MBARI procedures for automated nutrient analyses using a modified Alpkem Series 300 Rapid Flow Analyzer

This report documents the methods used at the Monterey Bay Aquarium Research Institute (MBARI) for analyzing seawater nutrient samples with an Alpkem Series 300 Rapid Flow Analyzer (RFA) system. The methods have been optimized for the particular requirements of this laboratory. The RFA system has been used to analyze approximately 20,000 samples during the past two years. The methods have been optimized to run nutrient analyses in a routine manner with a detection limit of better than -±1% and a within run precision of -±1% of the full scale concentration range. The normal concentration ranges are 0-200 ~M silicate, 0-5 ~M phosphate, 0-50 ~M nitrate, 0-3 ~M nitrite, and 0-10 ~M ammonium. The memorandum is designed to be used in a loose-leaf binder format. Each page is dated and as revisions are made, they should be inserted into the binder. The revisions should be added into the binder. Retain the old versions in order to maintain a historical record of the procedures. (88 pages)

An Easy-to-Construct Automated Winkler Titration System

The instrument described in this report is an updated version of the high precision, automated Winkler titration system described by Friederich et al.(1984). The original instrument was based on the work of Bryan et al. (1976) who developed a colorimetric endpoint detector and on the work of Williams and Jenkinson (1982) who produced an automated system that used this detector. The goals of our updated version of the device described by Friederich et al. (1984) were as follows: 1) Move control of the system to the MS-DOS environment because HP-85 computers are no longer in production and because more user-friendly programs could be written using the IBM XT or AT computers that control the new device. 2) Use more "off the shelf" components and reduce the parts count in the new system so that it could be easily constructed and maintained. This report describes how to construct and use the new automated Winkler titration device. It also includes information on the chemistry of the Winkler titration, and detailed instructions on how to prepare reagents, collect samples, standardize and perform the titrations (Appendix I: Codispoti, L.A. 1991 On the determination of dissolved oxygen in sea water, 15pp.). A disk containing the program needed to operate the new device is also included. (pdf contains 33 pages)

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate maps from James Island to Ozette Lake, Washington Outer Coast

Without knowledge of basic seafloor characteristics, the ability to address any number of critical marine and/or coastal management issues is diminished. For example, management and conservation of essential fish habitat (EFH), a requirement mandated by federally guided fishery management plans (FMPs), requires among other things a description of habitats for federally managed species. Although the list of attributes important to habitat are numerous, the ability to efficiently and effectively describe many, and especially at the scales required, does not exist with the tools currently available. However, several characteristics of seafloor morphology are readily obtainable at multiple scales and can serve as useful descriptors of habitat. Recent advancements in acoustic technology, such as multibeam echosounding (MBES), can provide remote indication of surficial sediment properties such as texture, hardness, or roughness, and further permit highly detailed renderings of seafloor morphology. With acoustic-based surveys providing a relatively efficient method for data acquisition, there exists a need for efficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), and through a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourier histogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures and classification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributed using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)

Benthic habitat mapping in the Olympic Coast National Marine Sanctuary: Classification of side scan sonar data from survey HMPR-108-2002-01: Version I

In September 2002, side scan sonar was used to image a portion of the sea floor in the northern OCNMS and was mosaiced at 1-meter pixel resolution using 100 kHz data collected at 300-meter range scale. Video from a remotely-operated vehicle (ROV), bathymetry data, sedimentary samples, and sonar mapping have been integrated to describe geological and biological aspects of habitat and polygon features have been created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). The data can be used with geographic information system (GIS) software for display, query, and analysis. Textural analysis of the sonar images provided a relatively automated method for delineating substrate into three broad classes representing soft, mixed sediment, and hard bottom. Microhabitat and presence of certain biologic attributes were also populated into the polygon features, but strictly limited to areas where video groundtruthing occurred. Further groundtruthing work in specific areas would improve confidence in the classified habitat map. (PDF contains 22 pages.)

Tracking Pacific bluefin tuna (Thunnus thynnus orientalis) in the northeastern Pacific with an automated algorithm that estimates latitude by matching sea-surface-temperature data from satellites with temperature data from tags on fish

Data recovered from 11 popup satellite archival tags and 3 surgically implanted archival tags were used to analyze the movement patterns of juvenile northern bluefin tuna (Thunnus thynnus orientalis) in the eastern Pacific. The light sensors on archival and pop-up satellite transmitting archival tags (PSATs) provide data on the time of sunrise and sunset, allowing the calculation of an approximate geographic position of the animal. Light-based estimates of longitude are relatively robust but latitude estimates are prone to large degrees of error, particularly near the times of the equinoxes and when the tag is at low latitudes. Estimating latitude remains a problem for researchers using light-based geolocation algorithms and it has been suggested that sea surface temperature data from satellites may be a useful tool for refining latitude estimates. Tag data from bluefin tuna were subjected to a newly developed algorithm, called “PSAT Tracker,” which automatically matches sea surface temperature data from the tags with sea surface temperatures recorded by satellites. The results of this algorithm compared favorably to the estimates of latitude calculated with the lightbased algorithms and allowed for estimation of fish positions during times of the year when the lightbased algorithms failed. Three near one-year tracks produced by PSAT tracker showed that the fish range from the California−Oregon border to southern Baja California, Mexico, and that the majority of time is spent off the coast of central Baja Mexico. A seasonal movement pattern was evident; the fish spend winter and spring off central Baja California, and summer through fall is spent moving northward to Oregon and returning to Baja California.

Indirect validation of the age-reading method for Pacific cod (Gadus macrocephalus) using otoliths from marked and recaptured fish

Two examples of indirect validation are described for age-reading methods of Pacific cod (Gadus macrocephalus). Aging criteria that exclude faint translucent zones (checks) in counts of annuli and criteria that include faint zones were both tested. Otoliths from marked and recaptured fish were used to back-calculate the length of each fish at the time of its release by using measurements of the area of annuli. Estimated fish size at time of release and actual observed fish size were similar, supporting the assumption that translucent zones are laid down on an annual basis. A second method for validating reading criteria used otolith age and von Bertalanffy parameters, estimated from the tagging data, to predict how much each fish grew in length after tagging. We found that otolith aging criteria applied to otoliths from tagged and recovered Pacific cod predicted quite accurately the growth increments that we observed in these specimens. These results provide further evidence that the current aging criteria are not underestimating the age of the fish and support our current interpretation of checks (i.e., as subannual marks). We expect these indirect validations to advance age determination for Pacific cod, which in turn would enhance development of stock assessment methods based on age structure for this species in the eastern Bering Sea.

River Dart Scale Reading Investigation Report on the 1965 Season

This is the fourth River Dart Scale Reading Investigation Report on the 1965 season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All it summarized in tables, and figures are included plotting weight distributions for each age classes and frequency distributions.

River Dart Scale Reading Investigation Report on the 1966 Season

This is the fifth River Dart Scale Reading Investigation Report on the 1966 Season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All it summarized in tables, and figures are included plotting weight distributions for each age classes and frequency distributions. It also compares the results of previous reports.

River Dart Scale Reading Investigation Report on the 1967 Season

This is the sixth and final River Dart Scale Reading Investigation Report on the 1967 Season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All it summarized in tables, and figures are included plotting weight distributions for each age classes and frequency distributions. It also compares the results of previous reports and gives a full summary for the investigation (including previous reports).

River Dart Scale Reading Investigation Report on the 1962 Season

This is the first River Dart Scale Reading Investigation Report on the 1962 season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. It reviews briefly the theory and mechanics of the scale-reading technique, the life history of the salmon, and the methods used for the collection of scales and the examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All are summarized in various tables and figures are also included, plotting weight distributions for each age classes and frequency distributions.

River Dart Scale Reading Investigation Report on the 1963 Season

This is the second River Dart Scale Reading Investigation Report on the 1963 season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All are summarized in tables, and figures are alo included plotting weight distributions for each age classes and frequency distributions. The report also remarks the similarity of the results with those for 1962.

River Dart Scale Reading Investigation Report on the 1964 Season

This is the third River Dart Scale Reading Investigation Report on the 1964 season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All are summarized in tables, and figures are also included plotting weight distributions for each age classes and frequency distributions. After three years of the investigation a pattern is emerging which shows that the Dart salmon population is mainly composed of four year old fish, which have spent two years in the river and then two year or little longer at sea.

River Dart Scale Reading Investigation 1971

This is the River Dart Scale Reading Investigation Report on the 1971 season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. In 1967 the final report on a five-year scale reading programme was summarised, at the time it was considered sufficient information to help with restocking programmes and the management of salmon population. But a further scale reading programme was started in an attempt to monitor changing patterns in salmon runs that may be caused by the new influences. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All are summarized in tables, and figures are also included plotting weight distributions for each age classes and frequency distributions.

River Dart Scale Reading Investigation 1972

This is the River Dart Scale Reading Investigation Report on the 1972 season by the Devon River Board. The object of this investigation is to examine, by means of scale-reading, the general biology of the salmon population of the River Dart. In 1967 the final report on a five-year scale reading programme was summarised, at the time it was considered sufficient information to help with restocking programmes and the management of salmon population. But a further scale reading programme was started in an attempt to monitor changing patterns in salmon runs that may be caused by the new influences. It reviews the methods used for collection of the scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All is summarized in tables, and figures are included showing weight distributions for each age classes and frequency distributions.

River Exe Scale Reading Investigation. 5th Annual Report for the 1970 Season

This is the 5th Annual Report of the Rive Exe Scale Reading Investigation for the 1970 season by the Devon River Authority. The object of this investigation is to examine, by means of scale reading, the biology of age classes of the salmon population of the River Exe. It reviews the methods used for the collection of scales and examination of the materials. It shows the results of the survey and the number of scales studied from each of the various sea-age classes, time of running with distribution of the sea-age groups throughout the season, fish sizes and smolt ages at migration. All is summarized in tables, and figures are included showing weight distributions for each age classes and frequency distributions.