ONC Echosounder Examples

This repository accompanies a conference poster on Ocean Networks Canada (ONC) long-term echosounder data products and provides ready-to-run examples for public use.

The poster can be found here: https://osm26.ipostersessions.com/Default.aspx?s=6A-29-A9-15-8D-96-A4-4C-0C-05-C6-29-3F-13-C8-7D

The goal is to make ONC bioacoustic data easier to explore by sharing:

• example MVBS (Mean Volume Backscatter) products,
  • The complete MVBS data products will eventually be available on Borealis (LINK COMING SOON)
• precomputed scalar time series (CM / center of mass and ABC / area backscatter),
• practical Jupyter notebooks that demonstrate analysis workflows.

Why this repository exists

ONC has collected long-term echosounder observations across multiple coastal sites, including deployments that generate very dense raw time series (often >1 GB/day). Raw data are powerful but can be computationally expensive to download, process, and interpret.

This repository lowers that barrier by sharing value-added examples and notebook workflows that are useful for:

• interdisciplinary researchers,
• students learning time-series analysis,
• users who want a reproducible starting point before building custom pipelines.

Conference-poster context

The examples contained in this repository focus on the exploration of:

• long-term, multi-frequency echosounder monitoring,
• cleaned MVBS products,
• descriptive scalar metrics for ecological interpretation,
• accessible open notebooks for re-use and extension.

The included examples are meant to illustrate how derived products can support analysis of diel, seasonal, and interannual variability in fish and zooplankton patterns.

Repository contents

• FolgerDeep_Upwelling.ipynb
  Demonstrates workflow for Folger Passage, including scalar time-series interpretation and optional comparison with supplementary ADCP-derived signals.
• SaanichInlet_Overturning.ipynb
  Demonstrates a workflow for Saanich Inlet, exploring temporal variability and notable events. This notebook includes pre-made plots so that it can be explored without the need to download python
• StraitOfGeorgia_SpringBloom.ipynb
  Demonstrates a workflow for the Strait of Georgia, for exploring temporal variability and the timing of the spring bloom.
• CM_ABC_examples/ and CM_ABC_averaged_examples/
  This is the complete set of CM and ABC data products. These scalar metric .mat files can be used to find interesting features in the echosounder data, and are demonstrated in the notebooks.
  • MVBS_examples/
    A select number of example MVBS .mat files. The full dataset will eventually be made available on Borealis.
• extra_data/
  Supplemental CSV data used by the Folger Deep notebook.

Quick start

1. Create and activate a Python environment.
2. Install dependencies:

pip install -r requirements.txt

3. Launch Jupyter:

jupyter lab

4. Open a notebook from the repository root and run cells top-to-bottom.

Dependencies

Dependencies are listed in requirements.txt and include scientific Python packages plus ONC client support.

Optional ONC API access

Some notebook sections demonstrate downloading additional data through the ONC API client.

To run those sections:

1. Create/sign in to an ONC account.
2. Generate an API token from your ONC profile.
3. Replace the placeholder token in notebook cells that call ONC(...).

Data and usage notes

• Included files are example products intended for exploration, teaching, and workflow development.
• High-resolution echosounder downloads can be large and slow, depending on request size.
• File names preserve key metadata fields (site, instrument, and time window) to support traceability.

License

Distributed under the terms in LICENSE.