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27 results for “san francisco estuary”
San Francisco Estuary Institute Phytoplankton eDNA and Toxin Monitoring, San Francisco Bay, CA, 2014-2023
From late 2014-present, San Francisco Estuary Institute has conducted molecular monitoring of phytoplankton in partnership with the US Geological Survey from several stations stretching from Rio Vista in the North Delta to the Lower South Bay, past the Dumbarton Bridge. These samples have been analyzed for 18S eDNA data in partnership with Timothy Otten at Bend Genetics, targeting the V7 region. The included dataset covers the 2014-2023 period, including data up to 2022, conducted with an Illumina MISEQ platform, and from 2022-2023 using a NEXTSEQ platform, which enabled much greater sampling depth. Two sets of taxonomic assignments are included in this data release, one using the Silva database, and the other using the PR2 database, two of the leading sources of phytoplankton taxonomic data aiding in assignments of OTUs to taxa. Raw sequence data will also be uploaded to NCBI for comparison. Data collection continues and this release will be updated as new time periods are added.
Interagency Ecological Program: Integrated Dataset of Phytoplankton Enumeration Data in the San Francisco Estuary, 1992-2024
Phytoplankton community composition is an important driver of zooplankton productivity and food supply for higher trophic levels in the San Francisco Estuary. Various monitoring surveys throughout the region collect phytoplankton enumeration data dating back to the 1990s. These include surveys from the CA Department of Water Resources (CADWR), CA Department of Fish and Wildlife (CDFW), the US Bureau of Reclamation (USBR), and the US Geological Survey (USGS). These surveys collect data via various sampling and laboratory methods which are not always directly comparable. This integrated dataset includes both enumeration counts and well-documented metadata to allow for informed decision-making in the integration of these data. It also standardizes taxonomic names between groups via a key list. Note that, in this dataset, we make conservative decisions about taxonomic resolution to ensure maximum compatibility between groups. For more detailed metadata and higher taxonomic resolution, refer to individual surveys’ publications or reach out to their primary contact.
Data from “Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary”
This publication includes the raw data from the manuscript: Lojkovic Burris, Z. P., R. D. Baxter, and C. E. Burdi. 2022. Larval and juvenile Longfin Smelt diets as a function of fish size and prey density in the San Francisco Estuary. California Fish and Wildlife Journal 108:e11. http://www.doi.org/10.51492/cfwj.108.11 Data includes the diets of larval and juvenile Longfin Smelt in the San Francisco Estuary from 2005 to 2008 in the form of diet by number, diet by weight, macroinvertebrate prey lengths, prey length-weight equations, and prey weight conversions.
Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program Data, 2016-2024
The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. The main purpose of EDSM is to provide information about endemic Delta Smelt (Hypomesus transpacificus) population sizes and distributions within the upper San Francisco Estuary. To track the life cycle of this annual species, larval trawling with a fine-mesh (20 mm) net is conducted during the spring months, and Kodiak trawling for juveniles and adults occurs during the summer, fall, and winter months. Sampling sites are chosen via a stratified random sampling design. A minimum of two tows are conducted at each site, and field staff typically sample between 18 and 41 sites weekly. All fish collected are identified and enumerated, and a subset are measured for body length. Environmental data (water temperature, conductivity, dissolved oxygen, turbidity, depth) are also measured. In addition to Hypomesus spp., this long-term monitoring dataset can also be useful in evaluating the status and trends of other species of interest, especially pelagic fishes. For more information: https://www.fws.gov/office/lodi-fish-and-wildlife
Interagency Ecological Program: Zooplankton abundance in the Upper San Francisco Estuary from 1972-2021, an integration of 7 long-term monitoring programs
The upper San Francisco Estuary is an inland inverse delta formed by the confluence of 5 major rivers that drain 40% of the land in California (USA). It is a central hub of water delivery in California and home to a number of commercially important and endangered fish, such as Chinook Salmon, Green Sturgeon, and Delta Smelt. To monitor the environmental impacts of water exports from this system, extensive ecological monitoring has been conducted since the 1960s. To track lower trophic levels, zooplankton abundance has been monitored from 1972 to present. Starting with just one survey (the CA Department of Water Resources’ [CDWR] and California Department of Fish and Wildlife’s [CDFW] Environmental Monitoring Program) in 1972, the suite of zooplankton surveys gradually expanded with time. Several surveys traditionally focused on monitoring fish abundance added zooplankton nets to their sampling programs. The CDFW 20-mm larval fish survey added zooplankton sampling in 1995, the CDWR Yolo Bypass Fish Monitoring Program add zooplankton in 1999, the CDFW Summer Townet Survey added zooplankton in 2005, and the Fall Midwater Trawl added zooplankton in 2007. Two new sampling programs, the Fish Restoration Program and Directed Outflow Project, began in 2015 and 2017, respectively. All sampling programs continue today. Each survey samples once or twice monthly at set of fixed or random stations that varies across surveys depending on their objectives. While the Environmental Monitoring Program samples year-round, the other surveys are mostly seasonal, although additional months were sampled in some years. Most surveys target open channels although the Fish Restoration Program samples in or near shallow tidal wetlands. Three size classes of zooplankton are targeted by these sampling programs with different net mesh sizes: micro zooplankton (copepods and rotifers) are targeted with a 43 µm mesh net, meso zooplankton (copepods and cladocerans) are targeted with 150 - 160 µm mesh
Interagency Ecological Program: Over four decades of juvenile fish monitoring data from the San Francisco Estuary, collected by the Delta Juvenile Fish Monitoring Program, 1976-2025
The United States Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP) has monitored juvenile Chinook Salmon Oncorhynchus tshawytscha and other fish species within the San Francisco Estuary (Estuary) since 1976 using a combination of surface trawls and beach seines. Since 2000, three trawl sites and 58 beach seine sites have been sampled weekly or biweekly within the Estuary and lower Sacramento and San Joaquin Rivers. As part of the Interagency Ecological Program (IEP) that manages the Estuary, the DJFMP has tracked the relative abundance and distribution of naturally and hatchery produced juvenile Chinook Salmon of all races as they outmigrate through the Sacramento-San Joaquin Delta for over four decades. The data that DJFMP collected has been used not only to help inform the management of Chinook Salmon, but also to monitor the status of native species of interest such as the previously listed Sacramento Splittail Pogonichthys macrolepidotus and invasive species such as Mississippi Silverside Menidia audens and Largemouth Bass Micropterus salmoides. DATA CORRECTION/UPDATE: Previous data versions 244.6, 244.7, and 244.8 contained an error and resulted in duplicated records of hatchery Chinook Salmon in the datasets. These datasets were removed from the data repository and the error was corrected in version 244.9 and after. DNA Data: Full more details of the DNA methods and results for juvenile Chinook salmon included in this dataset, please check out Blankenship, S.M., J. Israel, E. Buttermore, and K. Reece. 2021. Knights Landing, California Department of Fish and Wildlife, Genetic Determination of Population of Origin 2017 through 2019 ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/85fbc988c0b1362e84c318e69c7a939e. For more information on the Delta Juvenile Fish Monitoring Program: https://www.fws.gov/project/delta-juvenile-fish-monitoring-program
Interagency Ecological Program San Francisco Estuary Smelt Larva Survey 2009 – 2025
The Interagency Ecological Program's Smelt Larva Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 2009 to monitor the distribution and abundance of newly hatched Longfin Smelt (Spirinchus thaleichthys) in the San Francisco Estuary. Surveys are conducted bi-weekly, and sampling begins in December and continues through mid-March. The SLS samples at fixed stations, from San Pablo Bay through Suisun Bay and into the Sacramento-San Joaquin River Delta. Napa River stations were added in 2014 and the San Pablo Bay expansion stations were added in December 2022. Each sampling week currently consists of 59 stations. At each station, one 10-minute stepped oblique (bottom to top) tow is conducted following a prescribed tow schedule. The net is a conical 500 µm mesh lashed to a D-shaped frame mounted on skis. Larval fish samples are preserved in the field in 10% formalin and brought back to the CDFW Stockton Lab for identification and enumeration under a microscope. Several types of data are collected at each station in addition to the larval fish sample, including the volume of water sampled by the net, surface water temperature, surface and bottom specific conductance (EC normalized at 25˚C), Secchi disk depth, tow duration, tidal condition, and surface water turbidity.
Hourly water temperature from the San Francisco Estuary, 1986 - 2019
Projected temperature increases due to global climate change are likely to have localized impacts on the San Francisco Estuary (SFE). Increased water temperature in the SFE will lead to challenges for managing water resources. Many native species, such as salmon and smelt, rely on cooler water, and will be further stressed by increased water temperature. While real-time water temperature is collected by several state and federal agencies in the San Francisco Estuary, a landscape-scale synthesis of available water temperature data has not been conducted for the SFE. For this dataset, we compiled continuous water temperature data and associated metadata from the SFE to generate an integrated and usable dataset of known quality for climate and ecological analysis. Data were obtained from the California Data Exchange Center (CDEC; https://cdec.water.ca.gov/) for consistency (data are untreated) and efficiency (existing code to download data directly from CDEC). Data were integrated and standardized to hourly water temperature data in degrees Celsius. A series of quality control (QC) checks were then applied in a consistent manner to all stations. Datasets included in this package include raw hourly data, flagged data, and filtered data (where flagged data are removed). Additionally, information regarding current and historical sensors used for water temperature data collection was obtained from station managers for each station, and compiled in a metadata table.
Six decades (1959-2022) of water quality in the upper San Francisco Estuary: an integrated database of 16 discrete monitoring surveys in the Sacramento San Joaquin Delta, Suisun Bay, Suisun Marsh, and San Francisco Bay
The upper San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated water quality data from 16 boat-based long-term monitoring surveys in the upper SFE. This integrated dataset includes measurements of temperature (surface and bottom), conductivity (surface), salinity (surface), Secchi depth, qualitative concentration of the toxic alga Microcystis (surface), Chlorophyll-a concentration (surface), nutrients (surface), and other parameters from 1959 - 2022. The component surveys range in sampling frequency from thrice weekly to monthly and range in duration from 5 – 60 years. Most component surveys sample at fixed stations, but the Enhanced Delta Smelt Monitoring survey uses random sites and some stations (with “EZ” in the station name) of the Environmental Monitoring Program follow the salinity field. It is highly recommended to inspect the documentation of the component surveys for more information on their methods.
Fish abundance in the San Francisco Estuary (1959-2024), an integration of 10 monitoring surveys.
The San Francisco Estuary (SFE) is simultaneously a central hub of water delivery in California and home to commercially important and endangered fishes, such as Chinook Salmon, Green Sturgeon, and Delta and Longfin Smelt. Extensive ecological monitoring has been conducted for over 50 years, mainly under the auspices of the Interagency Ecological Program for the San Francisco Estuary (https://iep.ca.gov/). We integrated fish catch and length data from 10 long-term monitoring surveys in the SFE. The integrated database contains survey-level data such as environmental variables and sampling effort in addition to the fish-level species, lengths, and counts. Zero catches have been filled in for any species not caught in a sample. The geographic scope includes San Francisco Bay through the upper estuary, and the timeseries spans 1959 to 2024. Sampling methods, gear, fish length metric, and other factors differ among the component surveys. Sampling designs (locations and temporal frequency) have also changed over time. Thus, it is highly recommended to inspect the documentation of the component surveys for more information on their methods.
Cyanobacteria abundance, cyanotoxin concentration, and water quality data for the upper San Francisco Estuary, California, USA: 2014-2019
The goal of these measurements was to quantify Microcystis abundance and microcystin concentration and associated water quality conditions during summer blooms in the upper San Francisco Estuary in California, USA. Blooms of harmful algae are a major ecological concern in the area because harmful algae produce toxins and other metabolites, which deteriorate water quality and negatively impact the aquatic ecosystem. Our research team collected biological, physical, and chemical data at 2-week to 4-week intervals during the summer and fall from 2014 through 2019. Data included surface measurements of Microcystis volume (area-based diameter) by microscopy (flowCAM digital imaging flow cytometry) and subsurface (1 m depth) measurements of Microcystis, Aphanizomenon and Dolichospermum cell abundance measured by quantitative PCR, cyanotoxin concentration (total microcystins, anatoxin a and saxitoxin) measured by protein phosphatase inhibition assay or enzyme linked immunosorbent assay, and a suite of water quality parameters (water temperature, dissolved oxygen, nutrient concentration, water transparency, specific conductance, turbidity, pH, and chlorophyll a concentration). Details for the field sampling and analytical methods are available in Lehman et al. (2017). We also performed shotgun metagenomic analyses to investigate biodiversity of cyanobacteria and other aquatic microorganisms and all the DNA sequencing data are publicity available (www.ncbi.nlm.nih. gov/; BioProject ID: PRJNA434758, Kurobe et al. 2018, Lehman et al. 2021). During the study, we experienced critically dry (2014 and 2015), below normal (2016 and 2018), and wet years (2017 and 2019), therefore data obtained in this study provided a unique opportunity to assess impacts of extreme conditions on the aquatic ecosystem (Kurobe et al. 2018, Lehman et al. 2020).
Interagency Ecological Program: Zooplankton and water quality data in the San Francisco Estuary collected by the Summer Townet and Fall Midwater Trawl monitoring programs.
The Interagency Ecological Program’s (IEP) Summer Townet Survey (STN) and Fall Midwater Trawl (FMWT) are two long-term monitoring projects conducted by the California Department of Fish and Wildlife (CDFW) to monitor fish abundance and distribution trends in the San Francisco Estuary (SFE) since 1959 and 1967, respectively. Starting in 2005, zooplankton monitoring was added and paired with fish tows to investigate food availability for young fishes. Food limitation has been a long-term issue and a focus of the Pelagic Organism Decline (POD) studies that began in 2005. By 2011, STN routinely conducted zooplankton monitoring at 40 stations, and FMWT at 32 stations in the upper SFE from Carquinez Strait to the Sacramento Deep Water Ship Channel and into the South Delta. STN samples every other week from June to August and FMWT samples once monthly from September to December. Both projects collect mesozooplankton samples using a modified Clarke-Bumpus (CB) net to target copepods and cladocerans, and FMWT also samples macrozooplankton (i.e. mysids and amphipods) using a mysid net. Flowmeters are used to measure the volume sampled to determine zooplankton catch per unit effort. Environmental variables such as water temperature, turbidity, secchi, and electrical conductivity are collected with each zooplankton sample. Concurrent fish and zooplankton tows conducted by STN and FMWT have allowed for comparisons of fish diet to the available zooplankton prey at the time of collection.
Interagency Ecological Program: Summer Townet Survey for Young Pelagic Fishes in the San Francisco Estuary
The Interagency Ecological Program’s (IEP) Summer Townet Survey (STN) is a long-term effort to monitor the annual recruitment success of young pelagic fishes in the upper San Francisco Estuary (California, United States). Conducted by the California Department of Fish and Wildlife (CDFW) since 1959, STN has sampled fixed locations from Eastern San Pablo Bay to Rio Vista on the Sacramento River, and to Stockton on the San Joaquin River; and a single station in the lower Napa River. The study area was expanded in 2011 to include the Sacramento Deep Water Ship Channel (SDWSC) and Cache Slough (CS). Currently, 40 stations are sampled as a “survey” every other week June through August for 6 surveys. A conical net, lashed to a fixed metal “D” frame, is pulled obliquely through the water column 2 to 3 times at each station. All fish and macro-invertebrates are identified and enumerated from each tow, with fork lengths (mm) of the first 50 of each fish species also recorded. Fish catch, length-frequency, and catch-per-unit-effort (CPUE) among stations is available with data visualization tools on the study website for all species (https://wildlife.ca.gov/Conservation/Delta/Townet-Survey). Data collected at historic 31 stations are used to calculate annual relative abundance indices for age-0 Striped Bass (Morone saxatilis) and Delta Smelt (Hypomesus transpacificus). The remaining 9 stations are sampled to expand our sampling range further upriver and increase our understanding of larval and juvenile fish abundance and distribution in the lower Napa River and the North Delta. A meso-zooplankton net targeting copepods and cladocerans is also used in parallel to assess fish food resources at each station and a subset of the fish collected are retained for diet analysis by CDFW researchers (beginning 2005, see STN and FMWT zooplankton data on EDI). The STN also measures habitat conditions via water temperature (°C), water clarity (Secchi disk depth in cm), Turbidity (NTU) and s
Delta Smelt (Hypomesus transpacificus) biomarker and genetic data from supplemental release into the San Francisco Estuary, 2022
Delta Smelt (Hypomesus transpacificus) is an endangered fish that is endemic to the San Francisco Estuary. As a conservation strategy, hatchery-reared Delta Smelt have been released into the San Francisco Estuary to supplement the wild population. State and federal agencies surveyed the abundance of Delta Smelt, collected fish specimens, and recorded associated environmental data from sampling sites. Delta Smelt specimens were preserved and transported to the University of California, Davis where a variety of biomarkers were assessed on individual fish. This project, including the supplementation of hatchery-reared Delta Smelt and data collection, is ongoing.
Interagency Ecological Program: Data for Synthesis for Ecological Impacts of Drought in the Upper San Francisco Estuary, 1975-2021
These data were collected for the special issue on Drought in the Sacramento-San Joaquin Delta published in San Francisco Estuary and Watershed Sciences, Volume 22, Issue 1, March of 2024. Multi-year droughts are important and impactful features of California’s Mediterranean climate and can fundamentally affect the water quality and the ecosystem response of the San Francisco Estuary and the Sacramento-San Joaquin Delta. This data set was assembled from data collected by long-term monitoring programs over the past 46 years (1975-2021) to evaluate how the estuary changed during multi-year droughts. Data include fish, zooplankton, jellyfish, clams, temperature, Secchi depth, and salinity as measured by fish and water quality surveys, as well as nutrients and chlorophyll measured by water quality surveys. These data are accompanied by hydrologic metrics including Delta Inflow, Delta Outflow, the position of the 2-PSU isohaline, residence time, and daily values of various continuous water quality stations located in the Delta.
Interagency Ecological Program San Francisco Estuary Larval Entrainment Study (LES)
Fish entrainment into California's State Water Project (SWP) and Central Valley Project (CVP) has been a source of mortality for native osmerid species, including Delta Smelt (Hypomesus transpacificus) and Longfin Smelt (Spirinchus thaleichthys). While entrained adult and juvenile fishes are collected, identified and enumerated, the facilities design does not allow for a quantifiable estimate of larval fishes being entrained. This knowledge gap makes it difficult for managers to make scientifically informed decisions regarding the endangered Longfin & Delta Smelt. The Larval Entrainment Study (LES) aims to address this gap by providing a high-resolution dataset and insights into the variable abundances of Smelt at risk of entrainment, the community composition surrounding them, and associated water quality data. Our study design utilizes a variety of gear types and maximizes replicates to improve the understanding of larval Smelt abundances within the southern reach of the Sacramento and San Joaquin River Delta, the zone of entrainment for the SWP and CVP. Sampling began in 2022 using 10-minute stepped oblique tows of a Smelt Larval Survey (SLS) sled mounted with a 500 μm net. Tows were conducted in West Canal, outside Clifton Court Forebay (CCF), where the risk of entrainment is highest. Sampling was conducted five days a week in 2022 and three days a week in the following years. . Beginning in mid-January 2023, a 940 μm mesh net with the same dimensions as the SLS net was added, with sampling alternating between the two. This provided an intermediate gear between SLS (500 μm) and 20mm (1600 μm) nets. In 2024 we expanded to sample a transect of sites within the Old and Middle River (OMR) corridor. This provides broader spatial resolution and improves our ability to detect Osmerids within the South Delta. Sampling alternated between a high priority day (with intensive sampling in the lower San Joaquin River, SLS stations 809 & 812) and a longer transect day that ran
Delta Smelt Enclosure Studies, North Delta Arc of the upper San Francisco Estuary, CA, 2019 - 2024
This dataset comprises data from seven different enclosure studies, each of which used Delta Smelt reared by the UC Davis Fish Conservation and Culture Laboratory (FCCL). Each study had unique study questions and utilized slightly different methods. Enclosure Prototype (Rio Vista (RV) and Sacramento Deep Water Ship Channel (SDWSC)) – these studies, conducted January through February (RV) and March (SDWSC) of 2019, were designed to test different enclosure mesh sizes to assess their effects on Delta Smelt growth, survival, and feeding efficacy over a period of four weeks. Three different enclosure designs were deployed at two locations (Rio Vista and the Sacramento Deep Water Ship Channel), with 60 to 64 fish per enclosure and a control group of 30 fish at FCCL. See Baerwald et al, 2023 for details. - https://doi.org/10.1371/journal.pone.0286027 North Delta Pilot – This study, conducted in July and August of 2019, was implemented to test the feasibility of using enclosures to evaluate a flow action designed to improve food for Delta Smelt in the Yolo Bypass, and test upper thermal limits in field conditions for cultured Delta Smelt. Three enclosures were placed at Rio Vista and one enclosure was placed in the Yolo Bypass. Each enclosure held 60 fish. A control group of 90 fish was held at FCCL. The study lasted for four weeks; however, the Yolo Bypass enclosures were removed after three weeks following a heat wave that was lethal to all enclosure fish at that site. Suisun Marsh Pilot – This study, conducted in October and November of 2019, tested the feasibility of using enclosures to evaluate a flow action designed to improve low salinity habitat for Delta Smelt in Suisun Marsh. Three enclosures per site were placed at three locations (Suisun Marsh, Rio Vista, and the Yolo Bypass). Each enclosure held 60 fish, and a control group of 90 fish was held at FCCL. The study lasted for four weeks. Domestication/Behavior – This study, conducted in January and February of 20
Fish Restoration Program Tidal Wetland Restoration Monitoring in Upper San Francisco Estuary, 2015-ongoing
The Fish Restoration Program Monitoring Team assesses the biological effectiveness of 8,000+ acres of tidal wetland restoration in the Upper San Francisco Estuary (Sacramento-San Joaquin Delta and Suisun Marsh) through a contract with the CA Department of Water Resources. The restoration is pursuant to requirements in the 2008/2009 and 2019 Biological Opinions for state and federal water project operations. Data on fish and invertebrate abundance on or near these sites was collected as baseline monitoring data and to determine the most efficient methods for monitoring wetlands. Understanding how invertebrate, fish, and phytoplankton communities change pre- to post-restoration is essential to evaluating the benefits of tidal wetlands to native fish species. Invertebrate data was collected using sweep nets, benthic cores, neuston nets, and zooplankton trawls. Fish data was collected using otter trawls, lampara nets, and beach seines. For each method, the team recorded the catch of fish, invertebrates, and other organisms, length of selected organisms, and a suite of environmental information, including: dissolved oxygen, water temperature, pH, specific conductance, turbidity, chlorophyll a, phycocyanin, and dissolved organic carbon. Additional water quality samples, processed for Chlorophyll a, Dissolved Ammonia, Dissolved Nitrite + Nitrate, Dissolved Organic Carbon, Dissolved Organic Nitrogen, Dissolved Ortho-phosphate, Pheophytin a, Total Kjeldahl Nitrogen, Total Organic Carbon, Total Phosphorus, and Total Suspended Solids, were collected at a subset of sampling sites. Data are collected before and after restoration at project and reference sites (Before-After-Control-Impact-design), as well as at adjacent water bodies.
Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey 2002 - 2021
The Interagency Ecological Program San Francisco Estuary Spring Kodiak Trawl Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 2002 to improve the detection rate of pre-spawning and mature Delta Smelt (hypomesus transpacificus). The survey began as the Spring Midwater Trawl Survey, an extension of the Fall Midwater Trawl Survey, in 1991 to assist with water management and export decisions in relation to the distribution of pre-spawning Delta Smelt. Net evaluations studies compared the relative catch efficiency of 3 types of nets and found that the Kodiak net was most effective for Sampling adult Delta Smelt. Objectives of SKT are to improve the ability to detect Delta Smelt, obtain maturity status for adult Delta Smelt, and provide results to scientist and managers on a near real-time basis to ais in resource management. SKT operates 6 monthly surveys December through May each lasting 4-5 days in length. Each survey, 40 fix sample locations are sampled using a standard 10 minute Kodiak trawl with a total length of 65 feet and a fully expanded mouth opening of 25 feet by 6 feet. The volume of water sampled is estimated using a General Oceanics flowmeter placed over the side of the boat. The net is constructed of green or black variable mesh ranging in dimension from 2 inches knoteted stretched mesh at the mouth and decreasing by ½ inch through a series of 5 panels to ¼ inch knotless stretched mesh at the cod-end. All fish sampled are identified to species and enumeration, Delta Smelt are staged in the field. At each station, environmental and water quality data are also collected, and include: temperature, electrical conductivity (normalized @ 25°C), water clarity, and tidal condition.
Interagency Ecological Program San Francisco Estuary 20-mm Survey 1995 - 2024
The Interagency Ecological Program San Francisco Estuary 20-mm Survey was initiated by the California Department of Fish and Wildlife (CDFW) in 1995 to monitor the distribution and abundance of post-larval and juvenile Delta Smelt (Hypomesus transpacificus). Delta Smelt are considered to be an annual fish endemic to the upper San Francisco Estuary that spawn in early spring and rear through the summer and fall in fresh to brackish water. Young of the Year (YOY) Delta Smelt are considered juveniles at sizes greater than or equal to 20-mm, and this survey targets those Delta Smelt. The 20-mm Survey currently samples 61 stations at fixed locations from San Pablo Bay through Suisun Bay and into the Sacramento-San Joaquin River Delta every other week from March to July. The survey has historically sampled between 41 and 55 stations. At each station, three 10-minute stepped oblique tows are conducted for fish. Each stepped oblique tow follows a tow schedule to sample the water column up to 32 ft, and the volume of water sampled is estimated using a General Oceanics flowmeter. The net is a cone shaped plankton net composed of 1600μm mesh and measuring 5.5 meters in length with a mouth area of 1.51m2 lashed onto a rigid D-frame with skis. Post-larval and juvenile fish samples are preserved in the field in 10% Formalin dyed with Rose Bengal and brought back to the CDFW Stockton Lab for identification to species and enumeration under a microscope. Fish are measured to fork length or total length when fork is not present. At each station, environmental and water quality data are also collected, and include: top temperature, top and bottom electrical conductivity (normalized at 25 degree C), secchi (cm), surface water clarity (FNU), and tidal condition.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.