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@fmi-basel Friedrich Miescher Institute for Biomedical Research

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    107 repositories

    • faim-robocopy

      Public
      A python-based UI for robocopy
      Python
      •
      MIT License
      •0•4•6•1•Updated Sep 7, 2026Sep 7, 2026

    • gfelsenb-anytrack

      Public
      Pipeline to track individual objects in videos with static backgrounds
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 3, 2026Sep 3, 2026

    • singlemolecule-tracking

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•3•0•Updated Sep 2, 2026Sep 2, 2026

    • faim-jetraw

      Public
      Python
      •
      Apache License 2.0
      •0•0•3•1•Updated Aug 31, 2026Aug 31, 2026

    • gfelsenb-flypad-analysis

      Public
      Python analysis script for the flyPAD system.
      Python
      •
      GNU General Public License v3.0
      •2•2•0•0•Updated Aug 21, 2026Aug 21, 2026

    • ATMC_Analysis

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 21, 2026Aug 21, 2026

    • sam_trainer

      Public
      A small package for augmenting images and training micro-sam models
      Python
      •0•0•0•0•Updated Aug 19, 2026Aug 19, 2026

    • compbio-nomeR

      Public
      R
      •
      Other
      •0•0•0•0•Updated Aug 2, 2026Aug 2, 2026

    • balance-controlled-plasticity

      Public
      Python
      •
      MIT License
      •0•5•0•0•Updated Jul 17, 2026Jul 17, 2026

    • gliberal-scMultipleX

      Public
      Feature extraction and linking of multiplexing data.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•14•23•0•Updated Jul 14, 2026Jul 14, 2026

    • 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, C…
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 3, 2026Jul 3, 2026

    • luciferase_reader_legacy

      Public
      GUI for molt annotation for C. elegans luciferase assays.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 18, 2026Jun 18, 2026

    • labbook-explog-fmi

      Public
      Obsidian plugin
      TypeScript
      •0•0•0•0•Updated Jun 15, 2026Jun 15, 2026

    • FMI_H3.4

      Public
      Scripts used for the H3.4 manuscript
      C
      •0•0•1•0•Updated Jun 1, 2026Jun 1, 2026

    • DynCogRep-2PVR

      Public
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • DynCogRep-VR

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 22, 2026May 22, 2026

    • ggiorget_ms2analysis

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated May 19, 2026May 19, 2026

    • latent_distribution_matching

      Public
      Paper code to "Understanding Self-Supervised Learning via Latent Distribution Matching"
      Jupyter Notebook
      •0•10•0•0•Updated May 6, 2026May 6, 2026

    • CaImagingTest

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 5, 2026May 5, 2026

    • gfriedri-em-alignment

      Public
      Alignment tools used in the Friedrich lab.
      Python
      •
      Apache License 2.0
      •0•3•9•0•Updated May 5, 2026May 5, 2026

    • gbuehler-MiniChip

      Public
      small collection of R functions for ChIPseq analysis
      HTML
      •1•3•0•0•Updated Apr 17, 2026Apr 17, 2026

    • Dreamer-CDP

      Public
      Python
      •
      MIT License
      •612•2•0•0•Updated Mar 24, 2026Mar 24, 2026

    • ggrossha_SWI

      Public template
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•18•1•Updated Mar 19, 2026Mar 19, 2026

    • gpeters-fetchNOMe

      Public
      R package for fetching NOMe-seq data from BAM files
      C++
      •
      Other
      •0•0•0•1•Updated Feb 27, 2026Feb 27, 2026

    • ripple-detection

      Public
      0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • stork

      Public
      A differentiable spiking neural network simulator
      Python
      •
      MIT License
      •5•26•0•1•Updated Dec 5, 2025Dec 5, 2025

    • recurrent-predictive-learning

      Public
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Nov 25, 2025Nov 25, 2025

    • Deep-learning-bZIPs

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