Advancing an Underwater Video Fish Counting System with Deep Learning and Integration with Volunteer Visual Monitoring and PIT Tagging to Improve Fisheries Management and Population Assessments

· 02/2024 - 01/2026

Lead PI: Linda Deegan, Woodwell Climate Research Center

Our objective is to develop new automated river herring monitoring systems based on underwater and deep machine learning to
count river herring coupled with volunteer monitoring and observation validation processes, to improve accuracy and reduce the
human, monetary, and time costs associated with monitoring and assessing annual river herring runs. By doing so, our goal is to
provide solutions for needs expressed by local, state, and federal fisheries and natural resources management stakeholder groups.


  1. Machine learning programming will involve sampling video and training DL algorithms to recognize and quantify target objects and estimate the herring run.
  2. Underwater video cameras to record fish as they pass by, The video recordings will be saved on a portable hard drive for DL training.
  3. Volunteer monitoring groups will visually count fish at ten-minute intervals as they pass through a fish ladder using DMF protocols.
  4. Volunteer PIT tagging will follow standard procedures.
  5. Education/Outreach will involve postdoc, undergraduate students, NOAA CEI program, and stakeholder workshops.

Accurate population assessments are critically important for fisheries management, and essential for Northeast River herring since fishery closed over a decade ago when populations declined to less than 3% of historical peaks. River herring migrate between freshwater and marine environments, contribute to fishing economies, culture and subsistence of tribal communities, and the functioning of marine and freshwater ecosystems. Town, state and federal managers, local watershed groups, and tribes have expressed concerns about the continued low population levels, leading to petitions for ‘threatened species’ listing, and hundreds of river restorations for fish passage and requests for technological advances to monitor herring.