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

1. 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

1. Open Image Capture software.
2. Click the Browse button to bring up the Sample Browser.
3. Select the sample you will be imaging, usually a section half or a piece from a hard rock section half.
4. Enter the offsets of the requested image in the top and bottom fields.
5. Select wet or dry depending on treatment.
6. Enter the comment from the close-up sheet.
7. 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.
8. 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

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

Acquiring an Image

1. Start up the Capture One software
   
2. Under the File menu open a session or create a new one.  This will set the file structure for the images.
   
3. 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.
4. Crop the image if necessary.
5. 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.
      
6. 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.
7. Go to Image Capture to tag and upload the images to the database.

Upload Images to Database

1. 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.
   
   
   
2. 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.
   
   
   
3. Next we need to associate this image with a sample, so click on the Browse button.
4. 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).
5. 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.
6. Add the comment and name of requestor from the close-up request sheet into the Comments field.
7. 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.
8. 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.
9. 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
10. 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.
11. 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.