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@talmolab Talmo Lab at the Salk Institute

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    61 repositories

    • sleap-nn

      Public
      Neural network backend for training and inference for animal pose estimation.
      Python
      •
      GNU General Public License v3.0
      •3•11•16•7•Updated Aug 10, 2025Aug 10, 2025

    • lablink

      Public
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•32•2•Updated Aug 8, 2025Aug 8, 2025

    • sleap

      Public
      A deep learning framework for multi-animal pose tracking.
      deep-learningbehavior-analysisleappose-estimationanimal-trackinganimal-pose-estimationsleap
      Python
      •
      Other
      •113•501•79•34•Updated Aug 7, 2025Aug 7, 2025

    • labelroi

      Public
      Python
      •0•0•0•0•Updated Aug 6, 2025Aug 6, 2025

    • 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•13•37•1•Updated Aug 6, 2025Aug 6, 2025

    • sleap-vizmo

      Public
      Lightweight app for visualizing `LabeledFrames` using sleap-io and marimo.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • sleap-mot

      Public
      Standalone multi-object tracking.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•7•2•Updated Jul 31, 2025Jul 31, 2025

    • webRTC-connect

      Public
      Python
      •
      MIT License
      •0•0•1•2•Updated Jul 31, 2025Jul 31, 2025

    • webRTC-auth

      Public
      Remote Authenticated CLI Training w/ SLEAP
      MIT License
      •0•0•0•1•Updated Jul 31, 2025Jul 31, 2025

    • sleap-io

      Public
      Standalone utilities for SLEAP pose tracking data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•19•9•2•Updated Jul 29, 2025Jul 29, 2025

    • sleap-cuda-container

      Public
      Dockerfiles and test data for a portable SLEAP container with GPU acceleration and various connections.
      Python
      •
      BSD 2-Clause "Simplified" License
      •2•0•2•3•Updated Jul 28, 2025Jul 28, 2025

    • dreem-plots

      Public
      Plotting code for DREEM
      Jupyter Notebook
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 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
      •2•10•14•3•Updated Jul 25, 2025Jul 25, 2025

    • webRTC-client

      Public
      webRTC client repo for pip package
      Python
      •
      MIT License
      •0•0•0•1•Updated Jul 22, 2025Jul 22, 2025

    • sleap-roots

      Public
      Analysis tools for SLEAP-based plant root phenotyping.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•13•17•0•Updated Jun 23, 2025Jun 23, 2025

    • standard-trait-analysis

      Public
      Data cleanup, exploratory data analysis, and dimensionality reduction of standard phenotypic traits with metadata output from Bloom and sleap-roots-pipeline.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • plate-timelapse

      Public
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • sleap-roots-pipeline

      Public
      Container orchestration for sleap-roots inference pipeline.
      Shell
      •
      BSD 2-Clause "Simplified" License
      •0•0•1•0•Updated May 8, 2025May 8, 2025

    • 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 May 8, 2025May 8, 2025

    • vnl-ray

      Public
      MuJoCo fruit fly body model and reinforcement learning tasks
      Python
      •
      Apache License 2.0
      •43•4•0•0•Updated Mar 25, 2025Mar 25, 2025

    • mujoco_playground

      Public
      An open-source library for GPU-accelerated robot learning and sim-to-real transfer.
      Jupyter Notebook
      •
      Apache License 2.0
      •174•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • 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•0•Updated Mar 5, 2025Mar 5, 2025

    • internal-dockerfiles

      Public
      dockerfiles for talmo
      Dockerfile
      •1•1•0•2•Updated Feb 25, 2025Feb 25, 2025

    • sleap-wandb-training

      Public
      Training using the SLEAP API and wandb integration
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • Brax-Tracking

      Public
      Brax Rodent Run training script
      Jupyter Notebook
      •2•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
      •2•22•13•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