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@talmolab Talmo Lab at the Salk Institute

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    51 repositories

    • stac-mjx

      Public
      Implementation of STAC using MJX for GPU acceleration. Part of VNL project.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•34•0•Updated Jan 17, 2025Jan 17, 2025

    • sleap-nn

      Public
      Neural network backend for training and inference for animal pose estimation.
      Python
      •
      GNU General Public License v3.0
      •0•5•9•6•Updated Jan 17, 2025Jan 17, 2025

    • sleap-cuda-container

      Public
      Dockerfiles and test data for a portable SLEAP container with GPU acceleration and various connections.
      Dockerfile
      •
      BSD 2-Clause "Simplified" License
      •0•0•1•2•Updated Jan 16, 2025Jan 16, 2025

    • lablink

      Public
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • vnl-ray

      Public
      MuJoCo fruit fly body model and reinforcement learning tasks
      Python
      •
      Apache License 2.0
      •10•4•0•0•Updated Jan 15, 2025Jan 15, 2025

    • sleap

      Public
      A deep learning framework for multi-animal pose tracking.
      deep-learningbehavior-analysisleappose-estimationanimal-trackinganimal-pose-estimationsleap
      Python
      •
      Other
      •101•446•56•30•Updated Jan 14, 2025Jan 14, 2025

    • dreem

      Public
      DREEM Relates Every Entities' Motion (DREEM). Global Tracking Transformers for biological multi-object tracking.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•9•7•Updated Jan 13, 2025Jan 13, 2025

    • sleap-io

      Public
      Standalone utilities for SLEAP pose tracking data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•13•14•7•Updated Nov 27, 2024Nov 27, 2024

    • cosyne_vm

      Public
      This repository stores the scripts that are locally available on every VM instance we spin up for the COSYNE 2024 conference.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Nov 19, 2024Nov 19, 2024

    • sleap-mot

      Public
      Standalone multi-object tracking.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•3•0•Updated Nov 18, 2024Nov 18, 2024

    • internal-dockerfiles

      Public
      dockerfiles for talmo
      Dockerfile
      •1•0•0•2•Updated Nov 4, 2024Nov 4, 2024

    • lab-website

      Public
      Website for Talmo Pereira's lab (https://talmolab.org)
      SCSS
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Nov 1, 2024Nov 1, 2024

    • sleap-roots

      Public
      Analysis tools for SLEAP-based plant root phenotyping.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•10•7•0•Updated Oct 29, 2024Oct 29, 2024

    • Brax-Tracking

      Public
      Brax Rodent Run training script
      Jupyter Notebook
      •3•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • sleap-deps

      Public
      Packages necessary for sleap build maintained by the SLEAP team.
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

    • JABS-behavior-classifier

      Public
      Behavior Classifier Component from the Jax Animal Behavior System
      Python
      •
      Other
      •2•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • sleap-anipose

      Public
      SLEAP to Anipose triangulation pipeline for 3D multi-animal pose tracking.
      Python
      •
      GNU General Public License v3.0
      •1•16•11•0•Updated Oct 11, 2024Oct 11, 2024

    • streamlit

      Public
      Create web apps using the Python `streamlit` library
      Python
      •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • janky-charuco-calibrator

      Public
      Jankily calibrating charucoly
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 24, 2024Aug 24, 2024

    • Brax-Rodent-Run

      Public
      Brax Rodent Run training script
      Jupyter Notebook
      •3•1•1•0•Updated Aug 20, 2024Aug 20, 2024

    • VNL-Brax-Imitation

      Public
      VNL Implementation of Rodent Imitation Learning
      Jupyter Notebook
      •1•3•0•0•Updated Aug 19, 2024Aug 19, 2024

    • sleap-tutorial-data

      Public
      Data for SLEAP tutorials.
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Aug 19, 2024Aug 19, 2024

    • multi-animal-dannce

      Public
      Jupyter Notebook
      •
      MIT License
      •3•0•0•0•Updated Jul 23, 2024Jul 23, 2024

    • conda_packages

      Public
      Shell
      •
      Apache License 2.0
      •0•2•0•1•Updated Jul 15, 2024Jul 15, 2024

    • cajal2024-tutorial-data

      Public
      Data for CAJAL 2024 QABVR tutorial
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • keiller-tutorial-data

      Public
      Data for Keiller Academy tutorial.
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated May 30, 2024May 30, 2024

    • VNL-TorchRL

      Public
      The VNL implementation with TorchRL as the deep learning backend.
      Jupyter Notebook
      •1•0•0•0•Updated Apr 17, 2024Apr 17, 2024

    • ndx-pose

      Public
      NWB extension to store pose estimation data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •12•1•1•0•Updated Mar 14, 2024Mar 14, 2024

    • cosyne-tutorial-data

      Public
      Cosyne 2024 SLEAP tutorial data.
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Feb 28, 2024Feb 28, 2024

    • Berrigan_et_al_sleap-roots

      Public
      Code for figures and analyses in Berrigan et al.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Feb 5, 2024Feb 5, 2024