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DeepEthogram

DeepEthogram is an open-source package for automatically classifying each frame of a video into a set of pre-defined behaviors. Designed for neuroscience research, it could be used in any scenario where you need to detect actions from each frame of a video.

Example use cases:

  • Measuring itching or scratching behaviors to assess the differences between wild-type and mutant animals
  • Measuring the amount of time animals spend courting, and comparing between experimental conditions

DeepEthogram uses state-of-the-art algorithms for temporal action detection. We build on the following previous machine learning research into action detection:

deepethogram schematic

Installation

For full installation instructions, see this readme file.

In brief:

  • install PyTorch
  • Install PySide2: conda install -c conda-forge pyside2
  • pip install deepethogram

Licensing

Copyright (c) 2020 - President and Fellows of Harvard College. All rights reserved.

This software is free for academic use. For commercial use, please contact the Harvard Office of Technology Development ([email protected]) with cc to Dr. Chris Harvey. For details, see license.txt.

Usage

To use the GUI, click

To use the command line interface, click

Dependencies

The major dependencies for DeepEthogram are as follows:

  • PyTorch, torchvision: all the neural networks, training, and inference pipelines were written in PyTorch
  • pyside2: for the GUI
  • opencv: for video and image reading and writing
  • opencv_transforms: for fast image augmentation
  • scikit-learn, scipy: for binary classification metrics
  • matplotlib: plotting metrics and neural network outputs
  • pandas: reading and writing CSVs
  • h5py: saving inference outputs as HDF5 files
  • hydra: for smoothly integrating configuration files and command line inputs
  • tifffile: for writing neural network outputs as tiff stacks
  • tqdm: for nice progress bars

Hardware requirements

For GUI usage, we expect that the users will be working on a local workstation with a good NVIDIA graphics card. For training via a cluster, you can use the CLI yourself.

  • CPU: 8 cores or more for parallel data loading
  • Hard Drive: SSD at minimum, NVMe drive is better.
  • GPU: DeepEthogram speed is directly related to GPU performance. An NVIDIA GPU is absolutely required, as PyTorch uses CUDA, while AMD does not. The more VRAM you have, the more data you can fit in one batch, which generally increases performance. a I'd recommend 6GB VRAM at absolute minimum. 8GB is better, with 10+ GB preferred. Recommended GPUs: RTX 3090, RTX 3080, Titan RTX, 2080 Ti, 2080 super, 2080, 1080 Ti, 2070 super, 2070 Some older ones might also be fine, like a 1080 or even 1070 Ti/ 1070.