Overview

This system is designed to assist the photographer in the capture and cataloging of close-up photographs.

Equipment

Hardware

The close-up imager consists of the following hardware

Polaroid Camera Stand
Calumet light system
Canon EOS 1D Mark III Camera
Cannon Compact-Macro Lens EF 50mm 1:2.5
HP LP3065 Wide Gamut 30” LCD Monitor
HP xw4400 PC workstation

Software

The close-up imager system makes use of the following pieces of software

Capture One
IODP in house “Image Capture” software

Safety

There are no outstanding safety issues associated with operation of this instrument

Standard Operation

The following steps describe the standard procedure for taking and cataloging close-up images aboard the JOIDES Resolution.

Close-Up Request Sheet

Print out blank close-up request sheets and place on the clipboard in the Core Lab with a sheet of yellow dot labels.

Instruct scientists on how to fill it out properly and completely, and to put a yellow dot on the endcaps of sections with requests.

Printing Labels for the Close-up Images

Open Image Capture software.
Click the Browse button to bring up the Sample Browser.
Select the sample you will be imaging, usually a section half or a piece from a hard rock section half.
Enter the offsets of the requested image in the top and bottom fields.
Select wet or dry depending on treatment.
Enter the comment from the close-up sheet.
Click Large for the large label format that will print to the Sample Table label printer or the small format, which will print out on the printer in the microscope lab.
Place the label on the stand and shoot the image. You will use Image Capture to upload the image to LIMS so it will be easier to do it one at a time since the info you enter for the label will be used by the uploader.

Setting up the capture area and sample

Prior to imaging, ensure the camera and lighting is set up correctly. Turn on camera and Calumet control box.
Lower the screen mounted on the overhead to protect the paleontologists from the flash.
Pull out the rulers, gray scale cards, and the various aids used to position everything.
Arrange the sample, ruler, gray card, and label compactly.
Adjust the height of the camera stand so that everything will fit into the field of view.
Focus the camera manually.

Acquiring an Image

Start up the Capture One software
Under the File menu open a session or create a new one. This will set the file structure for the images.
Take an image using the shutter button on the camera or use the Capture button in Capture One but make sure no body parts are in the way of the flashes. The flashes should go off and the image will appear in Capture One. If the image is out of focus or something needs adjusting, make the adjustments and take another image.
Crop the image if necessary.
Adjust the image using the Eye drop tool on the tool bar.
1. Right click the eye drop and select “Pick White Balance” then click on the medium gray card.
2. Right click the eye drop and select “Pick Highlight Level” then click on the white card.
3. Right click the eye drop and select “Pick Shadow Level” then click on the dark gray card.
Process the image by entering Ctrl-D on the keyboard or right click the image and select Process. This will create the jpg and tiff images.
Go to Image Capture to tag and upload the images to the database.

Upload Images to Database

Open the IODP Image Capture software and login using your LIMS username and password. In the settings menu, select the destination folder of the images taken by Capture One and select the Closeup Mode.
Once you have logged in to the software you will notice a listing of images in the upper left corner. These are the images which were just taken (the JPG files specifically). Click on one of the images to select it for uploading.
Next we need to associate this image with a sample, so click on the Browse button.
After clicking browse select a site and hole to pick a sample from. The sample type will be defaulted to Section half and a list of available thin sections will appear in the window on the right. Click on the appropriate sample then swap back to the main window (you can close/minimize/ignore the sample browser window at your discretion. If you close it then it will open back to the same location).
Note that the sample textid field has been populated, and a new label has been generated in the top right. This label indicates what the renamed filename will be, and is based on the sample selected. If multiple pictures are taken the filename will be appended with _2, _3, _4 etc. based on the number of previous images already taken *and processed*. Fill out the rest of the values based on the conditions when you took the image.
Add the comment and name of requestor from the close-up request sheet into the Comments field.
When upload was clicked a window will pop up indicating the upload status. When the upload process is finished another dialog will appear indicating that the process is complete.
At this point the previously selected image will have been removed from the pending uploads list and will be loaded into LIMS. You can continue processing additional images. Go to LORE reports and verify that the images are uploaded.
The images themselves, after upload, are moved to the archive folder (at the same level as the capture folder). Under the archive folder there will be 3 subfolders:
1. JPEG
2. TIFF (Tiff’s will not generally be created in the standard workflow)
3. RAW
These folders will contain a hierarchy in the form of \{Expedition}\{SiteHole}\filename.ext of all the files. (Essentially pictures will be organized by type, expedition, and sitehole when put in the archive folder.) These pictures do not need to be backed up (as they are already in lims/asman) but can be taken by the photographers, etc. for alternate archiving if desired.
Note that these images may be deleted at any time, without notice, by the technicians or other scientists. They are always available via LIMS, and if you wish to save a local copy you may do so.

Shut Down the Instrument

LIMS Component Table

The following table contains all of the LIMS components for the entire CLOSEUP process.

ANALYSIS	TABLE	NAME	ABOUT TEXT
CLOSEUP	SAMPLE	Exp	Exp: expedition number
CLOSEUP	SAMPLE	Site	Site: site number
CLOSEUP	SAMPLE	Hole	Hole: hole number
CLOSEUP	SAMPLE	Core	Core: core number
CLOSEUP	SAMPLE	Type	Type: type indicates the coring tool used to recover the core (typical types are F, H, R, X).
CLOSEUP	SAMPLE	Sect	Sect: section number
CLOSEUP	SAMPLE	A/W	A/W: archive (A) or working (W) section half.
CLOSEUP	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.
CLOSEUP	SAMPLE	sample_number	Sample Number: automatically generated database identifier for a sample. This is the primary key of the SAMPLE table.
CLOSEUP	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.
CLOSEUP	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.
CLOSEUP	SAMPLE	x_sample_state	Sample state: Single-character identifier always set to "W" for samples; standards can vary.
CLOSEUP	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
CLOSEUP	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
CLOSEUP	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
CLOSEUP	SAMPLE	x_sampling_tool	Sampling tool: sampling tool used to take the sample (e.g., syringe, spatula)
CLOSEUP	SAMPLE	changed_by	Changed by: username of account used to make a change to a sample record
CLOSEUP	SAMPLE	changed_on	Changed on: date/time stamp for change made to a sample record
CLOSEUP	SAMPLE	sample_type	Sample type: type of sample from a predefined list (e.g., HOLE, CORE, LIQ)
CLOSEUP	SAMPLE	x_offset	Offset (m): top offset of sample from top of parent sample, expressed in meters.
CLOSEUP	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)
CLOSEUP	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)
CLOSEUP	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
CLOSEUP	SAMPLE	x_orig_len	Original length (m): field for the original length of a sample; not always (or reliably) populated
CLOSEUP	SAMPLE	x_length	Length (m): field for the length of a sample [as entered upon creation]
CLOSEUP	SAMPLE	x_length_cm	Length (cm): field for the length of a sample. This is a calculated field (length, converted to cm).
CLOSEUP	SAMPLE	status	Status: single-character code for the current status of a sample (e.g., active, canceled)
CLOSEUP	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
CLOSEUP	SAMPLE	original_sample	Original sample: field tying a sample below the CORE level to its parent HOLE sample
CLOSEUP	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)
CLOSEUP	SAMPLE	standard	Standard: T/F field to differentiate between samples (standard=F) and QAQC standards (standard=T)
CLOSEUP	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])
CLOSEUP	SAMPLE	login_date	Login date: creation date of the sample
CLOSEUP	SAMPLE	legacy	Legacy flag: T/F indicator for when a sample is from a previous expedition and is locked/uneditable on this expedition
CLOSEUP	TEST	test changed_on	TEST changed on: date/time stamp for a change to a test record.
CLOSEUP	TEST	test status	TEST status: single-character code for the current status of a test (e.g., active, in process, canceled)
CLOSEUP	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
CLOSEUP	TEST	test test_number	TEST test number: automatically generated database identifier for a test record. This is the primary key of the TEST table.
CLOSEUP	TEST	test date_received	TEST date received: date/time stamp for the creation of the test record.
CLOSEUP	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)
CLOSEUP	TEST	test analysis	TEST analysis: analysis code associated with this test (foreign key to the ANALYSIS table)
CLOSEUP	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
CLOSEUP	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
CLOSEUP	CALCULATED	Top depth CSF-A (m)	Top depth CSF-A (m): position of observation expressed relative to the top of the hole.
CLOSEUP	CALCULATED	Bottom depth CSF-A (m)	Bottom depth CSF-A (m): position of observation expressed relative to the top of the hole.
CLOSEUP	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.
CLOSEUP	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.
CLOSEUP	RESULT	aperture	RESULT aperture: aperture setting for the camera (e.g. F/22)
CLOSEUP	RESULT	bottom_offset	RESULT bottom offset (cm): bottom offset of the close-up request expressed in cm from top of section
CLOSEUP	RESULT	camera	RESULT camera: vendor and model of camera used for closeup photo
CLOSEUP	RESULT	date_taken	RESULT date taken: date/time stamp for when the image was captured
CLOSEUP	RESULT	focal_length	RESULT focal length (unit varies): focal length of lens (e.g., 50 mm); unit is expressed in the entry field
CLOSEUP	RESULT	iso	RESULT iso number: ISO number of the light sensitivity of the camera
CLOSEUP	RESULT	jpeg_asman_id	RESULT jpeg image ASMAN_ID: serial number of ASMAN record for the JPG/JPEG format image
CLOSEUP	RESULT	jpeg_filename	RESULT jpeg image filename: file name for the JPG/JPEG format image
CLOSEUP	RESULT	raw_asman_id	RESULT raw image ASMAN_ID: serial number of ASMAN record for the raw camera format image
CLOSEUP	RESULT	raw_filename	RESULT raw image filename: file name for the raw camera format image
CLOSEUP	RESULT	shutter_speed	RESULT shutter speed (s): shutter speed of the camera, usually expressed in a fraction of a second
CLOSEUP	RESULT	state	RESULT sample state: field to record sample state (e.g., wet or dry)
CLOSEUP	RESULT	tiff_asman_id	RESULT tiff image ASMAN_ID: serial number of ASMAN record for the TIF/TIFF format image
CLOSEUP	RESULT	tiff_filename	RESULT tiff image filename: file name for the TIF/TIFF format image
CLOSEUP	RESULT	top_offset	RESULT top_offset (cm): top offset of the close-up request expressed in cm from top of section
CLOSEUP	SAMPLE	sample description	SAMPLE comment: contents of the SAMPLE.description field, usually shown on reports as "Sample comments"
CLOSEUP	TEST	test test_comment	TEST comment: contents of the TEST.comment field, usually shown on reports as "Test comments"
CLOSEUP	RESULT	result comments	RESULT comment: contents of a result parameter with name = "comment," usually shown on reports as "Result comments"

Laboratory Manuals, Guides, and Resources

Close-up Capture User Guide