avian-src 1.0.0

Streamlined, modular, multi-source YOLO training & detection pipeline for research.

AVIAN

Automated Visual Inference & Activity Network

An open-source, automated animal-behavior detection pipeline.

Overview

AVIAN (1.1.17) is a research-oriented, Ultralytics-based pipeline designed to make custom deep-learning model training & behavioral detection accessible to field & laboratory researchers.

Supports:

• Multi-source real-time inference (video & live camera feeds).
• Structured logging of detections, interactions, & per-frame aggregate statistics.
• Automatic metadata extraction for precise timestamping for video & camera sources.
• Full configurability & modular design for research reproducibility.

This project remains open-source & under active development as part of an undergraduate research initiative. Contributions & feedback are always welcome!

Features

Model Training

• Supports transfer learning or training from scratch of an existing model.
• Automatically exports training metrics to:
  • Weights & Biases (W&B)
  • quick-summary.txt (local lightweight summary)
• Supports aggressive data augmentation & auto-detection of new data for retraining.

Detection Pipeline

• Multi-threaded inference across multiple sources (camera feeds & videos).
• Metadata-aware timestamping for accurate temporally-aligned measurements.
• Centralized message handling using unified DetectUI for all info, warnings, errors, & save confirmations.
• Robust exception handling for model initialization, frame errors, & I/O failures.

Classes & Configuration

• The pipeline uses user-defined class configurations:
  • FOCUS_CLASSES: primary subjects (e.g., animal species)
  • CONTEXT_CLASSES: contextual or environmental elements (e.g., feeders, water trays, etc)
• Class lists are stored in & managed through classes_config.yaml within the config folder, allowing for easy modification without editing code.

Here is an example of a default classes config YAML file:

FOCUS_CLASSES:
- F
- M
- Feeder
- Main_Perch
- Nesting_Box
- Sky_Perch
- Wooden_Perch

CONTEXT_CLASSES: []

A model's class list is extracted straight from its model.pt file to prepare a class_config.yaml file, which will be located in the /configs/<model_name> path.

This allows for a class list to be divided between focus & context classes that simplifies output statistics & terminal logs.

This class setup is intended to set specific classes as objects for focus classes to interact with, giving context to those interactions primarily.

Please ensure that the [] are removed if defining context classes!

Measurement System

• Data collection centralized in single helper utility that handles:
  • Passive presence tracked by logging current class counts on a user-defined time interval.
  • Interval-level aggregation for logging raw detection tracks within a user-defined time interval.
  • Session summaries
  • Interaction tracking (focus vs. context classes)
  • Motion
• Exports structured .csv summaries:
  • counts.csv, average_counts.csv
  • interval_results.csv, session_summary.csv
  • interactions.csv Supports automatic calculation of ratios (e.g., M:F) & normalized detection rates.

Directory and Output Structure

Integrates a clean, timestamped log structure for both camera feeds & videos:

Camera sources:

/AVIAN/logs/<model_name>/measurements/camera-feed/<usb>/<system_timestamp>/<measurements>/
├── recordings/
│   └── <usb>.mp4
└── scores/
    ├── <usb>_metadata.jsonw=
    ├── counts/
    │   ├── counts.csv
    │   ├── average_counts.csv
    │   ├── frame_counts.csv
    │   └── session_summary.csv
    ├── interactions/
    │   └── interactions.csv
    ├── motion/
        ├── motion_counts.csv
        ├── motion_intensity.csv
        └── motion_prevalence.csv

Video sources:

/AVIAN/logs/(model_name)/measurements/video-in/<video>/<video_timestamp>/measurements/
├── recordings/
│   └── <video>.mp4
└── scores/
    ├── source_metadata.json
    ├── frame-data/
    │   ├── interval_results.csv
    │   └── session_summary.csv
    ├── counts/
    │   ├── counts.csv
    │   └── average_counts.csv
    └── interactions/
        └── interactions.csv

• Folder names are automatically sanitized to avoid filesystem errors.
• Each source has its own isolated measurement subdirectory.

Terminal UI

Note that AVIAN is a headless detection pipeline, meaning that live display windows will not appear while running inference. Instead, the terminal logs & tracks initiation, FPS, & basic statistics.

Here is an example of what to expect from the terminal:

Detection
----------------

model: <model>

<video>: Frames:-- | FPS:-- | Time:-- | ETA:--
  class1:-
  class2:-
  OBJECTS:-

<usb>: Frames:-- | FPS:-- | Time:--
  class1:-
  class2:-
  OBJECTS:-

------------------------------------------------------------------------------------------------

model: <model>

info: Loaded 6 classes: ['class1', 'class2', 'class3', 'class4', 'class5', 'class6']
info: Recording initialized at mm/dd/yyy hh:mm:ss
info: Source '<video>' completed.

------------------------------------------------------------------------------------------------

exit: Stop signal received. Terminating pipeline...
exit: Saving CSV spreadsheets...

------------------------------------------------------------------------------------------------

model: <model>

save: Measurements for <video>
save: Measurements saved to: "measurements/video-in/<video>/<video_timestamp>/scores"
      - <video>.mp4
      - <video>_metadata.json
      - counts.csv
      - average_counts.csv
      - interval_results.csv
      - session_summary.csv
      - interactions.csv

save: Measurements for <usb>
save: Measurements saved to: "measurements/camera-feeds/<usb>/<system_timestamp>/scores"
      - <usb>.mp4
      - <usb>_metadata.json
      - counts.csv
      - average_counts.csv
      - interval_results.csv
      - session_summary.csv
      - interactions.csv

exit: All detection threads safely terminated.

Default example model trained on 7 classes:

• M (Male Passer domesticus)
• F (Female Passer domesticus)
• Feeder
• Main_Perch
• Wooden_Perch
• Sky_Perch
• Nesting_Box

The model was trained using this pipeline & has been used for primary testing purposes.

The purpose of this model in particular is use for tracking & logging basic behavioral attributes of captive Passer domesticus subjects influenced by various intestinal microbial communities over an individual's development.

To be clear, the model is still in development & included for users to demonstrate a custom model trained through the pipeline.

Installation

1. Install MiniConda or Conda:

https://www.anaconda.com/docs/getting-started/miniconda/main

https://www.anaconda.com/download

2. Create & activate environment using:

conda create -n AVIAN python=3.10

conda activate AVIAN

3. Install the package:

pip install avian-cv

Prerequisites

• Must use Python 3.10 or older.
• Keep in mind, training & detection require entirely separate system requirements.
• A computer with a relatively powerful CPU or has a GPU with CUDA enabled is required.

Execution

Initiate Training

- Transfer-learning by default:

avian train

Option to specify weights from either OBB or standard YOLO model:

avian train model=(yolo11n, yolo11l-obb, yolov8m, etc.)

This will default to using YOLO11n.pt if not specified.

Option to name the model:

avian train name="my awesome run!!"

Option to specify dataset within data folder.

avian train data="my awesome dataset!!

This will default to the most recent dataset within the /data folder.

- Train a model only from custom dataset:

Option to specify weights from either OBB or standard YOLO model.

avian train architecture=(yolo11, yolo12, yolov8-obb, etc.)

This will default to YOLO11.yaml if not specified.

- Designed to allow users to debug training operation:

avian train test

- Process Label-Studio export folders:

avian train labelstudio="my awesome export!!"

NOTE: Many of these commands can be set together, so here are a few examples:

avian train labelstudio=geckos model=yolo11m architecture=customgeckomodel

avian train data=geckos model=yolo12 test

Initiate Detection

- Defaults to mostly recently trained model & initiates usb0:

avian detect

- Initiate multiple sources in parallel:

avian detect usb0 usb1 "video1.type" "video2.type"

- Run inference using an official YOLO model or custom model:

avian detect model=(yolo11, yolo12, yolov8-obb, etc.)

- Designed to allow users to route to debug model:

avian detect test