Close-up Capture User Guide
- jr_crowder
- jr_houpt
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.
Right click the eye drop and select “Pick White Balance” then click on the medium gray card.
Right click the eye drop and select “Pick Highlight Level” then click on the white card.
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:
JPEG
TIFF (Tiff’s will not generally be created in the standard workflow)
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" |