Dataset Card for Fish-Visual Trait Analysis (Fish-Vista)

Note that the '' option will only load the CSV files. To download the entire dataset, including all processed images and segmentation annotations, refer to Instructions for downloading dataset and images. See [Example Code to Use the Segmentation Dataset])(https://huggingface.co/datasets/imageomics/fish-vista#example-code-to-use-the-segmentation-dataset)

Figure 1. A schematic representation of the… See the full description on the dataset page: https://huggingface.co/datasets/imageomics/fish-vista.

Dataset Card for Fish-Visual Trait Analysis (Fish-Vista)

  Dataset Deetails





  Dataset Description

The Fish-Visual Trait Analysis (Fish-Vista) dataset is a large, annotated collection of 60K fish images spanning 1900 different species; it supports several challenging and biologically relevant tasks including species classification, trait identification, and trait segmentation. These images have been curated through a sophisticated data processing pipeline… See the full description on the dataset page: https://huggingface.co/datasets/egrace479/fish-vista-test.

The EcoTrends project was established in 2004 by Dr. Debra Peters (Jornada Basin LTER, USDA-ARS Jornada Experimental Range) and Dr. Ariel Lugo (Luquillo LTER, USDA-FS Luquillo Experimental Forest) to support the collection and analysis of long-term ecological datasets. The project is a large synthesis effort focused on improving the accessibility and use of long-term data. At present, there are ~50 state and federally funded research sites that are participating and contributing to the EcoTrends project, including all 26 Long-Term Ecological Research (LTER) sites and sites funded by the USDA Agriculture Research Service (ARS), USDA Forest Service, US Department of Energy, US Geological Survey (USGS) and numerous universities. Data from the EcoTrends project are available through an exploratory web portal (http://www.ecotrends.info). This web portal enables the continuation of data compilation and accessibility by users through an interactive web application. Ongoing data compilation is updated through both manual and automatic processing as part of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA). The web portal is a collaboration between the Jornada LTER and the LTER Network Office. The following dataset from Santa Barbara Coastal (SBC) contains animal density of fish measurements in numberPerMeterSquared units and were aggregated to a yearly timescale.

This data set includes 7 georeferenced and clipped versions of aerial photographs from August 1960, taken over Monte Vista National Wildlife Refuge. A georeferenced mosaic of the photographs is included in the data set. Like other historic photos, this image allows for interpretation of habitat types on the refuge in 1960. Change over time estimates can be made from this image using current imagery for comparison. This image, along with others, are being used by refuge staff to assist in understanding and visualizing the historical content of the lands within the refuge and how they have changed. The original black and white aerial photograph was acquired in digital form from USGS EarthExplorer. Individual frames were referenced to the 2009 NAIP color imagery with ArcMap 10.0. The resolution of the image is 3 meters. This image should be used for resource-level interpretation only.

These data describe the abundance and size of fish species as part of SBCLTER's kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area. The table in this data package documented the annual benthic fish community survey which was conducted once a year around late July or early August. The time period of data collection for the annual benthic fish community survey varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The monthly fish survey at ABUR (Transect 1, 2, and 3), AQUE (Transect1), and MOHK (Transect 1) in 2002. The Transect 2 and 3 at ABUR were discontinued in June 2006. See Methods for more information.

These data describe the abundance and size of fish species as part of SBCLTER’s kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA, and the dataset is updated periodically throughout the year. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area.

Values shown are mean temperature from February to May for each year, the number of spawning days available for Delta Smelt for each period based on temperature (15–20°C), and the median day of year for each spawning period (where January 1st = 1).

This data package is formatted as a Darwin Core Archive (DwC-A, event core). For more information on Darwin Core see https://www.tdwg.org/standards/dwc/. This Level 2 data package was derived from the Level 1 data package found here: https://pasta.lternet.edu/package/metadata/eml/edi/189/2, which was derived from the Level 0 data package found here: https://pasta.lternet.edu/package/metadata/eml/knb-lter-sbc/17/35. The abstract below was extracted from the Level 0 data package and is included for context: These data describe the abundance and size of fish species as part of SBCLTER's kelp forest monitoring program to track long-term patterns in species abundance and diversity. This study began in 2000 in the Santa Barbara Channel, California, USA. The abundance and size of all taxa of resident kelp forest fish encountered along permanent transects are recorded at nine reef sites located along the mainland coast of the Santa Barbara Channel and at two sites on the north side of Santa Cruz Island. These sites reflect several oceanographic regimes in the channel and vary in distance from sources of terrestrial runoff. In these surveys, fish were counted in either a 40x2m benthic quadrat, or in the water parcel 0-2m off the bottom over the same area. The two tables in this data package include: 1) The annual benthic fish community survey which was conducted on 11 reefs once a year around late July or early August; and 2) The monthly fish survey which was conducted once a month at a subset of the sites (3 of the annual sites) The time period of data collection for the annual benthic fish community survey varied among the 11 kelp forest sites. Sampling at BULL, CARP, and NAPL began in 2000, sampling at the other 6 mainland sites (AHND, AQUE, IVEE, GOLB, ABUR, MOHK) began in 2001 (transects 3, 5, 6, 7, 8 at IVEE were added in 2011). Data collection at the two Santa Cruz Island sites (SCTW and SCDI) began in 2004. The monthly fish survey at ABUR (Transect 1, 2, and 3), AQUE (Transect1), and MOHK (Transect 1) in 2002. The Transect 2 and 3 at ABUR were discontinued in June 2006. See Methods for more information. The primary research objective of the Santa Barbara Coastal LTER is to investigate the importance of land and ocean processes in structuring giant kelp (Macrocystis pyrifera ) forest ecosystems. As in many temperate regions, the shallow rocky reefs in the Santa Barbara Channel, California, are dominated by giant kelp forests. Because of their close proximity to shore, kelp forests are influenced by physical and biological processes occurring on land as well as in the open ocean. SBC LTER research focuses on measuring and modeling the patterns, transport, and processing of material constituents (e.g., nutrients, carbon, sediment, organisms, and pollutants) from terrestrial watersheds and the coastal ocean to these reefs. Specifically, we are examining the effects of these material inputs on the primary production of kelp, and the population dynamics, community structure, and trophic interactions of kelp forest ecosystems.

Summary of Delta Smelt survival by enclosure type for Rio Vista (RV) and Deepwater Shipping Channel (DWSC) deployments.

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 specific conductance (µs/cm). Historically, STN began in response to the development of Central Valley Project pumping plants exporting water from the South Delta. STN continues to monitor fish abundance and distribution in relation to water diversions, for the operation of the Central Valley Project and the State Water Project, and management flow actions to improve summer-fall habitat conditions. Managers and researchers use the data collected by STN to inform decisions and improve our understanding of the health of the upper San Francisco Estuary.

The endangered Delta Smelt Hypomesus transpacificus is an osmerid fish endemic to the upper San Francisco Estuary. A captive breeding program for the species led by the Fish Culture and Conservation Laboratory (FCCL), University of California, Davis, began in 1996 to create a refuge population. In order to better understand how captive Delta Smelt would fare in conditions outside of the hatchery, we placed captive-reared fish in enclosures in the Sacramento San-Joaquin Delta, and evaluated their ability to survive, feed, and maintain condition. Fish were acclimated in the hatchery at FCCL, tagged, swabbed, weighed, measured, and transferred to enclosures in the field. There were three types of enclosures (n=2 for each type), varying in mesh size and wrap condition. In January 2019, 384 adult Delta Smelt (243 days post hatch) were transferred to enclosures in Rio Vista. In February 2019, 360 adult Delta Smelt (278 days post hatch) were transferred to enclosures in the Deepwater Shipping Channel. For each deployment, fish remained in enclosures for approximately one month, then were retrieved from enclosures, euthanized, identified, weighed and measured. A subset were also analyzed for diet contents. During the one-month long deployments, cages were checked for biofouling, damage, and dead fish, and water quality measurements and zooplankton samples were collected.

The global aquatic feed attractants market is experiencing robust growth, driven by increasing demand for high-quality aquaculture products and a rising global population requiring sustainable protein sources. The market's expansion is fueled by several key factors, including advancements in attractant technology leading to improved feed efficiency and reduced feed waste. This is further complemented by the growing adoption of sustainable aquaculture practices, emphasizing the need for efficient feed utilization and minimal environmental impact. Major market players are investing heavily in research and development to introduce innovative attractants with enhanced palatability and improved nutritional profiles, catering to the diverse needs of various aquatic species. The market segmentation, encompassing different types of attractants based on their origin (natural vs. synthetic) and target species (shrimp, fish, etc.), offers diverse growth opportunities. Regional variations in market growth are expected, with regions exhibiting strong aquaculture production likely to show higher demand. While challenges like fluctuating raw material prices and stringent regulatory frameworks for feed additives exist, the overall market outlook remains positive. The forecast period (2025-2033) is projected to witness continued expansion, driven by ongoing technological innovation, increasing consumer awareness of sustainable seafood, and expanding aquaculture operations globally. The competitive landscape is marked by the presence of both established players and emerging companies, fostering innovation and market diversification. Strategic partnerships, mergers, and acquisitions are anticipated as major companies seek to expand their market share and product portfolios. Continuous improvements in attractant efficacy and cost-effectiveness are crucial for sustaining the market's growth trajectory.

This report is a summary a trip to Alamosa National Wildlife Refuge and Monte Vista National Wildlife Refuge in 1991, and focuses on the hydrology and soil habitat types. It is part of the moist-soil expert system research project in collaboration with the Missouri Cooperative Fish and Wildlife Research Unit.

To manage the critically low 2021 water supply for beneficial uses, DWR installed the temporary emergency drought barrier (EDB) on West False River in the Sacramento–San Joaquin Delta (Delta), approximately 5 miles south of Rio Vista, California, in Contra Costa County in June 2021. To monitor the effectiveness and impacts of the EBD, a monitoring program was initiated to track changes in hydrodynamics, water quality, fish, harmful algal blooms, and aquatic weeds in the vicinity of the EDB. This data set includes all data collected as part of that monitoring program and subsets of ongoing monitoring programs that were used in the 2021 effectiveness report for the EDB.

Conservation of endangered fishes commonly includes captive breeding, applied research, and management. Since 1996, a captive breeding program has existed for the federally threatened and California endangered Delta Smelt Hypomesus transpacificus, an osmerid fish endemic to the upper San Francisco Estuary. Although this program serves as a captive refuge population, with experimental releases being initiated to supplement the wild population, it was uncertain how individuals would survive, feed, and maintain condition outside hatchery conditions. We evaluated this and the effects of three enclosure designs (41% open, 63% open, and 63% open with partial outer mesh wrap) on growth, survival, and feeding efficacy of cultured Delta Smelt at two locations (Sacramento River near Rio Vista, CA and in Sacramento River Deepwater Ship Channel) in the wild. Enclosures exposed fish to semi-natural conditions (ambient environmental fluctuations and wild food resources) but prevented escape and predation. After four weeks, survival was high for all enclosure types (94–100%) at both locations. The change in condition and weight was variable between sites, increasing at the first location but decreasing at the second location. Gut content analysis showed that fish consumed wild zooplankton that came into the enclosures. Cumulatively, results show that captive-reared Delta Smelt can survive and forage successfully when housed in enclosures under semi-natural conditions in the wild. When comparing enclosure types, we observed no significant difference in fish weight changes (p = 0.58–0.81 across sites). The success of housing captive-reared Delta Smelt in enclosures in the wild provides preliminary evidence that these fish may be suitable to supplement the wild population in the San Francisco Estuary. Furthermore, these enclosures are a new tool to test the efficacy of habitat management actions or to acclimate fish to wild conditions as a soft release strategy for recently initiated supplementation efforts.

This data set includes 31 georeferenced versions of original black and white aerial photographs acquired in digital form from the National Archives and Records Administration (NARA) for Monte Vista National Wildlife Refuge. These photo in this collection, from 1941, is one of the earliest know for this area and were part of the USDA's Agricultural Adjustment Administration's effort to capture the extent and condition of farmland across the US. Individual frames were referenced to the 2009 NAIP color imagery with ArcMap 10.0. The resolution of the image is 0.8 meters. This image should be used for resource-level interpretation only.

These data describe the average size and abundance of fishes, understory algae, and benthic invertebrates across 5 sampling sites (Arroyo Quemado, Naples, Isla Vista, Mohawk, Carpentaria) along the Santa Barbara Coast and 2 sites at Santa Cruz Island (San Pedro Point, and Cavern Point). Sampling began September 2021 and is conducted seasonally every 3 months. Data are collected within two circular plots at each sampling site. Plot 1 represents the control plot with no giant kelp removal and plot 2 represents the kelp clearing plot where all giant kelp are removed. Additionally, understory algae are removed seasonally from half of the rock plates for both plots (Plot 1 rock plates #1-6 and Plot 2 rock plates #13-18).

The second component of this project synthesizes the results of the CCVA with key metrics of current landscape integrity. The outputs are a series of “scorecards” for each Priority Linkage Area (PLA) that summarize elements of connectivity, climate change vulnerability, and current condition, which was modeled using NatureServe’s Vista decision support tool. The scorecards are designed to provide decision makers with a quick, visual display of relevant information for conservation strategy development.

The San Luis Valley was chosen as a contaminant study site under the U.S. Fish and Wildlife Service's (Service) Region 6 "Hot Spot" study program in 1987. The Service "Hot Spot" studies were designed to monitor certain areas for contaminants in fish and wildlife. These "Hot Spots" are of significant biological importance and were selected with regard to environmental and geological factors that create potential contaminant problems for fish and wildlife. In many cases, previous information has suggested the possibility of a contaminant problem. Geologically speaking, the northern half of the San Luis Valley is a "closed basin" system that contains and accumulates all of the water that enters the northern portion of the valley. As a result, this closed basin has a valuable ground water supply in the form of both confined and unconfined aquifers (U.S. Geological Survey, 1989). A network of irrigation and drainage ditches provides some of this water to other areas of the valley. With a variety of water sources, especially from the surrounding mountains, the valley's water supply could potentially accumulate environmental contaminants as it enters the valley and is stored in this unique hydrologic system. If present, these contaminants could be trapped in the valley, become available to fish and wildlife, and possibly endanger the ground-water supply. Results of this study identify three major stream drainages that are apparently being directly impacted by past and present mining activity in the area. These streams are Willow Creek, Kerber Creek, and Wightman Fork. Biota, water, and sediment samples from these areas and downstream sites contain high concentrations of metals including aluminum, cadmium, copper, lead, mercury, and zinc. In addition, liver samples from great blue herons found dead on Monte Vista National Wildlife Refuge contained high concentrations of mercury and selenium.