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    95 repositories

    • gliberal-scMultipleX

      Public
      Feature extraction and linking of multiplexing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•12•20•2•Updated Jan 6, 2026Jan 6, 2026

    • faim-robocopy

      Public
      A python-based UI for robocopy
      Python
      •
      MIT License
      •0•3•6•1•Updated Jan 5, 2026Jan 5, 2026

    • gpeters-fetchNOMe

      Public
      R package for fetching NOMe-seq data from BAM files
      C++
      •
      Other
      •0•0•0•1•Updated Jan 3, 2026Jan 3, 2026

    • compbio-nomeR

      Public
      C++
      •
      Other
      •0•0•0•1•Updated Jan 1, 2026Jan 1, 2026

    • faim-jetraw

      Public
      Python
      •
      Apache License 2.0
      •0•0•3•1•Updated Dec 22, 2025Dec 22, 2025

    • sam_trainer

      Public
      A small package for augmenting images and training micro-sam models
      Python
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • stork

      Public
      A differentiable spiking neural network simulator
      Python
      •
      MIT License
      •4•24•0•0•Updated Dec 5, 2025Dec 5, 2025

    • labbook-explog-fmi

      Public
      Obsidian plugin
      TypeScript
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • recurrent-predictive-learning

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Nov 25, 2025Nov 25, 2025

    • ggrossha_SWI

      Public template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•18•1•Updated Nov 25, 2025Nov 25, 2025

    • Deep-learning-bZIPs

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2025Nov 8, 2025

    • au-smfish-flow

      Public
      Batch smFISH pipeline for MIP-based cell/nucleus segmentation (Cellpose), spot detection (big-fish), SNR filtering, per-cell nuc/cyto counts; outputs AnnData, CSVs, and PDF reports.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 20, 2025Oct 20, 2025

    • gfelsenb-2p-analysis-warnecke-2025

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 2025

    • spiking-sqp

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 29, 2025Sep 29, 2025

    • gmatthia_mg132-timecourse

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • ggrossha-ce-chromatin-oscillations-TF-modelling

      Public
      R
      •0•0•0•0•Updated Aug 13, 2025Aug 13, 2025

    • RosEM

      Public
      Pipeline and GUI for cryoEM model refinement using Rosetta and Phenix
      guirefinementmodellingrosettaphenixcryoem
      Python
      •
      Apache License 2.0
      •1•2•0•0•Updated Aug 8, 2025Aug 8, 2025

    • balance-controlled-plasticity

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Jul 28, 2025Jul 28, 2025

    • gfriedri-brainmaps-api

      Public
      Python
      •1•0•0•0•Updated Jul 8, 2025Jul 8, 2025

    • gthoma_rosetta-density-crosslink-docking

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • gthoma_scan-factor

      Public
      PyMOL plugin to move a probe DNA (e.g. TF bound to free DNA) along a target DNA (e.g. nucleosome) and calculate clashes
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • gbuehler-MiniChip

      Public
      small collection of R functions for ChIPseq analysis
      HTML
      •1•3•0•0•Updated May 22, 2025May 22, 2025

    • 1Photon_Analysis

      Public
      This repository is a streamlined Miniscope Analysis pipeline that utilizes open source projects to motion correct, extract curate and align Miniscope data.
      matlabcalcium-imagingminiscope-imaging
      MATLAB
      •
      MIT License
      •2•2•0•0•Updated May 16, 2025May 16, 2025

    • 2Photon_Analysis

      Public
      This repository is a streamlined Two-Photon Imaging pipeline that utilizes open source projects to motion correct, extract and curate data collected with a Bruker 2Photon microscope.
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • neuRoi

      Public
      MATLAB
      •5•1•7•0•Updated Apr 19, 2025Apr 19, 2025

    • gfelsenb-fictrac

      Public
      FicTrac: A webcam-based method for tracking spherical motion and generating fictive animal paths. This is a fork to make installation work on new Windows 11 machines with FLIR cameras (Spinnaker SDK).
      C++
      •
      Other
      •36•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • gchao_translation-site-imaging

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•1•0•Updated Apr 10, 2025Apr 10, 2025

    • faim-cryoflare

      Public
      CryoFLARE: FMI Live Analysis and Reconstruction Engine for single particle Cryo EM data
      C++
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Jan 27, 2025Jan 27, 2025

    • latent-predictive-learning

      Public
      Code to accompany our paper "The combination of Hebbian and predictive plasticity learns invariant object representations in deep sensory networks"
      deep-learningself-supervised-learninghebbian-plasticity
      Jupyter Notebook
      •
      MIT License
      •7•29•0•0•Updated Jan 14, 2025Jan 14, 2025

    • neural-decoding-RSNN

      Public
      Recurrent spiking neural networks (RSNNs) for decoding of motor signals from cortical spike trains
      Python
      •
      MIT License
      •5•13•0•0•Updated Jan 8, 2025Jan 8, 2025