I. INTRODUCTION

The IODP Core Lab Cookbook is intended to guide Marine Laboratory Specialists (Techs) sailing onboard the R/V JOIDES Resolution in basic core lab procedures. All Techs assigned to the core lab share the responsibility of processing core and maintaining the lab. Below is a drawing of the core lab to help illustrate the procedures described in this Cookbook.

II. SUPPLYING THE LAB

At the beginning of an expedition, the core lab should be fully stocked and stock levels maintained during the cruise. Supplies can be obtained from Upper Tween, Pallet and Hold Reefer stores. Please remember to check out all supplies on the check-out sheets located in each storage area. In the core entry area there is a list of supplies for the core lab and where they are stored. Following is a detailed list of the supplies needed for the each area:

Catwalk Supplies

• clear, blue, and yellow end caps
• acetone in red squirt bottles (with “acetone” label)
• clean, absorbent rags
• wooden meter sticks (~149cm)
• 4" stainless steel spatulas
• permanent red markers (Marks-a-lot)
• chisel and mallet for harder sediment and hard rock
• liner puncture tool or drill for gassy sediments
• hammer, hacksaw, plunger, core catcher tools
• china markers for hard rock and marking liners on wet days
• core liner cutters with good blades
• liner patch
• Nitrile gloves, various sizes (bin by catwalk entry door)
• safety glasses (bin by catwalk entry door)
• hearing protection (bin by catwalk entry door)

These supplies must be clean. Meter sticks should be trimmed slightly short to yield 150 cm core sections. Rusty tools should be cleaned or replaced - a small amount of rust can ruin core material for paleomagnetics.

The chem techs provide their own supplies for taking headspace and vacutainer samples. IW samples require no special supplies. You should work with the Curatorial Specialist to maintain the supply of equipment for any special catwalk sampling such as MBIO.

Description Table Supplies

• glass slides
• toothpicks
• mounting media (Norland Optical Adhesive for ultraviolet curing)
• coverslips
• smear slide cases, smear slide labels
• glass sample vials with snap lids
• miscellaneous glassware
• desk supplies, including pens, pencils, Liquid Paper, rulers, etc.
• gloves for those who do not remove their jewelry
• GLAD™ Plastic Wrap

D-Tube Rack Supplies

• black (working) or red (archive) D-tube end caps
• d-tubes
• black (working) or red (archive) Permanent Markers
• waxed core boxes
• polyethylene tape (d-tube tape)
• core box stapler and staples
• shrink wrap

Sample Table Supplies

            The bins under the sample table should be stocked with:

• 5 and 10 cc sample tubes and scoops
• 5 and10cc foam plugs
• pop top vials
• sample bags
• foam rods
• "Kapak" bags
• ceramic-bladed knives
• P-Mag cubes
• other supplies as labeled

Splitting Room

• hook, utility and core cutter blades
• cleaning sponges
• acetone
• hard rock dividers, halved end caps (blue and clear)
• split foam rods
• PAL spacer foam, both black and red for sediment cores
• permanent red and black markers, china markers
• spatulas, various sizes
• squirt bottle with DI water

III. IODP CORE NAMING

IODP has a specific naming convention for identifying cores, data and samples. All are named with the leg number, site number, hole letter, core number, core type, section number, and which half (working or archive) plus Text ID. Samples and data will also include the sample interval.

Here is an example for scribing core liner in the Laser Engraver or by hand if needed

323-U1243B-6R-5W, ß, SHLF55443322

Here is an example for a sample:

323-U1243B-6R-5W, 25-30 cm, CYL55443322

Core Types

The following is a list of all the valid core types and their associated code with the most commonly used in bold:         

IV. CORE RECOVERY - CATWALK

After the liner is removed from the core barrel, it is placed on the catwalk holders (working side up, denoted by the double-lines on the core liner), where it is temporarily capped at either end to keep sediment from falling out during the initial handling stages. Full core barrels are usually 9.5 meters long, yield six sections, a shorter seventh section, and a core catcher. Recovery of material in length to the cored interval is considered full, or 100% recovery. However, the length of the recovered material may differ from the length of the cored interval. Recovery less than the cored interval may occur for a variety of reasons. Apparent recovery greater than the cored interval may also occur, typically a result of gaseous expansion of the sediment.

Cores taken from a hole are numbered serially from the top of the hole downward. When full recovery is obtained, the core sections are numbered 1 through 7, the last section being shorter than 1.5 meters. For sediments, the core catcher sample is extruded into a short piece of plastic liner and is treated as a separate section below the last core section. For hard rock, material recovered in the core catcher is included at the bottom of the last section.

The Curatorial Specialist and techs measure and mark the ends of each section, labeling each with core, core type and section number and an arrow pointing 'up'. At the section breaks, the liner is cut with a circular cutting tool and cut through the contained sediment with a spatula. If the material is well lithified a hacksaw or hammer & chisel is used to section the core. After separating into sections, whole round (aka catwalk samples, see next section) samples are taken. After the whole round and head space samples are removed from the catwalk, the rest of the core may be capped and glued with acetone. Blue end caps are placed at the top of each section, clear end caps at the bottom, and yellow end caps at the end of any section from which a whole round sample was taken.  Once labeled, sectioned and capped, the core is ready to be brought into the Core Lab for processing.

For obtaining good measurement on the NGR, a section needs to be minimum of 50 cm, preferably more than 50 cm. Curator/ALO should mark the second to last section accordingly to ensure the last section is at least 50 cm. For example – if the last two sections measure 200 cm, it is better to measure the last two as 120 and 80 cm, rather than 150 and 50 cm, or if the last two sections measure 175 cm, it is better to measure the second to last as 100 and the last 75 cm.

V. CATWALK SAMPLING

In addition to the usual hard rock/soft rock sample requests taken from the split core at the sample table, shipboard scientists will most likely take samples on the catwalk. Because most of these analyses are sensitive to the geochemical nature of the material it is important to keep the catwalk area acetone-free until the shipboard scientists and chem techs have finished taking their samples. All samples taken on the catwalk must be recorded in Sample Master.

Paleo Samples (PAL)

(PAL = paleontology) -  Paleontologists receive material from the core catcher for biostratigraphic dating of the core. Generally, 5 cm is sufficient, but in unfossiliferous material a greater volume may be required. This sample typically comes from the bottom of the core catcher.

After the PAL sample is taken, the core catcher is placed in plastic liner, capped and glued with acetone, and labeled with black marker. Leave an empty space in the liner where the PAL sample was removed. A foam spacer will be added after the liner is split. The PAL sample should be recorded as sample code PAL in Sample Master.

Head Space/Gas Analyses (HS, VAC)

The Shipboard Chemist or Chemistry Technician will take at least one 5cc sample for analysis of hydrocarbon composition and concentration. These include a sediment sample for headspace gas analysis (HS) and, if present, free gas samples (VAC or Vacutainer Samples). These samples are immediately analyzed to determine if it is safe to continue drilling.

Headspace samples are taken from the top or bottom of a freshly cut section, depending on the condition and lithology of the core, usually adjacent to the IW (interstitial water whole round sample). The cylinder used for headspace sampling removes material from the working side of the core. In the case of lithified sediments, scrapings or chips are taken. These samples are entered in Sample Master as sample code HS.

When gassy voids are present, the chemist may need to take free gas samples using a puncture tool and a vacutainer. Shipboard scientists may take as many vacutainer gas samples as desired for immediate or later analysis. The location of each sample must be entered in Sample Master as sample code VAC.

Interstitial Water Samples (IW)

Interstitial waters for geochemical analysis samples are generated from the whole round samples removed on the catwalk. In less consolidated sediments at the top of a borehole, IW samples are generally 5cm long (176cc). The size of the sample may be increased as the sediment becomes more lithified with depth. The Co-Chief Scientists, Staff Scientist, and Curatorial Specialist work together to come up with an IW sampling plan that best meets the needs of the shipboard party. These samples are entered in Sample Master as sample code IW.

When core recovery is less than about two sections, whole round sampling is often suspended. However, there is no official policy limiting the amount of whole-round sampling when recovery is low. The unofficial policy is that the co-chiefs, staff scientist, and the Curatorial Specialist define appropriate limits on whole round sampling to safeguard the scientific interests of the cruise. Always get the Curatorial Specialist’s (or his/her representative’s) OK to cut IW samples.

VI. IN THE LAB

The Curatorial Specialist or ALOs then enter the pertinent data into Sample Master to generate the bar coded labels for each section.

The marine technicians engrave the working (double line) and archive (single line) side of the liners with the Laser Engraver. Standard IODP identifier, "EXP-SITE-HOLE-CORE-CORETYPE-SECTION and TEXT ID" (e.g. 323-U1340A-1H-1W, ß, SHLF55443322). This ensures that each section is permanently and uniquely distinguished. The Laser Engraver is generally used to engrave the cores, however if the Laser Engraver does fail the sections must be labeled with the dremel tool.  View the Laser Safety training presentation that can be obtained from the ALO’s before using the Laser Engraver and read the user guide for Laser Katjie program. If engraving by hand (using Dremel™ tool) the engraving should be as legible as possible. The blue end caps of each section should be marked with the core, core type and section number like so:

Place sections 1-4 inside the engraver, working end (double lines) facing up.  Make sure that the area to be engraved falls within the two black arrows marked on the forward end of the engraver.  If the core section is too short, use the Small Format.

After placing the sections in the engraver, make sure the engraver door is completely closed.  The Laser system contains safety switches that will not allow you to use the engraver with the door opened.

Warning! The laser engraver utilizes a Class IV laser. Follow all of the safety procedures for this tool!

Warning! If any of the safety features of the laser engraver seem to be malfunctioning, call an ET immediately! The Class IV laser is very dangerous if its safety measures are not all in place.

Open the Laser Katjie software if it is not already open.   The monitor is a touch screen for easy use.  In order to be engraved, the cores have to be entered into Sample Master by the driller and ALO’s/Curator.  Select the Expedition>Site-Hole>Core of the sections to be engraved.  The first four sections should automatically pop up.  If you do not want to use one of the positions, for example, one section is too short, etc, simply select “not used” for that position. 

Once your sections are selected, hit “Engraver” on the touch screen.  The engraver will begin engraving your sections.  After ~10 seconds, it will finish the working halves and prompt you to rotate the sections to the archive half.  Open the door and rotate all sections 180 degrees to archive half up.  Close the door and hit next on the software to enable the engraver.  After ~10 sec, the engraver will complete the archive half engraving process and a light will prompt you that it is safe to open the engraver door and remove the cores. 

Once properly marked and recorded, the sections are moved to the next available spot in the rack to equilibrate to room temperature before they are measured on the tracks and measured for thermal conductivity.

Physical Properties Whole Rounds  

Sometimes physical properties whole round samples are chosen after the core has been run through the tracks. The Curatorial Specialist or ALOs will cut the whole round on the catwalk and then seal the samples in wax as soon as possible. Once the sample has been sealed in wax, it should be stored upright in a salt water bath in the reefer.

Splitting Core

After whole round measurements have been made, the sections are ready to be split. Verify with the ALOs or Curatorial Specialist that sections are ready to be split. A program called LIVE (LIMS data Viewer) can be used to confirm data on WR tracks is ok. Sections are split longitudinally from the bottom of the section to the top on the core splitter with either the wire (for soft sediments) or the supersaw (for lithified material) along an axis halfway between the double line and the opposing single line scribed on the liner. Lithified cores split with the supersaw should have the melted plastic that accumulates on the edges of the section due to sawing cut away with a hooked razor blade for safe handling (the plastic is sharp) and for better quality photographs and digital images. The sections should be gently rinsed and lightly scrubbed with a sponge to remove the cutting slurry before leaving the splitting room. The bottom to top direction that must be used when splitting a core is to prevent downward contamination. Biostratigraphic ages are based on the youngest fossils present in a sample. If the core is split from top to bottom, we would cause younger fossils to move downward into older age material.

Archive Half

The archive half is placed on the description table in the Core Lab. The core describers describe the core in detail, making smear slides to examine under the microscope. The core describers also run the sections through the Imaging (SHIL) and Section Half Multi Sensor Logger (SHMSL). The Paleomagnetists will measure the archive halves, one at a time, through the Cryogenic Magnetometer (Cryomag). After the cores have been described and run through the Cryomag the archive half is placed in the D-Tubes. (See section on Storing Core below).

Close-up Photos: Check the close-up photo request sheet to see if a close-up has been requested for that core. If so, place the sections in the d-tube but do not tape it closed. Place a yellow dot on the endcap.

Working Half

The working half sections are taken to the sample table where physical properties measurements are made and discrete samples are taken by the Phys Props scientists. Once Phys Props is done, a rotating team of scientists takes samples for the shipboard party. Once the core is sampled, the scientists will put the cores in pre-labeled (prepared by techs) D-tubes in the working half rack. It’s a good idea to stay ahead of the scientists by preparing a few cores worth of D-tubes in advance. The Curatorial Specialist will keep an eye on sampling activities during his/her shift, but during off-hours, it’s very helpful (and greatly appreciated) if you check on things at the sample table. Assist where needed.

Note on Core Flow

All techs assigned to the Core Lab watch over core flow by staying in touch with fellow techs and scientists in the lab. Ask if another core needs splitting or if supplies are low. Let them know you are available to assist with all core flow activities, including feeding the tracks. During slow times or if you need to work in another lab, check back frequently to see if you need to lend a hand to split, box core, etc..

VII. HARD ROCK CORES

Core Handling

When a hard rock (igneous or metamorphic) core arrives on deck, the liner is placed on the catwalk core holders. If hard rock pieces are scattered along the length of the liner, the upper end is raised slightly to shunt the pieces to the lower end to provide a more accurate recovery measurement. Place contents of the core catcher into the bottom of the liner in order.  Sometimes it’s not possible to make room for the CC in the last section, especially if the rocks are jammed in the liner and won’t push up.  In this case just give the CC the next sequential section.  The sections are then measured starting at the bottom of the recovered material and working upwards (i.e. toward the top of the core). Be sure to label the sections in the correct order. Measure until you get to the last section (i.e. Section 1). You may find when you get to Section 1, it could be either very full of rock or it may only contain small amount. Now it is time to estimate if you will need additional empty liners to give you extra space to “curate” the core. To “curate” a hard rock core is to add dividers between non-continuous rock pieces. This almost always expands the core. Once all the sections (including CC) are numbered on the catwalk, measure the recovered rock inside the liner to get your total recovery. The Curator or ALO will estimate the number of sections to enter into Sample Master with the total recovery adding up to the length of core (rocks) received. For example, if the total length of core is 205 cm and it is estimated to take up 2 sections with dividers enter the sections into Sample Master as Section 1 = 100cm and Section 2 = 105cm, so total length is 205cm.

Note: We also drill without a liner on occasion. When this is the case the core is shaken from the core barrel into split liners. Make sure to mark the bottom of the core pieces, when applicable, and keep them in order.

Unlike sediment cores, hard rock cores do not always break at 1.5 meters. They are sectioned at fractures or other natural breaks as close to 1.5 m intervals as possible. Sometimes pieces longer than 1.5 meters are recovered; then it is necessary to break the core at some appropriate point with a hammer and chisel. However, try to use natural fractures rather than breaking a core for sections.

Hard rock sections are carried into the core entry area where the recovery (recovery = liner length in Sample Master) is recorded on paper form. The recovery is then entered into Sample Master as sections and the record saved (but do not print labels at this point – wait for final curated length). The true “curated length” will not be correct until the core is fully spaced-out (i.e. curated). Engrave the sections but no labeling. Note: when working with hard rock, it is always helpful to have a plentiful supply of pre-cleaned and pre-split core liners on hand. Carry the core to the splitting room.

The Curatorial Specialist or senior tech will start to curate the cores shaking the rock piece out of the liner into split liners (not the engraved liners but split liners we use as holders, labeled 1, 2, 3, 4, 5, etc). Starting from the top of the section, mark the bottom with a red/blue wax china marker of every piece which is long enough not to have rolled in the liner (the pieces that roll are called rollers and cannot be oriented). It is not important which color china marker is used.

All rock pieces need to be thoroughly washed and dried before putting into the engraved clean split liner.

With the help of the igneous petrologist or structural geologist (or both), broken or beveled rock pieces that have recognizable features (e.g. foliation directions, connecting veins) are aligned from piece to piece and fitted together (Figure 2). The inspecting scientist(s) will mark a splitting line on the rock pieces with Working or Archive half clearly marked (Figure 3). Subpieces that fit together should have hatch marks drawn to help maintain connections between subpieces when cutting on the rock saw (Figure 4). Hard rock pieces that do not fit together are separated from each other in the core liner by plastic dividers. The dividers are then acetoned (or sonic welded) in the engraved split liner. Once the pieces in each section are spaced out and the dividers attached, the Curatorial Specialist or ALO will measure the curated length and enter it in Sample Master.  The length of each bin (space between dividers) is also recorded and entered into Sample Master along with the piece number.  It’s important to recalculate offsets, and re-build depths after entering curated lengths, as the depth calculation method used for hard rocks uses the curated lengths, not catwalk recovery length. 

At this point it is possible to make several fatal errors when entering and changing curated lengths and section numbers.  It may be necessary to delete a section that originally had catwalk recovery assigned.  If so, be sure to add the recovery length to the length of one of the other sections, so the overall core recovery length does not change.  Just deleting the section and associated recovery length will result in errors with depth calculations.  There is only 1 proper way to delete a section.  It must be deleted LIME and the text-ID associated with the section  Once again, re-calculate offsets, upload, and rebuild depths when these edits are complete.

Hard rock core pieces are split on the rock saws in the splitting room along the splitting line marked by the petrologists. Sometimes the Supersaw is used to cut long, solid pieces that do not fit on the table top saws. Similarly, a series of long pieces may be more conveniently cut on the Supersaw. Before making any cuts, check again to be sure that the bottoms of all orientable pieces are marked with wax pencil. Ideally, pieces are split symmetrically with regard to any contacts, veins or other special features, so as to preserve part of the feature in each section half. Pieces which fit together or which have contiguous features are split along a single line drawn on all the pieces when they are fitted together. Shattered rock which can be pieced together by hand may be held together with Parafilm™, masking tape or shrink tubing and cut as one unit.  

Once split, the hard rock core pieces are returned to their respective liners and set flat side down (Figure 5). They can be air dried with aid of a fan, dried with a heat gun (the heating element in the 'off' position), or with compressed air. Applying direct heat to the core can affect alteration products and demagnetize the rocks so be careful.