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SLEAP v1.1.3
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@talmo talmo released this 26 Mar 04:02
· 343 commits to main since this release
v1.1.3
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Release of SLEAP v1.1.3.

Includes several bug fixes and documentation improvements.

Full changelog

  • #498: Fix training when frames have no instances (fixes #480).
  • #503: Fix errors occurring sometimes after training (fixes part of #500)
  • #505: Add miscellaneous utilities/fixes
    • Add --open-in-gui flag to sleap-track to launch GUI on predictions
    • Add PredictedInstance.numpy() to convert predicted instances to numpy arrays
    • Fix visualization during single instance training
    • Add Skeleton.find_neighbors() to return parents and children of a node
    • Fix serialization of MediaVideo after loading from sleap.load_video() or sleap.load_file().
    • Add Instance.fill_missing() to initialize missing nodes (e.g., after importing from DLC)
  • #501/#519/#524: Fix multi-size video support in training and inference (fixes #510, #516, #517)
  • #523: Fix using sleap-track with zipped model folders
  • Revamped docs and notebooks to clarify the Colab-based workflow (especially Training and inference on your own data using Google Drive), which are now linked from the GUI as well
  • Fix regression in v1.1.2 (#528)

Installing

We recommend using Miniconda to install and manage your Python environments. This will also make GPU support work transparently without installing additional dependencies.

Using Conda (Windows/Linux)

  1. Delete any existing environment and start fresh (recommended):
conda env remove -n sleap
  1. Create new environment sleap (recommended):
conda create -n sleap -c sleap sleap=1.1.3

Or to update inside an existing environment:

conda install -c sleap sleap=1.1.3

Using PyPI (Windows/Linux/Mac)

  1. Create a new conda environment (recommended):
conda create -n sleap python=3.6
conda activate sleap
  1. Install from PyPI:
pip install sleap==1.1.3

Or to upgrade an existing installation:

pip install --upgrade --force-reinstall sleap==1.1.3

From source (development)

  1. Clone the repository at this tag:
git clone https://github.com/murthylab/sleap --branch v1.1.3 sleap_v1.1.3
cd sleap_v1.1.3
  1. Install conda environment and activate:
conda install -f environment.yml -n sleap_v1.1.3
conda activate sleap_v1.1.3
  1. Changes made in the code will be immediately reflected when running SLEAP in this environment.
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