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    50 repositories

    • in_silico_framework

      Public
      An in silico framework for multi-scale modeling and analysis of in vivo neuron-network mechanisms
      pythonneurosciencecomputational-neurosciencebrainin-silicomulti-compartment-modelingneuron-simulatormulti-scale-modeling
      Python
      •
      GNU General Public License v3.0
      •1•3•19•3•Updated Aug 20, 2025Aug 20, 2025

    • gpujob-viewer

      Public
      SLURM GPU job performance monitoring tool.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • spermull-bonn

      Public
      Hackaton project for a spermull frontend app.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

    • in_silico_framework_hot_zone

      Public
      An in silico framework for multi-scale modeling and analysis of in vivo neuron-network mechanisms
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jun 6, 2025Jun 6, 2025

    • amadeusgpt

      Public
      We turn natural language descriptions of behaviors into machine-executable code
      Python
      •
      Apache License 2.0
      •13•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • ood-amadeus-gpt

      Public
      Configure AmadeusGPT to launch using Open OnDemand
      MIT License
      •0•0•0•0•Updated Jun 2, 2025Jun 2, 2025

    • howto-cellpose

      Public
      a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •515•0•0•0•Updated May 29, 2025May 29, 2025

    • segment-anything-2

      Public
      The repository provides code for running inference with the Meta Segment Anything Model 2 (SAM 2), links for downloading the trained model checkpoints, and example notebooks that show how to use the model.
      Jupyter Notebook
      •
      Apache License 2.0
      •2k•0•0•0•Updated May 28, 2025May 28, 2025

    • braid-opto-arena

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 24, 2025May 24, 2025

    • jobstats-viewer

      Public
      JavaScript
      •0•0•0•0•Updated May 20, 2025May 20, 2025

    • isf-pandas-msgpack

      Public
      In-Silico-Framework Pandas Msgpack
      Python
      •
      Other
      •21•0•0•0•Updated May 14, 2025May 14, 2025

    • sleap

      Public
      A deep learning framework for multi-animal pose tracking.
      Python
      •
      Other
      •114•0•0•0•Updated Apr 22, 2025Apr 22, 2025

    • submitit

      Public
      Python 3.8+ toolbox for submitting jobs to Slurm
      Python
      •
      MIT License
      •141•0•0•0•Updated Apr 1, 2025Apr 1, 2025

    • bc_ollama_jupyter

      Public
      Ollama + Jupyter OOD Application for SOMA at MPINB
      HTML
      •
      MIT License
      •3•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • multi_gpu_training

      Public
      jupyter notebooks discussing multi GPU training and performance profiling
      Python
      •
      MIT License
      •49•0•0•0•Updated Mar 6, 2025Mar 6, 2025

    • Kaleido

      Public
      Fast static image export for web-based visualization libraries with zero dependencies
      HTML
      •
      MIT License
      •47•0•0•0•Updated Feb 21, 2025Feb 21, 2025

    • alphafold

      Public
      Open source code for AlphaFold 2.
      Python
      •
      Apache License 2.0
      •2.5k•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • msemalign

      Public
      serial section multibeam scanning electron microscopy volume alignment
      Python
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated Dec 3, 2024Dec 3, 2024

    • Augmentor

      Public
      Data augmentation for training 3D convolutional nets
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • swipe-labeler

      Public
      Swipe Labeler is a Graphical User Interface based tool that allows rapid labeling of image data.
      Jupyter Notebook
      •6•0•0•0•Updated Oct 23, 2024Oct 23, 2024

    • waterz

      Public
      Simple watershed and agglomeration library for affinity graphs.
      C++
      •25•0•0•0•Updated Oct 9, 2024Oct 9, 2024

    • sparseANNs

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • .github

      Public
      0•0•0•0•Updated Sep 5, 2024Sep 5, 2024

    • yolov8_ros

      Public
      Ultralytics YOLOv8 for ROS 2
      Python
      •
      GNU General Public License v3.0
      •183•0•0•0•Updated Jul 31, 2024Jul 31, 2024

    • swarm-scripts

      Public
      scripts for a basic method of scaling on a SLURM HPC cluster
      Python
      •0•1•0•0•Updated Mar 21, 2024Mar 21, 2024

    • BastFruengelEtAl

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Mar 1, 2024Mar 1, 2024

    • gauss-em

      Public
      Example that demonstrates computationally solving the order of unordered serial slices
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jan 19, 2024Jan 19, 2024

    • connected-components-3d

      Public
      Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants.
      C++
      •
      GNU General Public License v3.0
      •46•0•0•0•Updated Dec 7, 2023Dec 7, 2023

    • n2v

      Public
      This is the implementation of Noise2Void training.
      Python
      •
      Other
      •117•0•0•0•Updated Nov 15, 2023Nov 15, 2023

    • rosbag2video

      Public
      converts image sequence in ros bag files to video files
      Python
      •
      GNU General Public License v2.0
      •118•0•0•0•Updated Sep 13, 2023Sep 13, 2023