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@berenslab Berens Lab @ University of Tübingen

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    91 repositories

    • retinal-rl

      Public
      Testing theories about retinal coding in reinforcement learning environments
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•22•2•Updated Nov 29, 2025Nov 29, 2025

    • hh_sbi

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Nov 27, 2025Nov 27, 2025

    • skeliner

      Public
      A lightweight neuromorphological mesh skeletonizer.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • bagnetsv2

      Public
      Updated version of bagnets (bag-of-local-features neural network).
      Jupyter Notebook
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • fundus_image_toolbox

      Public
      A Python package for fundus image processing.
      Jupyter Notebook
      •
      MIT License
      •4•19•0•1•Updated Nov 24, 2025Nov 24, 2025

    • jaxley-retina

      Public
      A biophysical model of the outer retina using Jaxley
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • graph-ne-paper

      Public
      Python
      •0•1•0•0•Updated Nov 17, 2025Nov 17, 2025

    • iclr-dataset

      Public
      ICLR dataset
      Jupyter Notebook
      •
      MIT License
      •8•43•1•1•Updated Nov 17, 2025Nov 17, 2025

    • flatone

      Public
      A command-line tool to flatten one EyeWire II neuron automatically.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Nov 14, 2025Nov 14, 2025

    • pywarper

      Public
      Conformal mapping-based warping of retinal meshes and skeletons.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 14, 2025Nov 14, 2025

    • text-embed-augm

      Public
      Companion repository to our González-Márquez et al. (2025) preprint "Cropping outperforms dropout as an augmentation strategy for training self-supervised text embeddings" (arXiv)
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 11, 2025Nov 11, 2025

    • contrastive-ne

      Public
      Contrastive neighbor embeddings
      Jupyter Notebook
      •
      MIT License
      •10•57•1•0•Updated Nov 7, 2025Nov 7, 2025

    • TRACE

      Public
      contrastive learning for timeseries (neuro) data
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • TRACE_experiments

      Public
      Repository to reproduce figures from TRACE: Contrastive learning for multi-trial time-series data in neuroscience by Schmors et al., 2025.
      MIT License
      •0•0•0•0•Updated Oct 23, 2025Oct 23, 2025

    • MorphoPy

      Public
      A Python package for feature extraction of neural morphologies
      Python
      •
      MIT License
      •11•43•0•0•Updated Oct 20, 2025Oct 20, 2025

    • cooplot

      Public
      Visualizing co-op between members and subgroups.
      Python
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • pygridfit

      Public
      Python port of gridfit (John D'Errico, 2006)
      Python
      •
      Other
      •0•0•0•0•Updated Oct 6, 2025Oct 6, 2025

    • MWKNeuroReha

      Public
      Code for MWKNeuroReha
      Jupyter Notebook
      •0•0•0•0•Updated Sep 15, 2025Sep 15, 2025

    • cell_mosaics

      Public
      Package to compute and plot cell mosaics and coverage.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 4, 2025Sep 4, 2025

    • llm-excess-vocab

      Public
      Delving into LLM-assisted writing in biomedical publications through excess vocabulary
      Jupyter Notebook
      •
      MIT License
      •9•48•0•0•Updated Aug 28, 2025Aug 28, 2025

    • DREAMS-CNE

      Public
      Contrastive neighbor embeddings with added regularization for global structure preservation.
      Jupyter Notebook
      •
      Other
      •10•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • DREAMS

      Public
      Extensible, parallel implementations of t-SNE with additional regularization for better global structure preservation.
      Python
      •
      Other
      •175•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • dreams-experiments

      Public
      DREAMS - Dimensionality Reduction Enhanced Across Multiple Scales
      Jupyter Notebook
      •
      MIT License
      •0•4•1•0•Updated Aug 26, 2025Aug 26, 2025

    • cell_types_lateral_habenula

      Public
      Cell-typing of lateral Habenula neurons based on spontaneous and stimulus-driven response features.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • dependence-measures-medical-imaging

      Public
      This repository contains the code for the paper "Benchmarking Dependence Measures to Prevent Shortcut Learning in Medical Imaging".
      disentangled-representationsshortcut-learningdomain-shift
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • FedAdapterProto

      Public
      Python
      •2•1•0•0•Updated Jul 9, 2025Jul 9, 2025

    • disentangling-retinal-images

      Public
      This repository contains the code for the paper "Disentangling representations of retinal images with generative models".
      deep-learninggenerative-modelspurious-correlationscausalityretinal-fundus-imagesdisentanglement-learning
      Python
      •1•3•0•0•Updated Jul 3, 2025Jul 3, 2025

    • pubmed-landscape

      Public
      The landscape of biomedical research
      Jupyter Notebook
      •
      MIT License
      •13•121•0•0•Updated Jun 23, 2025Jun 23, 2025

    • sBNN

      Public
      A sparse bottleneck neural network to predict electrophysiological properties of neurons from their gene expression.
      visualizationmachine-learninglassosparseneural-networkselectrophysiologyomicsbottleneck
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated May 20, 2025May 20, 2025

    • t-simcne

      Public
      Unsupervised visualization of image datasets using contrastive learning
      visualizationdimensionality-reduction
      Python
      •14•116•1•1•Updated May 19, 2025May 19, 2025