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@berenslab Berens Lab @ University of Tübingen

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    98 repositories

    • retinal-rl

      Public
      Testing theories about retinal coding in reinforcement learning environments
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•32•5•Updated Jul 9, 2026Jul 9, 2026

    • nako-eye

      Public
      Description of the NAKO opthalmology dataset.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 8, 2026Jul 8, 2026

    • OrdinalDiffusionModels

      Public
      Python
      •1•4•0•0•Updated Jun 23, 2026Jun 23, 2026

    • hybrid_biophysical_models_preprint

      Public
      Code for "Learning Hybrid Biophysical Neuron Models with Neural ODEs"
      Jupyter Notebook
      •0•1•0•0•Updated Jun 15, 2026Jun 15, 2026

    • interpretable_FM

      Public
      Dual-IFM: an interpretable foundation model for retinal images.
      Python
      •0•0•0•0•Updated Jun 11, 2026Jun 11, 2026

    • medirater

      Public
      A web app for medical image evaluation.
      HTML
      •0•1•0•0•Updated Jun 10, 2026Jun 10, 2026

    • read-normalization

      Public
      Companion repository to our Lause et al. (2023) preprint "Compound models and Pearson residuals for normalization of single-cell RNA-seq data without UMIs" (bio…
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jun 5, 2026Jun 5, 2026

    • fundus_image_toolbox

      Public
      A Python package for fundus image processing.
      Jupyter Notebook
      •
      MIT License
      •5•24•0•0•Updated May 29, 2026May 29, 2026

    • MIDL24-segmentation_quality_control

      Public
      Experiments for MIDL 2024 Paper: Efficiently correcting patch-based segmentation errors to control image-level performance in retinal images
      Jupyter Notebook
      •2•2•0•0•Updated May 29, 2026May 29, 2026

    • cooplot

      Public
      Visualizing co-op between members and subgroups.
      Python
      •0•0•0•0•Updated May 28, 2026May 28, 2026

    • llm-excess-vocab

      Public
      Delving into LLM-assisted writing in biomedical publications through excess vocabulary
      Jupyter Notebook
      •
      MIT License
      •9•52•0•0•Updated May 22, 2026May 22, 2026

    • pubmed-ophtha

      Public
      Python
      •
      MIT License
      •0•2•0•0•Updated May 20, 2026May 20, 2026

    • bagnetsv2

      Public
      Updated version of bagnets (bag-of-local-features neural network).
      Jupyter Notebook
      •0•1•0•0•Updated May 19, 2026May 19, 2026

    • pmo-parser

      Public
      A Python library and CLI tool for extracting figures and captions from scientific publication PDFs, originally developed for PubMed-Ophtha.
      Python
      •
      MIT License
      •0•0•0•0•Updated May 11, 2026May 11, 2026

    • TRACE

      Public
      contrastive learning for timeseries (neuro) data
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 29, 2026Apr 29, 2026

    • RFEst

      Public
      A Python 3 toolbox for neural receptive field estimation using splines and Gaussian priors.
      matrix-factorizationsplinesjax
      matrix-factorizationsplinesjaxreceptive-fieldevidence-optimization
      Python
      •
      GNU General Public License v3.0
      •3•27•4•0•Updated Apr 28, 2026Apr 28, 2026

    • pywarper

      Public
      Conformal mapping-based warping of retinal meshes and skeletons.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•1•Updated Apr 24, 2026Apr 24, 2026

    • skeliner

      Public
      A lightweight neuromorphological mesh skeletonizer.
      Python
      •
      GNU General Public License v3.0
      •2•5•0•1•Updated Apr 10, 2026Apr 10, 2026

    • pygridfit

      Public
      Python port of gridfit (John D'Errico, 2006)
      Python
      •
      Other
      •1•0•0•0•Updated Mar 26, 2026Mar 26, 2026

    • flatone

      Public
      A command-line tool to flatten one EyeWire II neuron automatically.
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Mar 18, 2026Mar 18, 2026

    • text-embed-augm

      Public
      Companion repository to our González-Márquez et al. (2026) paper "Cropping outperforms dropout as an augmentation strategy for self-supervised training of text …
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 17, 2026Mar 17, 2026

    • cell_mosaics

      Public
      Package to compute and plot cell mosaics and coverage.
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 10, 2026Mar 10, 2026

    • medical-shortcut-mitigation

      Public
      This repository contains the code for the paper "Mitigating Shortcut Learning via Feature Disentanglement in Medical Imaging: A Benchmark Study".
      disentanglementconfounderlatent-space-regularization
      disentanglementconfounderlatent-space-regularizationshortcut-learningdomain-shiftdependence-measure
      Python
      •
      MIT License
      •0•1•1•0•Updated Feb 24, 2026Feb 24, 2026

    • disentangling-retinal-images

      Public
      This repository contains the code for the paper "Disentangling representations of retinal images with generative models".
      deep-learninggenerative-modelspurious-correlations
      deep-learninggenerative-modelspurious-correlationscausalityretinal-fundus-imagesdisentanglement-learning
      Python
      •
      MIT License
      •3•3•0•0•Updated Feb 4, 2026Feb 4, 2026

    • iclr-dataset

      Public
      ICLR dataset
      Jupyter Notebook
      •
      MIT License
      •14•60•2•2•Updated Jan 7, 2026Jan 7, 2026

    • DREAMS-CNE

      Public
      Contrastive neighbor embeddings with added regularization for global structure preservation.
      Jupyter Notebook
      •
      Other
      •10•1•0•0•Updated Dec 19, 2025Dec 19, 2025

    • DREAMS

      Public
      Extensible, parallel implementations of t-SNE with additional regularization for better global structure preservation.
      Python
      •
      Other
      •176•1•0•0•Updated Dec 19, 2025Dec 19, 2025

    • dreams-experiments

      Public
      DREAMS - Dimensionality Reduction Enhanced Across Multiple Scales
      Jupyter Notebook
      •
      MIT License
      •0•6•1•0•Updated Dec 19, 2025Dec 19, 2025

    • hh_sbi

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•4•0•0•Updated Nov 27, 2025Nov 27, 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
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