Repositories list

• skeliner

  Public
  A lightweight neuromorphological mesh skeletonizer.

  Python

  •

  GNU General Public License v3.0

  •33 forks in berenslab/skeliner•77 stars in berenslab/skeliner•00 issues in berenslab/skeliner•11 pull request in berenslab/skeliner•Updated Oct 27, 2026Oct 27, 2026

• fundus_image_toolbox

  Public
  A Python package for fundus image processing.

  Jupyter Notebook

  •

  MIT License

  •66 forks in berenslab/fundus_image_toolbox•2727 stars in berenslab/fundus_image_toolbox•00 issues in berenslab/fundus_image_toolbox•11 pull request in berenslab/fundus_image_toolbox•Updated Oct 24, 2026Oct 24, 2026

• cell_mosaics

  Public
  Package to compute and plot cell mosaics and coverage.

  Jupyter Notebook

  •

  MIT License

  •11 fork in berenslab/cell_mosaics•11 star in berenslab/cell_mosaics•00 issues in berenslab/cell_mosaics•00 pull requests in berenslab/cell_mosaics•Updated Oct 22, 2026Oct 22, 2026

• retinal-rl

  Public
  Testing theories about retinal coding in reinforcement learning environments

  Python

  •

  GNU Affero General Public License v3.0

  •11 fork in berenslab/retinal-rl•22 stars in berenslab/retinal-rl•3131 issues in berenslab/retinal-rl•44 pull requests in berenslab/retinal-rl•Updated Oct 22, 2026Oct 22, 2026

• nako-eye

  Public
  Description of the NAKO opthalmology dataset.

  Jupyter Notebook

  •

  MIT License

  •00 forks in berenslab/nako-eye•00 stars in berenslab/nako-eye•00 issues in berenslab/nako-eye•00 pull requests in berenslab/nako-eye•Updated Oct 19, 2026Oct 19, 2026

• hh_sbi

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks in berenslab/hh_sbi•55 stars in berenslab/hh_sbi•00 issues in berenslab/hh_sbi•00 pull requests in berenslab/hh_sbi•Updated Oct 17, 2026Oct 17, 2026

• pywarper

  Public
  Conformal mapping-based warping of retinal meshes and skeletons.

  Python

  •

  GNU General Public License v3.0

  •11 fork in berenslab/pywarper•11 star in berenslab/pywarper•00 issues in berenslab/pywarper•00 pull requests in berenslab/pywarper•Updated Oct 16, 2026Oct 16, 2026

• ssl_neuron

  Public
  Code to the paper "Self-Supervised Graph Representation Learning for Neuronal Morphologies"

  Jupyter Notebook

  •

  MIT License

  •1111 forks in berenslab/ssl_neuron•00 stars in berenslab/ssl_neuron•00 issues in berenslab/ssl_neuron•00 pull requests in berenslab/ssl_neuron•Updated Oct 2, 2026Oct 2, 2026

• TRACE

  Public
  contrastive learning for timeseries (neuro) data

  Python

  •

  MIT License

  •00 forks in berenslab/TRACE•11 star in berenslab/TRACE•00 issues in berenslab/TRACE•00 pull requests in berenslab/TRACE•Updated Sep 30, 2026Sep 30, 2026

• MorphoGNN

  Public
  Morphological embedding for single neuron with graph neuron networks

  Python

  •

  Apache License 2.0

  •55 forks in berenslab/MorphoGNN•00 stars in berenslab/MorphoGNN•00 issues in berenslab/MorphoGNN•00 pull requests in berenslab/MorphoGNN•Updated Sep 23, 2026Sep 23, 2026

• leverage-data

  Public
  Jupyter Notebook

  •00 forks in berenslab/leverage-data•00 stars in berenslab/leverage-data•00 issues in berenslab/leverage-data•00 pull requests in berenslab/leverage-data•Updated Sep 20, 2026Sep 20, 2026

• jaxley_retinaretreat_workshop

  Public
  This repository contains the material for the Workshop "Differentiable biophysical models of the Retina", given at the Eulerlab Retina retreat Sep. 2026

  HTML

  •

  MIT License

  •11 fork in berenslab/jaxley_retinaretreat_workshop•00 stars in berenslab/jaxley_retinaretreat_workshop•00 issues in berenslab/jaxley_retinaretreat_workshop•00 pull requests in berenslab/jaxley_retinaretreat_workshop•Updated Sep 18, 2026Sep 18, 2026

• interpretable_FM

  Public
  Dual-IFM: an interpretable foundation model for retinal images.

  Python

  •

  MIT License

  •00 forks in berenslab/interpretable_FM•11 star in berenslab/interpretable_FM•00 issues in berenslab/interpretable_FM•00 pull requests in berenslab/interpretable_FM•Updated Sep 16, 2026Sep 16, 2026

• bagnetsv2

  Public
  Updated version of bagnets (bag-of-local-features neural network).

  Jupyter Notebook

  •00 forks in berenslab/bagnetsv2•22 stars in berenslab/bagnetsv2•00 issues in berenslab/bagnetsv2•00 pull requests in berenslab/bagnetsv2•Updated Sep 14, 2026Sep 14, 2026

• neuron_hulls

  Public
  Python

  •

  MIT License

  •00 forks in berenslab/neuron_hulls•00 stars in berenslab/neuron_hulls•00 issues in berenslab/neuron_hulls•00 pull requests in berenslab/neuron_hulls•Updated Sep 14, 2026Sep 14, 2026

• pubmed-ophtha

  Public
  Python

  •

  MIT License

  •00 forks in berenslab/pubmed-ophtha•33 stars in berenslab/pubmed-ophtha•00 issues in berenslab/pubmed-ophtha•00 pull requests in berenslab/pubmed-ophtha•Updated Sep 7, 2026Sep 7, 2026

• pmo-experiments

  Public
  Python

  •

  MIT License

  •00 forks in berenslab/pmo-experiments•00 stars in berenslab/pmo-experiments•00 issues in berenslab/pmo-experiments•00 pull requests in berenslab/pmo-experiments•Updated Sep 7, 2026Sep 7, 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

  •00 forks in berenslab/pmo-parser•11 star in berenslab/pmo-parser•00 issues in berenslab/pmo-parser•00 pull requests in berenslab/pmo-parser•Updated Sep 7, 2026Sep 7, 2026

• MorphoPy

  Public
  A Python package for feature extraction of neural morphologies

  Python

  •

  MIT License

  •1111 forks in berenslab/MorphoPy•4848 stars in berenslab/MorphoPy•00 issues in berenslab/MorphoPy•00 pull requests in berenslab/MorphoPy•Updated Aug 19, 2026Aug 19, 2026

• pygridfit

  Public
  Python port of gridfit (John D'Errico, 2006), with some improvement.

  Python

  •

  GNU General Public License v3.0

  •11 fork in berenslab/pygridfit•00 stars in berenslab/pygridfit•00 issues in berenslab/pygridfit•00 pull requests in berenslab/pygridfit•Updated Aug 18, 2026Aug 18, 2026

• RFEst

  Public
  A Python 3 toolbox for neural receptive field estimation using splines and Gaussian priors.

  matrix-factorizationsplinesjax+ 2

  matrix-factorizationsplinesjaxreceptive-fieldevidence-optimization

  Python

  •

  GNU General Public License v3.0

  •44 forks in berenslab/RFEst•2727 stars in berenslab/RFEst•44 issues in berenslab/RFEst•00 pull requests in berenslab/RFEst•Updated Aug 18, 2026Aug 18, 2026

• OrdinalDiffusionModels

  Public
  Python

  •11 fork in berenslab/OrdinalDiffusionModels•55 stars in berenslab/OrdinalDiffusionModels•00 issues in berenslab/OrdinalDiffusionModels•00 pull requests in berenslab/OrdinalDiffusionModels•Updated Jun 23, 2026Jun 23, 2026

• hybrid_biophysical_models_preprint

  Public
  Code for "Learning Hybrid Biophysical Neuron Models with Neural ODEs"

  Jupyter Notebook

  •00 forks in berenslab/hybrid_biophysical_models_preprint•22 stars in berenslab/hybrid_biophysical_models_preprint•00 issues in berenslab/hybrid_biophysical_models_preprint•00 pull requests in berenslab/hybrid_biophysical_models_preprint•Updated Jun 15, 2026Jun 15, 2026

• medirater

  Public
  A web app for medical image evaluation.

  HTML

  •11 fork in berenslab/medirater•11 star in berenslab/medirater•00 issues in berenslab/medirater•00 pull requests in berenslab/medirater•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

  •00 forks in berenslab/read-normalization•44 stars in berenslab/read-normalization•00 issues in berenslab/read-normalization•00 pull requests in berenslab/read-normalization•Updated Jun 5, 2026Jun 5, 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

  •22 forks in berenslab/MIDL24-segmentation_quality_control•22 stars in berenslab/MIDL24-segmentation_quality_control•00 issues in berenslab/MIDL24-segmentation_quality_control•00 pull requests in berenslab/MIDL24-segmentation_quality_control•Updated May 29, 2026May 29, 2026

• cooplot

  Public
  Visualizing co-op between members and subgroups.

  Python

  •00 forks in berenslab/cooplot•00 stars in berenslab/cooplot•00 issues in berenslab/cooplot•00 pull requests in berenslab/cooplot•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

  •1111 forks in berenslab/llm-excess-vocab•5656 stars in berenslab/llm-excess-vocab•00 issues in berenslab/llm-excess-vocab•00 pull requests in berenslab/llm-excess-vocab•Updated May 22, 2026May 22, 2026

• flatone

  Public
  A command-line tool to flatten one EyeWire II neuron automatically.

  Python

  •

  GNU General Public License v3.0

  •22 forks in berenslab/flatone•11 star in berenslab/flatone•00 issues in berenslab/flatone•00 pull requests in berenslab/flatone•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

  •00 forks in berenslab/text-embed-augm•22 stars in berenslab/text-embed-augm•00 issues in berenslab/text-embed-augm•00 pull requests in berenslab/text-embed-augm•Updated Mar 17, 2026Mar 17, 2026