Repositories list

• utils_behavior

  Public
  Utility functions to manipulate and analyze behavior videos and associated data (tracking...) acquired in various setups and settings.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• Tracking_Analysis

  Public
  This repository comprises a set of tools used to perform tracking on behaviour arena data, analysis and plotting.

  active-dev

  Jupyter Notebook

  •

  MIT License

  •0•1•1•0•Updated Feb 3, 2025Feb 3, 2025

• flygym

  Public
  Simulating embodied sensorimotor control with NeuroMechFly v2

  biomechanicsphysics-simulationmujoco+ 3published-articleneuroaistable-infrastructure

  Python

  •

  Apache License 2.0

  •7•34•7•2•Updated Feb 3, 2025Feb 3, 2025

• vnc_networks

  Public
  Code to analyse the MANC connectome and perform connectome-constrained modelling

  Jupyter Notebook

  •

  MIT License

  •0•0•2•0•Updated Jan 30, 2025Jan 30, 2025

• DeepFly2D

  Public
  published-article

  Jupyter Notebook

  •1•0•0•0•Updated Jan 30, 2025Jan 30, 2025

• sequential-inverse-kinematics

  Public
  Sequential inverse kinematics pipeline.

  inverse-kinematicsdrosophila-melanogaster

  Python

  •

  Apache License 2.0

  •0•9•2•0•Updated Jan 22, 2025Jan 22, 2025

• kinematics3d

  Public
  Pipeline for calibration, triangulation, and data processing using DeepLabCut and Anipose.

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• antennal-grooming

  Public
  Repository hosting the analysis code for Ozdil et al 2024.

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• Sociability_Learning

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 4, 2025Jan 4, 2025

• DeMotion5D

  Public
  Remove sample movement from 5D microscopy data (xyz+time+color)

  Python

  •0•0•0•0•Updated Dec 17, 2024Dec 17, 2024

• sleap_tools

  Public
  A repository to regroup useful code to manipulate sleap objects and h5 exports, as well as help and method to setup tracking routines.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• farms_mujoco

  Public
  FARMS package for interfacing to the MuJoCo simulator

  Python

  •3•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• farms_core

  Public
  FARMS core

  Python

  •

  Apache License 2.0

  •3•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• farms_sim

  Public
  FARMS package for running simulations with physics engines

  Python

  •1•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• utils2p

  Public
  Utility functions for data generated with ThorImage and ThorSync.

  2-photonthor-imagethor-sync+ 1stable-infrastructure

  Python

  •2•0•0•1•Updated Nov 13, 2024Nov 13, 2024

• DeepFly3D

  Public
  Motion capture (markerless 3D pose estimation) pipeline and helper GUI for tethered Drosophila.

  deep-learningmotion-capturedrosophila-melanogaster+ 2published-articlepose-estimation

  Jupyter Notebook

  •

  GNU Lesser General Public License v3.0

  •17•90•1•0•Updated Oct 28, 2024Oct 28, 2024

• PyBundleAdjustment

  Public
  published-article

  Jupyter Notebook

  •1•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• dn_networks

  Public
  Repository holding the code for Braun et al. 2023

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• neuromechfly-workshop

  Public
  NeuroMechFly workshop.

  Jupyter Notebook

  •

  Apache License 2.0

  •0•1•0•0•Updated Oct 19, 2024Oct 19, 2024

• NeuroMechFly

  Public archive
  A neuromechanical model of adult Drosophila melanogaster.

  evolutionary-algorithmslocomotionpybullet+ 4drosophila-melanogasterpublished-articlegait-optimizationsimulation

  Python

  •

  Apache License 2.0

  •2•47•1•0•Updated Oct 11, 2024Oct 11, 2024

• _media

  Public
  This repository is for larger media files (eg. GIFs/videos on the README).

  Shell

  •0•0•0•0•Updated Oct 5, 2024Oct 5, 2024

• .github

  Public
  0•0•0•0•Updated Sep 23, 2024Sep 23, 2024

• utils_video

  Public
  Video utility functions for 2p imaging data and behaviour.

  behaviour2pstable-infrastructure+ 1video

  Python

  •0•2•7•2•Updated Sep 4, 2024Sep 4, 2024

• nmf2-videos

  Public archive
  NMF2 videos linked from preprint. DO NOT DELETE OR REMOVE THIS REPOSITORY.

  Apache License 2.0

  •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

• SeptaCam

  Public
  Code for controlling the seven-camera system

  published-article

  C

  •

  MIT License

  •0•1•0•0•Updated Aug 5, 2024Aug 5, 2024

• multimaze_recorder

  Public
  Tools to operate Matthias' high-throughput recording setup

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

• nmf2-paper

  Public archive
  Code for generating some figures in for the NeuroMechFly v2 paper.

  published-article

  Jupyter Notebook

  •

  Apache License 2.0

  •0•2•0•0•Updated Jul 19, 2024Jul 19, 2024

• flyvis

  Public
  A connectome constrained deep mechanistic network (DMN) model of the fruit fly visual system

  Python

  •

  GNU General Public License v3.0

  •13•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• object_preference

  Public
  This repository contains tools for analysising food object preferece in the scope of Alice Canuti and Samara Santarelli's project

  Jupyter Notebook

  •

  MIT License

  •1•1•0•0•Updated Jun 14, 2024Jun 14, 2024

• df3dPostProcessing

  Public
  Functions for postprocessing DeepFly3D results, such as, align 3d model and calculate leg angles

  stable-infrastructure

  Python

  •

  MIT License

  •0•2•0•1•Updated Jun 3, 2024Jun 3, 2024