRESULT shutter speed (s): shutter speed, usually expressed in a fraction of a second (e.g., 1/640 sec.)
TSIMAGESAMPLEsample descriptionSAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments"
TSIMAGETESTtest test_commentTEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments"
TSIMAGERESULTresult commentsRESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments"

Archive Versions

PICAT User Guide - 24022020