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ReTune Commons

TRR 295 ReTune: Retuning dynamic motor network disorders using neuromodulation

ReTune Commons

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This is the coding part of the ReTune Commons initiative. The joint github organization is 1 aspect of the overarching aims of ReTune Commons in common data standards, common data infrastructure and common data exchange, in which raw and standardized data can be exchanged on joint GDPR-conform data infrastructure, in order to be analysed with containerized analytic workflows and open-source ReTune-specific softwares. The key element is the integration of the ReTune Commons into the Virtual Research Environment as the major digital research flagship of the Charité – Universitätsmedizin Berlin, Berlin Institute of Health (BIH) and Universitätsklinikum Würzburg.

The open-source coding repositories of ReTune Commons are collected here:

Open-source toolboxes

GitHub name Github Link Short description Publications
ANTx2 LINK toolbox for small animal neuroimaging atlas registration Koch et al. (2019) DOI
bart LINK toolbox for atlas registration of rodent brain histology de Bortoli et al. (2021) DOI
rodentDtiConnectomics LINK mrtrix scripts for reconstruction of rodent dMRI Kuffner et al. (2022) DOI
separating periodic from aperiodic PSD LINK code based on FOOOF for separating periodic from aperiodic power spectral densities Gerster et al. (2022) DOI
ROIconnect LINK functional connectivity analysis between regions of interests (ROIs) on source level. Pellegrini et al. (2023) DOI
FCSim LINK Matlab code for the paper "Identifying best practices for detecting inter-regional functional connectivity from EEG" Pellegrini et al. (2023) DOI
Lead-DBS LINK toolbox facilitating Deep Brain Stimulation electrode reconstructions and computer simulations based on postoperative MRI & CT imaging. Horn et al. (2019) DOI
ReTap LINK open-source published finger tapping accelerometer assessment tool Habets et al. (2023) DOI
Graph Diffusion Reclassification LINK algorithm for graph semi-supervised learning Peach et al. (2020) DOI
Highly Comparative Graph Analysis LINK  highly comparative graph analysis toolbox performs a massive feature extraction from a set of graphs, and applies supervised classification methods. Peach et al. (2021) DOI
Multiscale centrality LINK Graph centrality is a question of scale - Multiscale centrality (MSC) is a scale dependent measure of centrality on complex networks. Arnaudon et al. (2020) DOI
PyGenStability LINK Markov Stability: Computing the Markov Stability graph community detection algorithm in Python Arnaudon et al. (2023) DOI
TVB-multiscale LINK DOI TVB Extension of TVB to cosimulate mean-field and spiking network models Meier et al. (2022) DOI
Virtual DBS model EBRAINS  Virtual DBS proof-of-concept model including all data Schirner et al. (2022) DOI
HCP pre-processed data LINK Readily available pre-processed data of Human Connectome Project data Schirner et al. (2023) DOI
BIDS input to TVB LINK Extension of TVB to input BIDS-conform data
BIDS extension proposal PR850 PR967 BIDS extension proposal for computational modeling data Schirner et al. (2021) DOI
IPID1 inferring phase isostable dynamics LINK implementation of the IPID-1 algorithm to infer phase/isostable response curves from time series data Cestnik et al. (2022) DOI
deepflash2 LINK segmentation of ambiguous bioimages Griebel et al. (2023) DOI
py_neuromodulation LINK toolbox allowing for real time capable processing of multimodal electrophysiological data Merk et al. (2022) DOI
ndx_ecg LINK extension to convert ECG data into NWB
Let_it_be_3D LINK pipeline for tracking mice movements from 2D in 3D
Findmycells LINK end-to-end bioimage analysis pipeline with state-of-the-art tools for non-coding experts
PyPerceive LINK toolbox (internal use) to import (perceive'd) Percept STN LFP data in Python
PyBispectra LINK A Python signal analysis toolbox for computing spectral-domain interactions using bispectra.
ReTune BIDS Standardization LINK Tools for input and conversion of human electrophysiology in BIDS
Sim2BIDS LINK sim2bids: an app with GUI that converts computational modeling data into BIDS
Dataset Filter kit LINK tool to filter BIDS datasets and divide it in subdataset
ReTune electrophysiology workshop LINK MATLAB workshop for electrophysiology provided by projects B03, C01 and INF
Perceive LINK Extract data from the Medtronic Percept bidirectional brain computer interface device for adaptive deep brain stimulation
Dynamic Graph Dimensionality LINK Dynamic Graph Dimensionality is a methodology for computing the relative, local and global dimension of complex networks
stats_n_plots LINK Computation and visualization of statistical analyses common in the Life sciences made easy
SignDCL LINK An easy-to-use GUI to perform contour tracking, extract immobility and freezing episodes.
neurokin LINK python package to support integrated analysis of neural and kinematic data
BSI-Zoo LINK python library for M/EEG simulation and source reconstruction
PAC LINK Matlab code for the manuscript in preparation "Distinguishing across- from within-site phase-amplitude coupling using antisymmetrized bispectra"
MARBLE LINK MARBLE or MAnifold Representation Basis LEarning is a fully unsupervised geometric deep learning method that can intrincally represent vector fields over manifolds, perform unbiased comparisons across dynamical systems and can operate in geometry-aware or geometry-agnostic modes
RVGP LINK Riemannian manifold vector field Gaussian Processes is a generalised Gaussian process for learning vector fields over manifolds, using the connection Laplacian operator, which introduces smoothness in the tangent bundle of manifolds.

Open-data Overview

The open-data of ReTune Commons are collected here:

Source Link to the Data Short description Publications
Data from: On the objectivity, reliability, and validity of deep learning enabled bioimage analyses Data DOI Animal Data: Images, training datasets, codes, deep learning models and model ensembles: cFOS Segebarth et al. (2020) DOI
Data from: A unified connectomic target for deep brain stimulation in obsessive-compulsive disorder Lead-DBS Human data: the joint DBS-based clinical improvement-predictive tract atlas of 50 patients with OCD is openly available within Lead-DBS software Li et al. (2020) DOI
Data from: Personalizing Deep Brain Stimulation Using Advanced Imaging Sequences Lead-DBS Human data: the joint hypointensity template and the probabilistic map derived from 36 patients with Essential Tremor using FGATIR sequences is openly available within Lead-DBS software Neudorfer et al. (2022) DOI
Human data: Replication data demonstrating that electrocorticography is superior to subthalamic local field potentials for movement decoding in Parkinson's disease Data DOI human neuroelectrophysiological data of 15 subjects with Parkinson's disease and DBS-ECOG implant Merk et al. (2022) DOI
Data from: Exploring transcriptome-wide changes in the brain-localized immune cells in a mouse model of Parkinson's Disease GEO Accession Viewer Genetic data (animal): Bulk mRNA sequencing data from the brain-localized immune cells in a mouse PD model Karikari et al. (2022) DOI
Data from: Analyzing the immune cell population changes in the brain and the gut of PD mice GEO Accession Viewer Genetic data (animal): Single-cell sequencing data from the CD4+, CD8+, and CD11c+ cells in the brain of a PD mouse model McFleder et al. (2023) DOI
Data from: Deep learning-enabled segmentation of ambiguous bioimages with deepflash2 Data DOI Animal data: Dataset, trained deep learning (benchmark) models, and Python Code for deepflash2 Griebel et al. (2023) DOI
Data from: Prediction of Stroke Outcome in Mice Based on Noninvasive MRI and Behavioral Testing Data DOI Animal data: raw MRI T2w images, lesion masks, and the registered atlases, the input for machine learning algorithms (lesion volume, segmented MRI, behavioral scores), the trained classifiers, and their output (predicted behavioral scores) Knab et al. (2023) DOI

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  1. let_it_be_3D let_it_be_3D Public

    2D to 3D tracking data conversion pipeline

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  2. InvasiveElectrophysiologyWorkshop_I InvasiveElectrophysiologyWorkshop_I Public

    This is the official ReTune repository for invasive neurophysiology workshop I, provided by projects B03, C01 and INF.

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  4. hackathon_2023 hackathon_2023 Public

    Repository for the ReTune Hackathon 2023

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  5. INF INF Public

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  6. PyBispectra PyBispectra Public

    Forked from braindatalab/PyBispectra

    A Python signal analysis toolbox for computing spectral-domain interactions using the bispectrum.

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