Berens Lab @ University of Tübingen

t-simcne

Unsupervised visualization of image datasets using contrastive learning

pubmed-landscape

The landscape of biomedical research

contrastive-ne

Contrastive neighbor embeddings

MorphoPy

RFEst

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

patch-seq-rrr

Sparse reduced-rank regression

iclr-dataset

ICLR dataset

elephant-in-the-room

Companion repository to our Lause, Berens & Kobak (2024) preprint "The art of seeing the elephant in the room: 2D embeddings of single-cell data do make sense" (bioRxiv)

neuroprobnum

Probabilistic numerics for common neuroscience models.

ephyspy

A Python package for electrophysiological feature extraction for patch-clamp experiments.

medical-t-simcne

This repository contains the codes to train a t-SimCNE model. This model has been shown to produce good representations on natural and medical images.

read-normalization

Companion repository to our Lause et al. (2023) preprint "Compound models and Pearson residuals for normalization of single-cell RNA-seq data without UMIs" (bioRxiv))

eff-ph

Persistent homology for high-dimensional data based on spectral methods

fundus_circle_cropping

Code for extracting a circular mask from fundus images and tightly cropping the images around the mask.

MIDL24-segmentation_quality_control

Experiments for MIDL 2024 Submission: Controlling Segmentation Quality per Image

retimgtools

Web-based tools for retinal image annotation and evaluation.

retinal_image_counterfactuals

Realistic retinal fundus and OCT counterfactuals using diffusion models and classifiers.

hh_sbi

DiffusionTempering

fslm

refactored fslm repository

fslm_repo

reproduce results of fslm paper

interpretable-sparse-activation

MA_LA_For_MML

Code for my Masters Thesis "Robust Uncertainty Estimation in Medical Machine Learning Applications with the Laplace Approximation". Mostly based on Laplace Redux -- Effortless Bayesian Deep Learning

ne_spectrum_scRNAseq

picasso

Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.

poisson-gpfa

Gaussian process factor analysis with Poisson observations

retinal-classification

non-rl experiments for the retinal-rl project

retinal-rl

Testing theories about retinal coding in reinforcement learning environments

retinal-rl-models

Code for the pytorch models used in the retinal-rl project (and related non-rl usages)

sbi-kigali-2023-student