Repositories list

• DREAMS-CNE

  Public
  Contrastive neighbor embeddings with added regularization for global structure preservation.

  Jupyter Notebook

  •

  Other

  •10•0•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

  •175•0•0•0•Updated Dec 19, 2025Dec 19, 2025

• dreams-experiments

  Public
  DREAMS - Dimensionality Reduction Enhanced Across Multiple Scales

  Jupyter Notebook

  •

  MIT License

  •0•4•1•0•Updated Dec 19, 2025Dec 19, 2025

• retinal-rl

  Public
  Testing theories about retinal coding in reinforcement learning environments

  Python

  •

  GNU Affero General Public License v3.0

  •1•0•22•3•Updated Dec 15, 2025Dec 15, 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•2•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•22•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

  •9•45•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•45•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•47•0•0•Updated Aug 28, 2025Aug 28, 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•2•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-correlations+ 3causalityretinal-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-learninglasso+ 5sparseneural-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•115•1•1•Updated May 19, 2025May 19, 2025