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Expedition 335 Scientists2


This chapter documents the procedures and methods employed in the various shipboard laboratories during Expedition 335 of the Integrated Ocean Drilling Program (IODP). This information applies only to shipboard work described in the Expedition Reports section of the Expedition 335 Proceedings volume. Also described is the information architecture for the population and extraction of curatorial information, as well as shipboard scientific observations and data from the Laboratory Information Management System (LIMS) database and the Sample Master and DESClogik interfaces. Methods for shore-based analysis of Expedition 335 samples and data will be described in the individual scientific contributions to be published in the Research Results section of the Expedition 335 Proceedings volume and in international peer-reviewed literature.


All shipboard scientists contributed to this volume. However, certain sections were written by discipline-based groups of scientists as listed below (group leaders and then alphabetically):

  • Expedition 335 summary: Expedition 335 Scientists

  • Methods and Hole 1256D:

  •     Background and objectives: Teagle and Ildefonse

  •     Operations: Grout, Ildefonse, Blum, and Teagle

  •     Igneous petrology: Lissenberg, Abe, Adachi, Dick, Koepke, Miyashita,     Oizumi, and Payot

  •     Alteration and metamorphism: Alt, Abily, France, Harris, and Python

  •     Structural geology: Anma, Deans, Endo, Ferre, and Till

  •     Geochemistry: Godard, Kurz, and Roy

  •     Paleomagnetism: Morris and Kim

  •     Physical properties: Tominaga and Baines

  •     Core section image analysis: Wilson

  •     Downhole measurements: Guerin, Zakharova, and Wilson

  •     Underway geophysics: Wilson

  • Deep drilling of intact crust: harnessing past lessons to inform future endeavors: Ildefonse and Teagle

Numbering of sites, holes, cores, and samples and computation of depth

Drilling sites are numbered consecutively from the first site drilled by the Glomar Challenger in 1968. Starting with IODP Expedition 301, the prefix “U” designates sites occupied by the US Implementing Organization (USIO) vessel, the R/V JOIDES Resolution. Site 1256 does not follow this nomenclature because it was started during Ocean Drilling Program (ODP) Leg 206 (although the “U” does currently appear in online database reports). At a site, multiple holes are often drilled. For all IODP drill sites, a letter suffix distinguishes each hole drilled at the same site. The first hole drilled is assigned the site number modified by the suffix “A,” the second hole takes the site number and the suffix “B,” and so forth. Hole 1256D was the fourth hole drilled at Site 1256 (Wilson, Teagle, Acton, et al., 2003).

While on site, ship location over a hole is maintained with respect to one or two positioning beacons deployed on the seafloor and in active communication with the Neutronics 5002 dynamic positioning (DP) system on the JOIDES Resolution. In general, the primary reference for DP is GPS; the beacon reference acts as a backup in the event that GPS becomes unreliable.

The cored interval is measured in meters below rig floor (mbrf) and reported in meters below seafloor (mbsf). Depth below seafloor is determined by subtracting the seafloor depth measured from the rig floor, as determined from the initial drill pipe measurement at Hole 1256B (3645.4 m) (Wilson, Teagle, Acton, et al., 2003) from the rig floor measurements. Note that according to the recent IODP Depth Scales Terminology version 2 (, the mbsf scale is defined as the core depth below seafloor, method A (CSF-A), with units of meters. The computations of mbsf and m (CSF-A) depths are exactly the same.

During most IODP expeditions, each cored interval is generally 9.5–9.8 m long, which is the length of a core barrel. However, one potential cause of poor recovery during hard rock coring is core jamming in the bit or in the throat of the core barrel. Once the opening in the bit is jammed, core is prevented from entering the core barrel. During ODP hard rock coring missions, core barrels were often extracted at shorter penetration intervals in order to mitigate loss of core when the bit was blocked. This strategy improved core recovery in Hole 1256D during Leg 206 and IODP Expedition 309 and was the standard operating procedure throughout IODP Expedition 312. All cores recovered from Hole 1256D during Expedition 335 were cored at intervals of 4.7 m half-cores or less.

Each core recovered is divided into 1.5 m sections that are numbered serially from the top. When full recovery is achieved, the sections are numbered sequentially as recovered, starting with 1 at the top of the core; the last section may be shorter than 1.5 m (Fig. F1). For the purpose of nominal depth calculation, the top depth of the core is equated with the top depth of the cored interval (in mbsf) by convention, to achieve consistency in handling analytical data derived from cores. All pieces recovered are placed immediately adjacent to each other in the core tray. Samples and descriptions of cores are designated by distance, measured in centimeters from the top of the section to the top and bottom of each sample or interval. A full identifier for a sample consists of the following information: expedition, site, hole, core number, core type, section number, section half identifier (if applicable), top and bottom offsets in centimeters measured from the top of section (half), and additional subsample names if applicable. For example, the designation “Sample 335-1256D-235R-1W, 0–1 cm (Thin Section 2)” represents the second thin section made during the expedition, of a billet removed from the interval between 0 and 1 cm at the top of working section half 1W in Core 235R (R designates that this core was taken with the rotary core barrel) of Hole 1256D from Expedition 335. In addition, core pieces are numbered sequentially from the top of each section, and if a core piece can be reassembled the piece numbers are annotated with the suffix “A, B,” and so forth.

Curation protocols for geologic and industrial materials recovered by fishing and hole cleaning operations during Expedition 335

Extensive hole cleaning operations undertaken during Expedition 335 recovered a large amount of geologically valuable materials from Hole 1256D, as well as metallic junk from drilling, fishing, and milling equipment. To preserve the operational information and source of samples retrieved by fishing, reaming, and cleaning operations, nomenclature was developed for identifying on which reentry and from what device the samples were collected. Materials were recovered from external (EXJB; when deployed in multiples, EXJB1 and EXJB2), bit sub (BSJB), flow-through (FTJB), and reverse circulation (RCJB) junk baskets and the fishing magnet (FM) (see Fig. F19 in the “Expedition 335 summary” chapter [Expedition 335 Scientists, 2012a]). A very large amount of sand-sized cuttings were recovered from the drill collars (DCs). Table T1 shows the nomenclature for identifying the reentry (run) number and the sample recovery device. Full operations details of the numerous hole-clearing runs are documented in “Operations” and Table T3, both in the “Expedition 335 summary” chapter (Expedition 335 Scientists, 2012a). For curatorial reasons, the original sample depth was assigned somewhere in Hole 1256D from the bottom of the 16 inch casing to the total depth (270–1520 mbsf). For many materials, tighter depth ranges can be assigned from operational (e.g., bit withdrawals) and geological (e.g., igneous texture, alteration, and metamorphism) information. Large rocks (>5 cm) were assigned individual identification letters (e.g., Run12-RCJB-Rock B). Cobble-sized samples were weighed and measured individually (see Table T6 in the “Site 1256” chapter [Expedition 335 Scientists, 2012b]), whereas smaller samples were clustered by texture and grain size. Shipboard analyses (e.g., thin sections and inductively coupled plasma–atomic emission spectroscopy [ICP-AES] analyses) could then be tied to a particular rock or cutting style (sand or rubble) from a specific tool on a specific reentry run (Table T1).

Core reference frame for sample orientation

Each core piece that has a length exceeding that of the core liner diameter is associated with its own core reference frame (CRF) (Fig. F2). The primary reference is the axial orientation (i.e., the top and bottom of the piece) based on the piece’s orientation when extracted from the core barrel. The core axis defines the z-direction, where positive is downcore. The secondary reference is an arbitrarily marked axis-parallel line on the whole-round surface of the piece. This is the cut line, which marks the plane through the cut line and the core axis where the piece will be split. The cut line is selected by scientists to maximize the dip angle of planar features on the split surface, which facilitates accurate structural measurements. The x-axis of the CRF is defined orthogonally to the cut plane, positive (000°) into the working half and negative (180°) into the archive half. The y-axis is orthogonal to the x-z plane and, using the right-hand cork-screw rule, is positive (090°) to the left and negative (270°) to the right when looking upcore onto the archive half.

Cube samples taken from the working half were marked with an arrow in the negative z-direction (upcore) on the working half surface (x-y plane), which defines the cube’s orientation unequivocally within the CRF. Thin section billets and thin sections made of billets were also marked with an upcore arrow, in addition to a “~” sign marking the 270° direction. Thin section billets taken from the x-y plane (i.e., bottom or top face of the piece) and thin sections made from such billets were marked with “Ø” and the “~” symbol for the 270° direction. For thin sections cut in the x-z plane, an arrow indicates the uphole direction, and “@” indicates the thin section faces 090°, whereas “$” indicates a 270° facing (Fig. F2).

Core handling and core flow

The 15 steps of the core handling and core flow process, from coring to shipboard sampling, are summarized in Figure F3. Nonmagnetic core barrels were used throughout Expedition 335. Because of high ambient temperatures at the bottom of ODP Hole 1256D (>100°C), and to minimize the risk of cores jamming, all cores during Expedition 335 were recovered without plastic liners. When the core came to the rig floor, the Curator, supported by USIO technicians, waited with presplit core liners at the end of the catwalk. Once the core barrel was lowered horizontally, each rock piece was removed from the core barrel one by one and placed in consecutive order in 1.5 m split plastic liners labeled “A” through “D” (“A” through “F” for 9 m cores), with “A” being the lowermost split liner section. Blue and colorless liner caps denote the top and bottom of each split liner, respectively. This convention was used throughout the curation process. Before each piece was removed from the core barrel, the curator marked the bottom of all oriented pieces with a red wax pencil. In some cases, pieces too small to be oriented with certainty were marked before they were extracted from the core barrel. Therefore, the red wax mark does not universally indicate that the core piece was oriented. The core catcher sample was added to the bottom of split section A. To minimize contamination of the core with platinum group elements and gold, all personnel handling and describing the cores or other sample material removed jewelry from their hands and wrists before handling. For cores where the selection of microbiological samples was planned, all personnel handling the cores wore nitrile gloves to reduce contamination.

Once all core material was removed from the core barrel, split sections were transferred to the catwalk or core splitting area, and the rock material in each section was measured and entered into Sample Master as Recovered Length (Fig. F4). This parameter was used to compute core recovery. While the core was being recovered from the core barrel on the catwalk, identification labels were put on prescribed split liners. After transport to the splitting room, core pieces were transferred into the prescribed and labeled liners. After all pieces were placed in the labeled split liners, the curator and one other technician washed the whole-round pieces, one piece at a time, and allowed them to dry.

The rocks in each section were then placed into sample bins, by inserting plastic core dividers between individual pieces. These spacers may represent substantial intervals of no recovery. Adjacent core pieces that could be fitted together along fractures were curated as single pieces. Core pieces that appeared susceptible to crumbling were encased in shrink-wrap. Once binning activities and curatorial measurements were completed, a digital photograph was taken of the unlabeled section for insurance against accident during the prelabeling handling of whole-round pieces.

A designated scientist was then called to the splitting room to check the binning and reconstruction of fractured pieces. A splitting line was marked on each piece with a red wax pencil so that the piece could be split into representative working and archive halves, ideally maximizing the expression of dipping structures on the cut face of the core while maintaining representative features in both archive and working halves (Fig. F2). To ensure a consistent protocol for whole-core imaging (see “Core section image analysis”), the splitting line was drawn so that the working half was on the right side of the line with the core upright. The working half of each piece was marked with a “W” to the right of the splitting line. Where magmatic fabrics were present, cores were marked for splitting with the fabric dipping to the east (090°) in the IODP CRF. This protocol was sometimes overridden by the presence of special features (e.g., xenoliths, mineralized patches, and dike margins) that were subdivided between the archive and working halves to ensure preservation and/or allow shipboard or postcruise sampling.

Once the split line was drawn, the curator secured the plastic spacers permanently with acetone between individual pieces into matching working and archive half split core liners. Spacers were mounted into the liners with the angle brace facing uphole. This ensured that the top of each piece had the same depth as the top of the curated interval for each bin. The length of each bin was entered into Sample Master as Bin Length. The cumulative length of all bins, including spacers, was entered as the Curated Length of the section. Oriented pieces were recorded at this stage. The caliper length (longest vertical dimension) of each piece was also measured by the curator and entered into Sample Master as Piece Length (Fig. F4). Once all curatorial information had been entered and uploaded, the empty section half with bins was placed over the full half and taped together in a few places to dry and equilibrate to core laboratory conditions (usually <1 h from arrival from the catwalk).

Once thermally equilibrated, the magnetic susceptibility and natural gamma radiation (NGR) signal of each section was measured using the shipboard Whole-Round Multisensor Logger (WRMSL) and the Natural Gamma Radiation Logger (NGRL), respectively (see “Whole-Round Multisensor Logger measurements” and “Natural Gamma Radiation Logger”), and the outer cylindrical surfaces of whole-round pieces were scanned with the adapted Section Half Imaging Logger (SHIL) using the split line marking for registration (see “Core section image analysis”).

Each piece of core was then split into archive and working halves, with the positions of plastic spacers between pieces maintained in both halves. Piece halves were labeled sequentially from the top of each section, beginning with number 1; reconstructed groups of piece halves were assigned the same number but were lettered consecutively. Pieces were labeled only on the outer cylindrical surfaces of the core. If the piece was oriented with respect to the way up, an arrow was added to the label, pointing to the top of the section. Digital images of the dry, cut faces of archive halves were captured with the SHIL (see “Core section image analysis”). Sections were then transferred to the Section Half Multisensor Logger (SHMSL) where laser piece height, color reflectance, and contact probe magnetic susceptibility were measured (see “Section Half Multisensor Logger measurements”).

Following sample curation, whole-round and section half measurement and imaging, and splitting (Fig. F3), the archive section halves of each core were described by expedition scientists, and observations were recorded using the DESClogik interface and uploaded into the LIMS database (for details, see individual disciplinary sections in this chapter). Archive section halves were also passed through the cryogenic magnetometer for magnetic remanence measurements (see “Paleomagnetism”).

Digital color close-up images were taken of particular features for illustrations in the summary of each site, as requested by individual scientists. Working section halves of cores were sampled for both shipboard characterization of cores and shore-based studies. Samples were routinely taken for shipboard physical properties (minicore or 8 cm3 cube), paleomagnetic (minicore or 8 cm3 cube), thin section (billet or slab), and geochemical (billet, slab, or quarter round) analyses, as described in the sections below. Each extracted sample was logged into the LIMS database using the Sample Master program, including the sample type and either the shipboard analysis (test) conducted on the sample or the name of the investigator receiving the sample for postcruise analysis. Records of all samples taken from the cores were stored in the LIMS database and are accessible online ( Extracted samples were sealed in plastic vials, cubes, or bags and were labeled.

Following shipboard initial scientific observations, measurements, and sampling, both core halves were shrink-wrapped in plastic to prevent rock pieces from moving out of sequence during transit. Working and archive halves were then put into labeled plastic tubes, sealed, and transferred to cold-storage space aboard the drilling vessel. At the end of Expedition 335, cores were transferred from the ship for permanent storage at the IODP Gulf Coast Repository in College Station, Texas (USA).

Information architecture

Laboratory Information Management System

The USIO LIMS database is an infrastructure to store all operational, sample, and analytical data produced during a drilling expedition. The LIMS database comprises an Oracle database and a custom-built asset management system, along with numerous web services to exchange data with information capture and reporting applications. More than 30 data capture applications, most of them USIO custom tools built to support specific shipboard workflows, collect information and store it in the LIMS database. Several data retrieval applications are available to access the data from the LIMS database for different purposes (Fig. F5).

Data capture tools

All samples collected during Expedition 335 were registered in the LIMS database using the Sample Master application. The program has workflow-specific interfaces to meet the needs of different users. Sample registration begins with the driller entering information about the hole and then the cores retrieved from the hole. IODP personnel entered additional core information, sections, pieces, and any other subsamples taken from these, such as cubes or thin section billets. One interface is designed for visiting scientists so they can autonomously enter subsample information according to the sampling plan.

Five imaging systems available on the JOIDES Resolution were used to produce six types of images:

  1. Whole-round section surface (360°) images using the converted SHIL, used for the first time during Expedition 335 (see “Core section image analysis”);

  2. Section half surface images using the SHIL;

  3. Core composite images combining multiple section half images into the traditional “core table” view;

  4. Close-up images taken to meet special imaging needs not covered with routine line scan images;

  5. Whole-area thin section images using a custom-built system; and

  6. Photomicrographs using commercial cameras mounted on optical microscopes.

All images were uploaded to the LIMS database immediately after capture and were accessible via browser-based reports. Images were provided in at least one generally usable format (JPG, TIFF, or PDF) and in multiple formats if appropriate.

Physical properties, paleomagnetic, and geochemistry analytical systems in the shipboard laboratories were used to capture instrumental data, as described in the following sections. In cases where no further user interaction was required, the data upload to the LIMS database was triggered automatically. In cases where quality control or data processing was needed before upload, the user triggered the upload to the LIMS database when the data were ready.

Descriptive and interpretive information (DESCINFO) was captured using the DESClogik custom software application, and all information was stored in the LIMS database. This system was still relatively new, and significant development occurred during Expedition 335 in terms of worksheet configuration for hard rock descriptions and application feature development. The main DESClogik interface is a spreadsheet with extensive data entry and data validation support. The columns and tabs are entirely configurable by USIO staff based on users’ definitions of what information should be collected (see “Core description overview”). USIO staff then enables entry columns based on sets of parameters that make up the DESCINFO data structure.

Data retrieval

Data tables were mostly populated using the recently deployed LIMS Reports (Fig. F5), where the user selects the type of desired information from ~30 available reports, selects a hole (and cores and sections), and uses additional report-specific filters, if desired, to view a report online or download information in a standard comma-separated value (CSV) file. For information reporting not yet implemented in LIMS Reports (a beta version was used during Expedition 335), the original Web Tabular Report (WTR) was used to access data. Information retrieved from the WTR generally represents all valid data stored in the LIMS database for a given analysis, but the formats are not always user friendly.

Another alternative for retrieving data from the LIMS database was to use LIMS2Excel, a highly configurable Java-based data extractor where users can save a specific configuration for any combination of data parameters and export it into a Microsoft Excel workbook.

Many data sets could also be viewed on LIMSpeak, a browser-based application that plots cores, sections, and samples along with a user-selected data set, including images and other data sets, against depth. The application is particularly useful for monitoring data acquisition, real-time quality control, and browsing images.

Core description overview

Work flow

Three teams were formed to describe igneous petrology, alteration and metamorphic petrology, and structural geology in all core sections and thin sections prepared onboard. This disciplinary team approach ensured that all members of a specialty group were able to see all recovered material and work in a coordinated fashion to produce consistent data sets. The teams were each assigned a 12 h shift, spaced out to provide sufficient time and space for each team to examine the cores and also to ensure overlap with the other teams for information exchange. The igneous petrology team started at 2400 h and was responsible for defining igneous units in the recovered section. The alteration and metamorphism group worked 0600–1800 h, and the structural geology team started at 1200 h. Daily science meetings with the entire expedition Shipboard Scientific Party were held to avoid the development of singular department achievement philosophies.

Descriptive data capture workbooks

At the beginning of the expedition, each group defined observables as Excel spreadsheet columns, and those specifications were subsequently implemented as columns, tabs, and workbooks in the DESClogik application. Observable parameters were of three types: controlled values, free text, and numbers. For the controlled value columns, subject matter experts defined specific value lists that were configured in DESClogik as drop-down lists to facilitate consistent data capture. These values are defined in each description team’s section. Free text fields had no constraints and were used for comments. Number columns were used to log abundance percentage, size, intensity, and rank (for plotting) of physical constituents, texture, and structures.

The three teams defined 640 data capture columns. Columns were arranged in tabs and workbooks as agreed upon within each description team and among the three teams. Arrangements were optimized to support the description workflow and to avoid overlaps and gaps in data collection (Table T2).

Section summary graphic (visual core descriptions)

With all observables specified, the science party selected a few of the parameters to be represented graphically on the section summary graphic, historically referred to as the visual core descriptions (VCDs). All the information for the VCDs was retrieved from the LIMS database via the LIMS2Excel tool. VCD information was plotted as symbols, patterns, and line plots with depth, along with some instrumental data, using the commercial plotting program Strater. Tabulated data summaries for the sections were generated using DESClogik and printed next to the plots postcruise. All information displayed on the VCDs was plotted or otherwise collected from the LIMS database in a semiautomated process supported by USIO staff.

1Expedition 335 Scientists, 2012. Methods. In Teagle, D.A.H., Ildefonse, B., Blum, P., and the Expedition 335 Scientists, Proc. IODP, 335: Tokyo (Integrated Ocean Drilling Program Management International, Inc.).

2Expedition 335 Scientists’ addresses.

Publication: 3 June 2012
MS 335-102