Friedrich Miescher Institute for Biomedical Research

latent-predictive-learning

Code to accompany our paper "The combination of Hebbian and predictive plasticity learns invariant object representations in deep sensory networks” bioRxiv 2022

LSTree

LSTree is a digital organoid and lineage tree extraction workflow for light sheet movies.

stork

A differentiable spiking neural network simulator

gliberal-scMultipleX

Feature extraction and linking of multiplexing data.

GUIFold

GUI for running jobs with a local installation of AlphaFold2. Supports submission to queuing systems.

faim-cryoflare

CryoFLARE: FMI Live Analysis and Reconstruction Engine for single particle Cryo EM data

faim-robocopy

A python-based UI for robocopy

gfriedri-em-alignment

Alignment tools used in the Friedrich lab.

implicit-var-reg

gbuehler-MiniChip

small collection of R functions for ChIPseq analysis

disinhibitory-control

gfriedri-em-alignment-flows

gliberal-lightsheet-2023

guifold-alphafold2

Open source code for AlphaFold.

neuRoi

ggiorget-spt-analysis

ggiorget-spt-parameter-sweep

ggiorget-spt-parameter-sweep

dl-utils

faim-ij1-io

A simple IJ2 wrapper for reading and writing TIFF files through IJ1

faim-ij2-ij

Simple headless SciJava wrappers around ImageJ plugins

faim-imagej-stitching

faim-jetraw

gbuehler-dinoR

R package for differential NOMe-seq data analysis.

gbuehler-NOMeConverteR

functions to convert between NOMe-seq data representation formats

gchao-koopa-flows

gchao_RPL-Myc

gpeters-fetchNOMe

R package for fetching NOMe-seq data from BAM files

guifold-rosettafold2

HT_OrganoidAnalysis

Code accompanying the manuscript "Dynamics and plasticity of stem cells in the regenerating human colonic epithelium" by Oost, Kahnwald et al. from the Liberali Lab.

surrogate-gradient-theory