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27 results for “san francisco estuary”
Surface and bottom hourly water temperature from the San Francisco Estuary, 2012-2019
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, which may cause them to seek microrefugia. While several state and federal agencies in the SFE collect real-time water temperature data, most of the water temperature collection sites are at a fixed location or floating near the surface of the water column. This dataset includes four real-time water quality stations that provide water temperature data for both the surface and bottom positions in the water column. We obtained surface water temperature data from an integrated hourly water temperature dataset (https://doi.org/10.6073/pasta/7385985f68b02c0deb2a9e425a9f3ad8). This dataset included data downloaded from the California Data Exchange Center (CDEC; https://cdec.water.ca.gov/) and cleaned with a series of quality control (QC) checks (see integrated dataset metadata). We obtained bottom temperature data from the California Department of Water Resources (DWR) internal database Water Quality Portal (WQP). Data were integrated and standardized to hourly water temperature data in degrees Celsius, and the same series of quality control (QC) checks from the surface dataset were applied in a consistent manner to all stations. Bottom temperatures were selected from surface temperatures to provide measures of temperature difference. Datasets included in this package include source hourly surface and bottom data, both obtained from DWR’s WQP, as well as an integrated dataset of cleaned hourly surface and bottom data, with calculated surface-bottom temperature differences. Both datasets are filtered to the timeframe used in an analysis of surface-bottom temperature differences. Additionally, information regarding current
California Department of Fish and Wildlife Enhanced Large Fish Study, San Francisco Estuary, California, 2023 Gillnet Survey
The Enhanced Large Fish Study (ELFS) was established and included in the Interagency Ecological Program (IEP) work plan in 2023 to fill some of the monitoring gap of fishes in the San Francisco Estuary (SFE), California. The fish monitoring of the IEP prior to ELFS primarily consisted of trawl- and seine-based surveys, which generally capture small and/or juvenile fishes due to survey gear and methodologies. In order to more effectively sample the large/adult fish portion of SFE fish communities, the ELFS uses American Fisheries Society experimental gillnets, plus the inclusion of the optional "large fish panel," to sample the waters of the SFE. The experimental gillnets measure 24.4m in length, 1.8m in depth, and includes eight 3m length panels with stretch mesh measurements of 76.2mm, 114.3mm, 50.8mm, 88.9mm, 38.1mm, 127.0mm, 63.5mm, and 101.6mm. The optional large fish panel measures 9.1m by 1.8m in depth and includes three 3m length panels with stretch mesh measurements of 152.4, 177.8, and 203.2mm. The ELFS conducted its first year of sampling in the North Delta, California, in 2023, and will be expanded to the greater Delta and Suisun Bay and Marsh in future sampling years. The ELFS is currently funded as a special study to inform future monitoring, with funding contracted through fiscal year 2026-2027.
Selected trait data for the most abundant phytoplankton, zooplankton, benthic invertebrates, and fishes of the Upper San Francisco Estuary
This data set includes selected trait data from published literature and online databases for the most common phytoplankton, zooplankton, benthic invertebrate, and fish taxa at long term monitoring stations in the Upper San Francisco Estuary, which includes the Sacramento-San Joaquin River Delta, Suisun Bay, and Grizzly Bay.
Time-varying flow-ecology relationships for an endangered fish population: Longfin Smelt in the San Francisco Estuary
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Disentangling abiotic and biotic controls of age-0 Pacific herring population stability across the San Francisco Estuary
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Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates
<p>Environmental DNA (eDNA) methods complement traditional monitoring and can be configured to detect multiple species simultaneously. One such approach, eDNA metabarcoding, uses high-throughput DNA sequencing to indirectly detect many different organisms, spanning broad taxonomic boundaries, from water samples. We are optimizing a non-invasive, low cost eDNA metabarcoding protocol to be used in conjunction with existing monitoring programs. One resource that is currently lacking for metabarcoding studies in general, including those in the San Francisco Estuary (SFE), is a comprehensive database of DNA barcode reference sequences. Without this foundational data, many species go undetected or misidentified in metabarcoding studies. To meet this need, we generated a custom barcode sequence database for the SFE by DNA sequencing and mining of public DNA seqeunce data for estuarine and freshwater species of interest to monitoring programs and ecological studies. Here we present custom reference sequence databases for three barcodes: Cytochrome C Oxidase I (COI), 12S MiFish and 16S.</p>
Reference sequence database for eDNA metabarcoding of San Francisco estuary fishes and invertebrates
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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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.