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K.M. Gillis, J.E. Snow, A. Klaus, G. Guerin, N. Abe, N. Akizawa, G. Ceuleneer, M.J. Cheadle, Á. Adrião, K. Faak, T.J. Falloon, S.A. Friedman, M.M. Godard, Y. Harigane, A.J. Horst, T. Hoshide, B. Ildefonse, M.M. Jean, B.E. John, J.H. Koepke, S. Machi, J. Maeda, N.E. Marks, A.M. McCaig, R. Meyer, A. Morris, T. Nozaka, M. Python, A. Saha, and R.P. Wintsch2


This chapter documents the procedures and methods employed in the various shipboard laboratories during Integrated Ocean Drilling Program (IODP) Expedition 345. This information applies only to shipboard work described in the Expedition Reports section of the Expedition 345 Proceedings volume. Also described is the information architecture for the population and extraction of curatorial information and 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 345 samples and data will be described in the individual scientific contributions to be published in articles in the open literature and in the Expedition Research Results section of the Expedition 345 Proceedings volume.

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 U.S. Implementing Organization (USIO) vessel, the R/V JOIDES Resolution. 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. Although all cored holes are routinely given these letter designations, during Expedition 345 jet-in tests were also given hole designations. This permitted documentation of jet-in test location and penetration information in the LIMS database.

While on site, the ship’s location over a hole is maintained using a Neutronics 5002 dynamic positioning system that utilizes positioning information from both a positioning beacon deployed on the seafloor and the shipboard GPS. Given the seafloor morphology surrounding the Hess Deep drill sites, the seafloor positioning beacons were conveyed to and placed on the seafloor using the camera system.

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 from the rig floor measurement of the depth of the bit below seafloor. Note that according to IODP Depth Scales Terminology v.2 (, the mbsf scale is defined as meters core depth below seafloor, method A (CSF-A). The computations of mbsf and meters CSF-A depths are exactly the same.

The cored interval was generally a maximum of ~9.5 m long, which is the length of a standard 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. Thus, core barrels were sometimes retrieved after shorter penetration intervals (usually ~4.7 m) to improve core recovery. In addition, core barrels were often deployed without a plastic liner.

Two types of cores were recovered with the rotary core barrel (RCB) coring system during Expedition 345. The first type includes RCB cores that penetrate into new formation at the bottom of the hole; these cores have the “R” designation in the core identifier. The second type includes cores in which the material enters the core barrel during substantial hole cleaning operations in previously cored or drilled intervals. These are termed “ghost cores” and are identified with a “G” core identifier instead. See “Operations” in each hole chapter for a listing of core intervals.

Each recovered core was divided into 1.5 m sections numbered serially from the top. The sections were 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 were placed immediately adjacent to each other in the core tray. Core pieces were 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 core piece 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 sample identifier “345-U1415A-5R-1W, 0–1 cm” represents a piece from the interval between 0 and 1 cm at the top of working section half 1W in Core 5R (R designates that this core was taken with the RCB) of Hole U1415A from Expedition 345. Core pieces are numbered sequentially from the top of each section, and if core pieces can be reassembled into a single coherent piece, the piece numbers are annotated with the suffix “A,” “B,” and so forth.

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 bottom was marked by red grease pencil on the bottom of the core piece. 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 was selected by a structural geology specialist to maximize the dip angle of planar features on the split surface, which facilitated 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 rule, is positive (090°) to the left and negative (270°) to the right when looking upcore onto the archive half. When viewing the working half upcore (e.g., for sampling), 090° is to the right and 270° to the left. Cube samples and thin sections taken from the working half were marked as shown in Figure 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. Routine steel core barrels were used unless otherwise noted in the operations sections. Cores may be recovered with or without a plastic liner, which is believed to reduce core jamming caused by angular fragments. When cores without liners came to the rig floor, the Curator, supported by 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 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 bottom of all pieces long enough to ensure vertical orientation was marked with an “X” using a wax pencil. In some cases, pieces too small to be oriented with certainty may have been marked as they were extracted from the core barrel but later identified to be a roller. Any core catcher sample recovered 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. In addition, no magnetic materials were used in the vicinity of the core to minimize the impact on the magnetic properties of the core.

Once all core material was removed from the core barrel and placed in split plastic liners, the liners were transferred to the core splitting room, 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 of the cores 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 placed into sample bins with 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 designated scientist (structural geology specialist) 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 structural fabrics were present, cores were marked for splitting with the fabric dipping to the east (090°) in the CRF. This protocol was sometimes overridden by the presence of special features (e.g., xenoliths, mineralized patches, and dike margins) that were divided between the archive and working halves to ensure preservation and/or allow shipboard or postcruise sampling.

Once the split line was drawn, the plastic spacers were permanently secured 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. Later, at the start of core description, the igneous petrologists measured the longest vertical dimension of each piece and entered by the curator 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 measurements”). The outer cylindrical surfaces of whole-round pieces were then 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 vertical, 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. Sections were then transferred to the Section Half Multisensor Logger (SHMSL), with which color reflectance and contact probe magnetic susceptibility were measured (see “Section Half Multisensor Logger measurements”).

Following core 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 to 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”) and selected half-round core pieces were measured for thermal conductivity measurements (see “Physical properties”).

Digital color close-up images were taken of particular features for illustrations, as requested by individual scientists. Working section halves of cores were sampled for both shipboard characterizations of cores and, later during the expedition, for shore-based studies. Samples were routinely taken for shipboard physical properties (8 cm3 cubes), paleomagnetism (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 initial shipboard 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 345, the cores remained on the ship. After the ship transited to Victoria, Canada, they were shipped to the IODP Gulf Coast Repository in College Station, Texas (USA).

Information architecture

Laboratory Information Management System

The 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 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 system for different purposes (Fig. F5).

Data capture tools

All core pieces collected and samples taken during Expedition 345 were registered in the LIMS database using the Sample Master application. The program has workflow-specific interfaces to meet the needs of different users. Core piece registration began with the driller entering information about the hole and then the cores retrieved from the hole. IODP staff entered additional core information, sections, pieces, and any other subsamples taken from these, such as cubes or thin section billets.

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 (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 cameras mounted on optical microscopes.

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

Physical property, paleomagnetism, and geochemistry analytical systems in the shipboard laboratories were used for the capture of 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 explicitly 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. The main DESClogik interface is a spreadsheet with extensive data entry and data validation support. The columns and tabs were entirely configurable by USIO staff based on users’ definitions of what information should be collected (see “Core description overview”). USIO staff then enabled entry columns based on sets of parameters that made up the DESCINFO data structure.

Data retrieval

Data tables were mostly populated using LIMS Reports (Fig. F5), with which the user selected the type of desired information from ~30 available reports, selected a hole (and core pieces and sections), and used additional report-specific filters as desired to view a report online or download information in a standard comma-separated value (CSV) file. For information reporting not yet implemented in the LIMS Reports, another program (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.

Another alternative was to use LIMS2Excel, a highly configurable Java-based data extractor with which users 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, 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. Each team was assigned shifts that were intended to provide time and space to examine the cores and also to ensure overlap with the other teams for information exchange.

At the beginning of the expedition, each group defined observables as Excel spreadsheet columns, with descriptive terminology and definitions defined as appropriate for each measurement. These 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, value lists were configured 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, for example, abundance percentage, size, intensity, and rank (for plotting) of physical constituents, texture, and structures.

Descriptive data capture workbooks

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

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 core section summary graphic, historically referred to as the visual core descriptions (VCDs). All information for VCDs was retrieved from the LIMS database with 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. All information displayed on the VCDs were plotted or otherwise collected from the LIMS database in a semiautomated process supported by USIO staff.

Thin section description overview

Work flow

Thin sections were prepared on board after the daily shipboard sample party. Metadata, including the rationale for taking each section, were recorded and entered into the LIMS database. Finished thin sections were available ~1 day after sampling and were given an immediate preliminary description by the igneous petrology team. Detailed descriptions were conducted by each of the three teams in turn, and observational data were recorded in DESClogik and all digital imaging (whole-round sections, split sections, and close-up images, and photomicrographs) uploaded into the LIMS database. Concise summaries of findings are presented in the section-by-section VCDs and thin section summaries.

1 Gillis, K.M., Snow, J.E., Klaus, A., Guerin, G., Abe, N., Akizawa, N., Ceuleneer, G., Cheadle, M.J., Adrião, Á., Faak, K., Falloon, T.J., Friedman, S.A., Godard, M.M., Harigane, Y., Horst, A.J., Hoshide, T., Ildefonse, B., Jean, M.M., John, B.E., Koepke, J.H., Machi, S., Maeda, J., Marks, N.E., McCaig, A.M., Meyer, R., Morris, A., Nozaka, T., Python, M., Saha, A., and Wintsch, R.P., 2014. Methods. In Gillis, K.M., Snow, J.E., Klaus, A., and the Expedition 345 Scientists, Proc. IODP, 345: College Station, TX (Integrated Ocean Drilling Program). doi:10.2204/iodp.proc.345.102.2014

2Expedition 345 Scientists’ addresses.

Publication: 12 February 2014
MS 345-102