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c2dbb06130517d229353efb937dd27d8fa602d4a0c2ef88a45d6f174d8b1288e | Text | 1,631 | 42 | # Meaningful Associations Redux
This repository contains the R code and materials for the paper:
**Meaningful Associations Redux: Quantifying and interpreting effect size in the context of the Adolescent Brain and Cognitive Development Study**
Anthony Steven Dick, Jonathan S. Comer, Mohammadreza Bayat, Marilyn Curt... |
53cfff123d517e43f5b06d72037cdcd54acf91156e2cc80c50a95f80cc72b07f | Text | 1,645 | 21 | # Controlling Donor and Newborn Neuron Migration and Maturation in the Eye Through Microenvironment Engineering
In this repository you may find the information for reproducing ... |
dfff51e880ad591f4d009b33369d413ccaaaafa2072737855bc294cb59853e88 | Text | 1,687 | 26 | # Traditional Imagined Speech Paradigm
This paradigm is based on the work of [Nguyen 2018](https://pubmed.ncbi.nlm.nih.gov/28745299/).
## How to run
0. Before Running
- Install OpenViBe Designer.
1. Setting up the Paradigm.
- Open "TraditionalParadigm.xml" using OpenViBE Designer
- On the "Lua Stimulator" box, chan... |
59df511174a74ea1806f60aadea16133c7cf88b7c554488e7f2eab2da57049ba | Text | 1,711 | 51 | # Stringer-AQP4-Classifier-QuPath
Pixel classifier for AQP4 quantification using QuPath (trained in v0.3.0, compatible with v0.5.1)
Stringer-AQP4-Classifier-QuPath
This repository contains a pixel-based classifier for quantifying Aquaporin-4 (AQP4) protein expression in human post-mortem brain tissue using QuPath.
Tr... |
6e084496681a002a2270868f3b24e679bdbba24a0a4bc9bfe54fcaa8b044eb7b | Text | 1,714 | 27 | # SpaGE
## Predicting whole-transcriptome expression of spatial transcriptomics data through integration with scRNA-seq data
### Implementation description
Python implementation can be found in the 'SpaGE' folder. The ```SpaGE``` function takes as input i) two single cell datasets, spatial transcriptomics and scRNA-... |
be98932aeff927a0f59d95f4f56437f5d5c2b5a0af08ef2197a8572a31fce595 | Text | 1,732 | 31 | # qbic-pipelines/rnadeseq
**Downstream differential gene expression analysis with DESeq2 package**.
[](https://www.nextflow.io/)
[](http://bioc... |
670ac1b42f2a8f0a695293e55db3c2bf9f18ae474142777defc41f29cde99a18 | Text | 1,737 | 8 | # VNLS
Implementation of the Variational Neural Linear Solver as presented in Toward Neural Network Simulation of Variational Quantum Algorithms by Oliver Knitter, James Stokes, and Shravan Veerapaneni. This implementation derives from the original released with the paper (https://github.com/oliverknitter/VNLS) and is... |
96b5144cd5b8b7a4e24a7c2418eb2586f01ed6f8a49c5527d637fe7839887d08 | Text | 1,745 | 7 | # Transcriptional dynamics of the oligodendrocyte lineage and its regulation by the brain erythropoietin system
Oligodendrocytes differentiate from oligodendrocyte progenitor cells (OPC) in early postnatal development, but some oligodendrogenesis is maintained throughout adulthood, where oligodendrocyte lineage dynami... |
55bad9333a442767f8c5b22bc6597c0582c59d2fb6de7f16208ec457132126c5 | Text | 1,756 | 39 | # Code for "Revealing how uncertainty computations drive1 hierarchical reasoning via CogLink Networks"
## Installation
It is highly recommended to use virtual environment to install the package.
> virtualenv env
To install all the dependency, we recommend to use pip to install.
>pip install -r requirements.txt
## Fi... |
83d772ed4ac4741096ac881885fdb23e0bcbe7c244c18485f457c36f764d74ee | Text | 1,763 | 39 | # Ex2p / Ex2pO
Extra lens mount for 2-photon microscope
- extend imaging capability
- excitation of neurons by optogenetic stimulation with narrow-band laser
|Imaging flexibility|Optogenetical stimulation (under-filled setting)|
|---|---|
|<img width="960" alt="image" src="https://github.com/rysk-t/ex2p/blob/main/i... |
169ecc6eb309a4115b645af1f3168f0bb5554223bd40e4a3dc41c7cb3754af1c | Text | 1,773 | 50 | # Neuropixels-footprint
Get footprint metric from all Neuropixels probe
## Description
This repository calculates footprint metric from Neuropixels mean waveforms, a metric to evaluate waveform spead from peak site.
Footprint is defined as the radius from peak site, at which the mean waveform peak voltage drops below ... |
da428e427a4dedda860633eef48a3e38d217c2ed8bf9474f2727b2877ec3ebe3 | Text | 1,775 | 43 | # ktan
ktan is a C++ program to perform data acquisition with the GNU/Linux operating system. This program was developed to work with the Evaluation board from Intan Technologies. The low level code to interface with the board comes from the RHD2000 interface software of Intan Technologies. The visual interface of kac... |
41abe52ea2b3eda60027d2e90c3f6f254ee3ed8411ad49f62780f023cf3089c3 | Text | 1,787 | 47 | # BrainSTEM
BrainSTEM (brain Single-cell Two tiEr Mapping) is a biologically-driven
multi-resolution mapping strategy to assess the transcriptional fidelity of
midbrain cultures via scRNA-seq. In the first tier, query datasets are projected
onto the fetal whole brain atlas to assess the brain region specificity of ... |
aef566d20de6e713efa58c3b99e58120cc660001965a74e4edd3e029e7b53b6f | Text | 1,791 | 35 | # prfVista
A small respository to call pRF functions in vistasoft without the need to set up vistasoft-specific data structures and session files. The assumption is that the fMRI time series are in NIFTI files, and the stimulus file is in either a NIFTI file or MATLAB file.
This requires the vistasoft tools on the pat... |
00e72a9b285896fcd02fa08c725245b30ae53e24d267a9333f4e47afed7dfe7a | Text | 1,800 | 35 | CorticalSim - cortical microtubule simulator
If you use CorticalSim in publications, please include a citation to:
[for general use] http://dx.doi.org/10.3389/fphy.2014.00019
[for microtubule dependent nucleation] http://dx.doi.org/10.1088/1478-3975/8/5/056002
[for microtubule severing] http://dx.doi.org/10.1073/pnas... |
21ecfeccd8999a97a3c10685ce3b92ffece6599c43d933763eed8a99b329dff2 | Text | 1,806 | 15 | # Sleep-biopsychosocial profiles
### Summary
This repository contains code to reproduce the analyses conducted for the manuscript entitled '**A multidimensional investigation of sleep and biopsychosocial profiles with associated neural signatures**' by Aurore A. Perrault, Valeria Kebets, et al.
### Abstract
Sleep is... |
9cb2b59227c30c32209d12c4c63482a570547b26b1f9acd0410a8f7901bf3f98 | Text | 1,817 | 34 | # abrWaveAnalyser
Marcotti's lab ABR wave analysis GUI. The software can be used to semi-automatically label thresholds and waves (wave I-IV supported) of auditory brainstem responses (ABRs).
## Installation
A python environment with the following libraries is required:
- `python 3.10`
- `pyqt 5`
- `pyqtgraph 0.... |
6388677e9c9f1e56f389c783bcf90b84db14dc0a24eca861ed5d1c8402c565c1 | Text | 1,836 | 33 | # dmrff
dmrff: identifying differentially methylated regions efficiently with power and control
Matthew Suderman, James R Staley, Robert French, Ryan Arathimos, Andrew Simpkin, Kate Tilling
bioRxiv 508556; doi: https://doi.org/10.1101/508556
*Background.* An epigenome-wide association study (EWAS) tests associations ... |
a168608e0be9bf391d8f39f1a5aeccd2b3b69eadc528b008ed09cbddc183aa79 | Text | 1,837 | 79 | # The OHBA Software Library for the analysis of electrophysiological data (osl-ephys)
Tools for MEG/EEG analysis.
Documentation: https://osl-ephys.readthedocs.io/en/latest/.
## Installation
See the [official documentation](https://osl-ephys.readthedocs.io/en/latest/install.html) for recommended installation instruc... |
7e5b0e05e2a502ad57522506da6ed353500b07a9a6ef7f48639028d905e61c88 | Text | 1,842 | 40 | Source code for paper: *Decoding multi-joint hand movements from brain signals by learning a synergy-based neural manifold*
## How to Run: Instructions for Users
### 1. **Download the Dataset**
Download the dataset and place it in the *Dataset* directory. The dataset is organized into the following three folders... |
869b9384fa4b3a0f5f85e4482857e2e5556d45926250c5e0b7a80801b5e83d5d | Text | 1,844 | 37 | JILL Real-Time Auditory Neuroscience Framework
----------------------------------------------
|ProjectStatus|_ |TestStatus|_ |License|_
.. |ProjectStatus| image:: https://www.repostatus.org/badges/latest/active.svg
.. _ProjectStatus: https://www.repostatus.org/#active
.. |TestStatus| image:: https://github.com/meliz... |
ba31a2c23ecb5f23b9729ce800602ba74bac2dbdf9c305fb3e938ea554744926 | Text | 1,879 | 34 | # iMFA: _In Vivo_ Metabolic Flux Analysis
The codes related to our manuscript **"Rewiring of Cortical Glucose Metabolism Fuels Human Brain Cancer Growth"** can be found in this repository.
We organized the codes into following folders and provided a detailed description for using the codes in each folder. Please clic... |
df903163e56ec45c7819b04dc607b4c2b656445c98ead538ea7975b2db19c5f8 | Text | 1,884 | 47 | hbMEP Paper
=====
This repository has code to reproduce results in the paper `Hierarchical Bayesian estimation of motor-evoked potential recruitment curves yields accurate and robust estimates <https://arxiv.org/abs/2407.08709>`_.
It uses the `hbmep v0.5.0 <https://github.com/hbmep/hbmep>`_. See `pyproject.toml <http... |
fdbc1d5a5626608f573908be85d847f52c8b8f8f9898731cf248592a18d8c275 | Text | 1,885 | 59 | # tms-nirs-connectivity
Source code and lab notes for the `tdcs-nirs-connectivity` study.
:page_facing_up: **Preprint**: <https://www.researchsquare.com/article/rs-7179811/v1>
## System dependencies
* [Python 3.12.0](https://www.python.org/downloads/release/python-3100/), to run the fNIRS preprocessing pipeline.
* ... |
4acad93bf6da5d0c177cf18f75948c364612a50af2cb830b348d1a88aee72128 | Text | 1,886 | 42 | # The best of two worlds: Decoding and source-reconstructing M/EEG oscillatory activity with a unique model
Britta U. Westner & Jean-Rémi King
## Repository
This repository contains the simulation and analysis code for the project _The best of two worlds: Decoding and source-reconstructing M/EEG oscillatory activity... |
8252fbc0983d8311019159cfbef8bd259d0bfe7b3a5fddf031c6a82c1c038ae9 | Text | 1,887 | 43 | # Hardness and Surface Roughness Prediction of 3D-Printed ASA Components Using Machine Learning and Deep Learning
This repository contains the dataset, source code, and experimental results for the study:
**“Hardness and Surface Roughness of 3D-printed ASA Components Subjected to Acetone Vapor Treatment and Different ... |
3ba0c0a66f85f955d11e35d30d78278616106cb142a6fa35e7887365bace5f2d | Text | 1,904 | 30 | # Pairwise-Importance-Estimate-Extension-with-Time-Series-adaptation
## Datasets
- Univariate Simulated Dataset 0
- Univariate Simulated Dataset 1
- Multivariate Simulated Dataset 0
- Multivariate Simulated Dataset 1
- [Occupancy](https://archive.ics.uci.edu/dataset/357/occupancy+detection)
- [HHAR](http://archive.ics... |
d2486096c8dad3ae5e8476220da4bd7e557020bb1dff9ddd4ac3fd605a0f1547 | Text | 1,907 | 68 | <div align="center">
<img src="https://github.com/user-attachments/assets/e12bcab1-3856-4c11-bebe-6fe148dad1b2" alt="Oncomark Poster">
</div>
<br>
**OncoMark** is a deep learning tool designed to systematically quantify hallmark activity using transcriptomics data from routine tumor biopsies. Ideal for applications ... |
3e5b6a53d8958413ff3f634398f12a42a4598efaf94261513e93b5680b42137e | Text | 1,912 | 51 | # High-resolution in vivo kinematic tracking with customized injectable fluorescent nanoparticles
## Authors
Emine Zeynep Ulutas<sup>1</sup>, Amartya Pradhan<sup>1,2</sup>, Dorothy Koveal<sup>1</sup>Jeffrey E. Markowitz<sup>1,2#</sup>
<br>
<sup>1</sup>Wallace H. Coulter Department of Biomedical Engineering, Georgia ... |
5742916f638ba641c33ea44d2ba4ee80e408d81ac083b090742a9dda12d150b7 | Text | 1,912 | 57 | # IEBCS
ICNS Event Based Camera Simulator
The code base has been recently cut down to a maintainable reference python implementation. For now, if you want the blender interoperability or the C++ implementation, download a previous version of this repository at your own risk.
This repository contains:
* /data/: Store... |
9c0a53e3197d94c66f5ba6472d1e96a62e439813aa9d98c1bfa675ab744c8ae6 | Text | 1,914 | 35 | # Source Code
This repo including the analysis code in the paper, **Regulatory networks of KRAB zinc finger genes and transposable elements changed during human brain evolution and disease** (DOI: 10.1101/2023.12.18.569574). You ca... |
e47ddcfaa360bb61cde48889c1c39defa94a4dc62e5a729f30fdc0730cd81244 | Text | 1,953 | 53 | # IML SpotifyTrackerOpen 🎧
A Python script to log Spotify playback activity for research purposes.
This script was developed as part of the Intentional Music Listening project to analyze participants’ music listening behavior.
## Features
- Detects when the Spotify app is opened or closed
- Logs:
- Track name, ... |
154e0318a8c298b5fefe750632c276f70328cc78ed978b4fc09d0ade1f02b366 | Text | 1,959 | 64 | .. image:: https://zenodo.org/badge/14752681.svg
:target: https://zenodo.org/badge/latestdoi/14752681
Microscope-Cockpit
==================
.. image:: cockpit/resources/images/cockpit.ico
:width: 400
:align: center
:alt: Cockpit Icon
Cockpit is a microscope graphical user interface. It is a flexible
and ea... |
99f5ea5a210b2cc59c8b330e65ca8fc14926342fb114d42f7f0c1ff4714a3e0d | Text | 1,959 | 48 | # Functional specialisation of multisensory temporal integration in the mouse superior colliculus
Code to reproduce the figures from Bianchini et al., "Functional specialisation of multisensory temporal integration in the mouse superior colliculus" available at https://www.biorxiv.org/content/10.1101/2025.02.11.637674v... |
f8806b43b8c757c5ca332c2deafd9a23bfaeb0464e637e7efdafbbfe767305a0 | Text | 1,959 | 27 | # WGCNA Application to Proteomics and Metabolomics Data
Progresses in mass spectrometric instrumentation and bioinformatics identification
algorithms made over the past decades allow quantitative measurements of relative
or absolute protein/metabolite amounts in cells in a high-throughput manner, which
has significantl... |
ad7d703ff279158128640908b8efc16c2a79459cb95478f4694ee22ee693c780 | Text | 1,962 | 16 | # ptx-spsp4d
This is a matlab script for designing parallel transmit (pTx) 4D spatial spectral (spsp) RF pulses with kT point parameterization.
You may run the demo script, `demo.m`, to grab an idea of how this toolbox can be used to design pTx 4D spsp (3D spatial + 1D spectral) pulses to create uniform water-selective... |
db4085906a6e08f30da0b86441fb1d26ec4051175feb828d181121112b550a55 | Text | 1,963 | 60 | # GenScore
GenScore is a generalized protein-ligand scoring framework extended from RTMScore, and it exhibits balanced scoring, ranking, docking and screening powers on multiple datasets.
<div align=center>
<img src="https://github.com/sc8668/GenScore/blob/main/zzz-3.jpg" width="600px" height="300px">
</div>
### R... |
a37d3d4700ec1a4080dfa6a29290b2ffd2e065e7a794491c60d95b7cb2ed66df | Text | 1,966 | 59 | DRA-coupling
Electrophysiological recordings reveal photoreceptor coupling in the dorsal rim areas of honeybee and bumblebee eyes
This repository contains files relevant to the manuscript "Electrophysiological recordings reveal photoreceptor coupling in the dorsal rim areas of honeybee and bumblebee eyes" by George... |
395853a8aca8fc463acc7f853657da2a2f0481389b6cdc488ea1ae606a75674f | Text | 1,969 | 49 | # <img src="https://github.com/hilgers-lab/SpliceFlow/blob/main/data/logo.jpg" alt="Logo" width="20%" align="left"> SpliceFlow
<!-- badges: start -->
[
# Molscrub
Process large numbers of small molecules for docking with AutoDock.
May be useful for structure-based modeling in general.
What happens:
- generate 3D coordinates using RDKit's ETKDGv3 and UFF minimization
- enumerate tautomers (aiming at low energy states only)... |
246554ace55c55f1de21a36a2fce7872ab0a73a5ac1732345ff12d1788328133 | Text | 1,981 | 40 | # Tensor-MP-PCA
Matlab implementation of MP-PCA based denoising of multidimensional data based on Olesen, JL, Ianus, A, Østergaard, L, Shemesh, N, Jespersen, SN. Tensor denoising of multidimensional MRI data. Magn Reson Med. 2022; 1- 13. doi:10.1002/mrm.29478. Usage is free, but please cite the paper above. The data ca... |
134bf346fbf73b19732dcbd3ecf0d01ccc1beaa78a9aef04f16a4b28827f5157 | Text | 2,018 | 47 | # Public code repository for the Journal of Engineering manuscript "Distance of bipolar re-referencing imparts nonlinear frequency-specific influences on intracranial recording signal measurements"
================================
## Package setup.
### 1. Required software
MATLAB (tested with Version 2023-2025). ... |
5f93ff8c0b69ff62dcc8ac6d97ddbb51840a20c7cb9708901812148d376c8409 | Text | 2,024 | 34 | # ibean
Data repo for the ibean project of the AIR lab.
This dataset is of leaf images taken in the field in different districts in Uganda by the Makerere AI lab in collaboration with the National Crops Resources Research Institute (NaCRRI), the national body in charge of research in agricul... |
3851485141a5cde2f211499d10490226b653ce0713bb6d1fb953cf70f0603f3d | Text | 2,031 | 57 | # Fast-Higashi: Ultrafast and interpretable single-cell 3D genome analysis
[https://www.cell.com/cell-systems/fulltext/S2405-4712(22)00395-7](https://www.cell.com/cell-systems/fulltext/S2405-4712(22)00395-7)
Fast-Higashi is an interpretable model that takes single-cell Hi-C (scHi-C) contact maps as input and jointly i... |
57119a84514e63a60c2105ceeebdbdc41c87c4bb8a084bf2fdf37115580bcbdf | Text | 2,035 | 53 | ## MARLIN
**M**ethylation- and **A**I-guided **R**apid **L**eukemia Subtype **In**ference
MARLIN is a deep neural network model for DNA methylation-based Acute Leukemia classification from sparse DNA methylation profiles.
For more information please refer to our paper.
## Installation
Get the repository:
`git clo... |
e7174bda69bdaa22e92818684dfa7828f4294aa19b678f70de4c08cea61ce4fe | Text | 2,045 | 47 | # Denk et al., 2025. "Text-to-music generation models capture musical semantic representations in the human brain"
This repo contains the code to reproduce the main results presented in Denk et al., 2025. "Text-to-music generation models capture musical semantic representations in the human brain".
## Setup
(Unless ... |
039e8165ae5a4fd2b5272ac6c0e680c99854f92daf6da34d090f7d78d8a569a7 | Text | 2,055 | 59 | <!-- PROJECT SHIELDS -->
[![Apache-2.0 License][license-shield]][license-url]
<!-- PROJECT TITLE -->
<p align="center">
<h3 align="center">Shotgun Lipidomics Assistant</h3>
<p align="center">
A python project to read and analysis Sciex Analyst output data
<br />
<a href="https://www.uclalipidomics.net/... |
d46410c807d454bcec9fcb2a00a0a73f8da557a0d31dc1d47ab6eba4bfd13ce8 | Text | 2,072 | 30 | # Machine-learning convergent melanocytic morphology despite noisy archival slide
## Requirements
To use the code in this repository, you will need to set up two different environments: one for WSI preprocessing and another for model training.
For WSI preprocessing, use the `wsi_pipeline.yml` environment.
For mode... |
6d65094bd18ac76f8cb7e108b7bbd47b0d3056d1a273c61b78a7e7366b43142a | Text | 2,075 | 23 | # Individualized neonatal functional connectivity
This repository contains the code for
> Derman D., Pham D. D., Mejia A. F., & Ferradal S. L. (2025). Individual patterns of functional connectivity in neonates as revealed by surface-based Bayesian modeling. [Imaging Neuroscience](https://direct.mit.edu/imag/article... |
aa6357ccd56e5665f747afb4d807c57d6a6aa1ff32de75eaf63569377b3366ec | Text | 2,091 | 59 | # Structure Tensor Analysis Toolkit
=================================
This project provides a set of Python tools to perform 3D Structure Tensor (ST) analysis on volumetric microscopy data.
It allows estimation of orientation vectors, local disarray, and fractional anisotropy from 3D image stacks, with options for vis... |
ec89c7a672f3d237dc45e562239fc2b0e6a0ae9291e3a7d731c929e5b3a0db9e | Text | 2,092 | 48 | Capcalc
=======
capcalc is a suite of python programs used to perform coactivation
pattern analysis on time series data. It uses K-Means clustering to find
a set of “activation states” that represent the covarying patterns in
the data.
HTML documentation is here: http://capcalc.readthedocs.io/en/latest/
NOTE
====
T... |
cf2e737367292f2d5113bab1a6702da9f1f7ead57fe407ed0c5d3b989ed4e478 | Text | 2,093 | 28 | <a href="https://doi.org/10.5281/zenodo.15595744"><img src="https://zenodo.org/badge/996283200.svg" alt="DOI"></a>
# Magnitude-Constrained Optimal Chaotic Desynchronization of Neural Populations
This repository contains the Matlab code for calculating magnitude-constrained optimal stimuli for desynchronizing neural po... |
9011b6599688c0f026713132830ed87f23ffa2691c3dc3d6dc88ba0bcb0b721b | Text | 2,106 | 52 | # Does *COMT* Play a Role in Parkinson's Disease Susceptibility Across Diverse Ancestral Populations?
`GP2 ❤️ Open Science 😍`
[](RELLENAR)
[](https://opensource.org/licenses/MIT)
**Last Updated:** Apr... |
7c43c8dab718618c5ceb96f0061faff597533d221e239c4b0f7878badfe0ec25 | Text | 2,112 | 27 | # miniature Bessel-beam two-photon microscope (miniBB2p)
## Description
This repository includes the optical design files, technical drawings, assembly protocol, and code for hardware control of miniBB2p. miniBB2p is a head-mounted miniature Bessel-beam two-photon microscope, published in Qian, et al.,"High-throughput ... |
a503e378671020cb709eab41adfac1ca45041717210712c82b01fc0bab929029 | Text | 2,113 | 22 | # Inference of vagus nerve parameters through optimization
This repository provides a proof-of-concept for the inference of vagus nerve structure through the use of optimization of model parameters to minimize the error between a ground truth and *in silico* evoked compoint action potential. The model of the eCAP is t... |
68f2e14253721e86ac12411dbd091d028b9ca8d90aa14feb82fdc926a0ab3e58 | Text | 2,116 | 63 | # SuCOS
SuCOS is an RDKit-based overlap measure that combines volumetric shape and pharmacophoric features to give a combined overlap score similar to OpenEye's Tversky Combo and [Malhotra and Karanicolas' COS measure](https://pubs.acs.org/doi/abs/10.1021/acs.jmedchem.6b00725).
For calculation of chemical feature ov... |
afc416939b8f0e792985bde85b43a9ee9d6831a24e80649dd26ffe61150136e0 | Text | 2,122 | 44 | # Ex2p / Ex2pO
Extra lens mount for 2-photon microscope
- extend imaging capability
- excitation of neurons by optogenetic stimulation with narrow-band laser
|Imaging flexibility|Optogenetical stimulation (under-filled setting)|
|---|---|
|<img width="960" alt="image" src="https://github.com/rysk-t/ex2p/blob/main/i... |
a509879f9497c8efc8747037f5533001516a422ee79476c78d1bcf47cdc65031 | Text | 2,137 | 52 | # Does *COMT* Play a Role in Parkinson's Disease Susceptibility Across Diverse Ancestral Populations?
`GP2 ❤️ Open Science 😍`
[](https://opensource.org/licenses/MIT)
[](https://doi.org/10.5281/zenodo.1... |
20ab157ec5a68dd98f5a2c0189a9b284b5a7ac1694c0f02cee903862512f2ec3 | Text | 2,139 | 73 | # molcloud [](https://whitead.github.io/molcloud/)[](https://badge.fury.io/py/molcloud)
This package draws molecules (or RNA, thanks to [@Shunsuke-1994](https://github.com/Shunsuke-1... |
b17910608e8a118bb10647f4b05e4b42e605a076fbe8f2ef6025c261e4d29f19 | Text | 2,139 | 19 | # ITEM
<h3>Inverse Transformed Encoding Models</h3>
This repository contains SPM-compatible MATLAB code for estimating inverse transformed encoding models (ITEM) based on first-level general linear models (GLMs) for functional magnetic resonance imaging (fMRI) data [1,2]. The ITEM approach allows trial-wise linear de... |
5ff7760d1696aa1053b3d7695b17d4632c913bc2e28e683ba482e80c4e94e316 | Text | 2,150 | 45 | # CUT-RUN-pipeline
This repository contains scripts for processing, normalizing, quantifying, and clustering CUT&RUN datasets. The pipeline is structured to facilitate downstream analysis.
## Pipeline Overview
### 1: Data Processing (`main_pipeline.sh`)
Processes paired-end FASTQ files into normalized BigWig files.... |
5b5dee5622e3b647c0b3ff8864248c572ed2988b95d90c0ad2df6b40104c3486 | Text | 2,152 | 41 | # Recurrent Predictive Learning (RPL)
This repository contains code for reproducing results reported in our preprint on RPL,
a JEPA model of predictive processing.
## Setup
We have provided the code as a python package. To setup your python environment
and run the code, clone this repository and follow the following s... |
6d5cfad33379490aa61d0591cd3d5285309778f283513d772060f519bf037ed9 | Text | 2,154 | 54 | # MorphoTrack-merger
MorphoTrack-Merger is a Python-based tool designed to extract morphological features from segmented images and merge them with tracking data from TrackMate or Manual Tracking (Fiji). This tool is particularly useful for researchers working in bioimaging and cell tracking, as it allows for seamless... |
6901660e40c7afb47fda3c3122eda53e9334142b4f9ddd7e305b47c57d1068c2 | Text | 2,159 | 42 | # Code and Materials for: <Manuscript Title>
**Repository DOI (Zenodo):** <to be added by PPMI Statistics Core upon deposit>
**Corresponding author:** <Name, email, affiliation>
**PPMI RRID:** <RRID: to be filled>
**PPMI data download date used in analysis:** <YYYY-MM-DD>
**PPMI code creation date:** 2025-08-3... |
f7e56569054bd2af894e08695970b28f44feb200b7cb640976cac8ac3d4b4a74 | Text | 2,162 | 67 | # MNI Template Rescaling
A MATLAB function for creating subject-specific rescaled MNI templates based on individual head measurements.
This tool helps improve the anatomical accuracy of neuroimaging analyses by accounting for individual head shape variations.
## Author
Hyunwoo Jang, Center for Consciousness Science,... |
71a66743065c3afa2e971acb3bb42ce757ff21daafe753e3d8fbf3cbeef6c662 | Text | 2,196 | 62 | #!/bin/csh
#
# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.7
# This folder contains GROMACS formatted force fields, a pre-optimized PDB structure, and GROMACS inputs.
# All input files were optimized for GROMACS 2019.2 or above, so lower version of GROMACS can cause some errors.
# We adopted the Verlet cut... |
4f1728521ab79de1c33e1cf8605b31037effed5de2a2fbbccba58d7b0a005ae7 | Text | 2,197 | 26 | AutoDock Vina: Docking and virtual screening program
----------------------------------------------------
[](https://opensource.org/licenses/Apache-2.0)
[](https://pypi.pyt... |
508193bc08180f5612de257c2fb478808e96a8022404eed1ebed3e13820c84e0 | Text | 2,198 | 46 | # XGBoost-ARAT Research Repository
### Overview
This repository contains code to reproduce the analyses from <https://doi.org/10.1186/s12984-025-01743-4>. We developed an XGBoost model to predict 6-month ARAT scores after stroke using longitudinal clinical measurements.
### Citation
If you use this code, please cit... |
64f6671799568f47565f72663e5d223e67a71f938243ff4057273fdb32fe273a | Text | 2,204 | 28 | README for Data and Code of [Coordinated hippocampal-entorhinal representations support human context-dependent spatial navigation]
This repository contains the data and analysis code used to generate the figures for the manuscript:
"Coordinated hippocampal-entorhinal representations support human context-dependent s... |
c0dbcbd7217dbd4d09f4e89d259f2ed2b9582e3205714e53af3d2481341d74f9 | Text | 2,212 | 34 | # Behavioural data: Distributed range adaptation in human parietal encoding of numbers
Arthur Prat-Carrabin, Gilles de Hollander, Saurabh Bedi, Samuel J. Gershman, Christian C. Ruff
Paper (preprint): https://doi.org/10.1101/2025.09.25.675916 · Code: https://github.com/ruffgroup/neural_priors · fMRI data: OpenNeuro (s... |
a913540d3dba6a1de6c4a12db5863168781ffd26dcb4bea9c275423a138a8dbe | Text | 2,214 | 17 | This repository is under active development. Scripts may contain unused code that has not been deleted yet.
# Interacting MT Simulation Files
This is an event-driven simulation where the main objects are the event list, MTs, and bundles. Conceptual details of this simulation can be found in my Master's thesis (DOI:10... |
64c6f72fabfb94f4bbe2a8b64aae03ed609796266a46c8c2155151d3c2da1388 | Text | 2,232 | 28 | # Corticom Unsupervised Neural VAD
Code repository for the paper "Real-time detection of spoken speech from unlabeled ECoG signals: A pilot study with an ALS participant" by Angrick et al.
## Installation
All dependencies can be found in the [requirements.txt](requirements.txt) file. This repository was tested with P... |
5ac16240426cdeeb64bedc08825692c43a30cab4343a2c4b032a0445f0bfcc7c | Text | 2,256 | 44 | # Human PVT Atlas: Histologically-Informed MRI Segmentation
This repository provides a publicly available, MRI-compatible atlas of the **paraventricular nucleus of the thalamus (PVT)** derived from histological and neuroanatomical landmarks. The mask is aligned to MNI152 (0.5 mm) space and is designed for use in in vi... |
c8b5a8e370c06af301b935c34106a50653e9551ef5a3aa1d3728419287d0b39c | Text | 2,258 | 31 | # Establishment of sea urchin (*L. variegatus*) embryonic cell lines
### The raw single cell RNA-sequencing and bulk RNA-sequencing data associated with this project are affiliated with NCBI BioProject PRJNA1109820
## Validating the identity of the cells in culture using 16S rDNA PCR and 18S rDNA targeted amplico... |
30d6917bde7f93c70a208afb8d1caf1e7404c4c4c8695d42b8f6f1361850ef89 | Text | 2,261 | 46 | # SPOT reproducibility package — Zenodo release candidate
This package accompanies the manuscript **Population connective field modeling reveals proto-retinotopic visual cortex organization in the prenatal human brain** by So-Hyeon Yoo,
Anne-Sophie Kieslinger, and Michael A. Skeide.
## Contents
- `code/pipeline/`: p... |
3a3ac759ea2af0946204b4326be68bb7304c4ddbd5022ac16e59bdfb30f690e8 | Text | 2,270 | 23 | 代码中：
先看train_student.py里面主要看 md_relation_pyr 对应的部分，opt.feature 代表使用S-RFD过程, opt.spatial 代表使用R-RFD过程， SampleAttentionModule对应 S-RFD模块，SpatialAttentionModule对应 R-RFD模块。老师网络已经预训练好了，不用再训练，直接可以load参数，这里只放了resnet56的teacher参数。我们主要通过train_student.py训练学生网络的性能。
python命令：看run.sh中的运行命令
```
FitNet
python train student.py --path t ... |
eaf5814871031f28b2fd0c4f540ead1276d96efb94b3a9786795c677cf79fb06 | Text | 2,270 | 51 | Analysis codes and main connectivity map outputs to accompany manuscript
**Cortical and subcortical mapping of the allostatic-interoceptive system in the human brain using 7 Tesla fMRI**
Jiahe Zhang1,2, Danlei Chen1, Philip Deming1, Tara Srirangarajan3, Jordan E. Theriault1,4,5, Philip A. Kragel6, Ludger Hartley1, K... |
7428fca2662f8e7a70c62a02b4ea92eba2ceffb258a5f9f065baceb4858c0967 | Text | 2,287 | 25 | # CoLoRSdb v1.1.0
The Consortium of Long Read Sequencing (CoLoRS) is an open coalition of international researchers focused on cataloging and providing frequency information, for all classes of variation found within the human genome, using long-read whole genome sequencing.
This repo contains four gzipped VCFs, two ... |
83cd2276443ed2059693b892a764e1ce9d1f42488e1e4ff2e9d8c77879ba10d8 | Text | 2,291 | 62 | # One-Click Image Reconstruction in Single-Molecule Localization Microscopy via Deep Learning
This repository accompanies the paper:
**_"One-click image reconstruction in single-molecule localization microscopy via deep learning"_**
> 📄 Please make sure to [cite the original paper](#c... |
07d2be7ec1d9bc706ea1370b4da070f1fddb87809501110fffc541abf53f8b52 | Text | 2,295 | 55 | <h1 align='center'>Flexutils Toolkit</h1>
<p align="center">
<img alt="Supported Python versions" src="https://img.shields.io/badge/Supported_Python_Versions-3.8_%7C_3.9_%7C_3.10_%7C_3.11_%7C_3.12-blue">
<img alt="GitHub Downloads (all assets, all releases)" src="https://img.shields.io/github/downloads/I2PC/F... |
ae36a91661e71d6ddfa294ed8f2c4f09ccf75d18bc3d568d9cd18e47702c9383 | Text | 2,304 | 53 | # Augmenting radiological assessment of imaging evident dementias with radiomic analysis
This work is published in _npj Dementia_ (https://doi.org/10.1038/s44400-025-00031-1).
## Overview
This repository provides a comprehensive pipeline for preprocessing, feature extraction, modeling, and evaluation of neuroradiolog... |
573dcea0bacd0e12a816de1f6af57842c75e136fd5a453997133bdc16129cc19 | Text | 2,308 | 18 | # mcPVS-Net
The mcPVS-Net can segment perivascular spaces (PVS) from 3D T1-weighted images.
# Introduction
Perivascular spaces (PVS) visible on magnetic resonance imaging (MRI) are significant markers associated with various neurological diseases. Traditionally, clinicians have assessed PVS using visual scores, which ... |
f02d24acc7523c7673e23f3bf12cb37d552beb76bf6f60d77329f0e14b1aa49a | Text | 2,315 | 61 |
# Noninvasive megapixel fluorescence microscopy through scattering layers by a virtual reflection-matrix
This repository contains the implementation of the I-CLASS algorithm for incoherent data, such as fluorescence, as described in "Noninvasive megapixel fluorescence microscopy through scattering layers by a virt... |
6a0df8f50b8ad339dec3c22d7ba9f0ca95c66c963e88fd7d59e2e5b2c4c0cc44 | Text | 2,322 | 37 | # Paper : Influence of gonadal and chromosomal sex on the brain transciptome in a mouse species with natural sex reversal
# Institute : Institut des Sciences de l'Evolution de Montpellier, Université de Montpellier, CNRS, IRD, 34095 Montpellier, France
Cite paper : Louise D Heitzmann, Paul A Saunders, Julie Perez, Pier... |
2d8535e03f74625200e19cc777de79a6877e514e11d0b88b1462d937f48c2f6e | Text | 2,325 | 68 | # IoT_Sentinel
[](https://scorecard.dev/viewer/?uri=github.com/andypitcher/IoT_Sentinel)
> Note: This project is originally from **2017** and has been modernized for Python 3 compatibility.
This program is an implementa... |
2fcbe28d34f9961f15149cb43a34bef5e783db4aab005f47d8f5d5f9ea7f1746 | Text | 2,346 | 11 | # Evaluating topological and graph-theoretical approaches to extract complex multimodal brain connectivity patterns in multiple sclerosis
## Abstract
Brain networks, or graphs, derived from magnetic resonance imaging (MRI) offer a powerful framework for representing the structural, morphological, and functional organ... |
94dca25124cd8cb849edf9ce29923e7cc2aebfeb933801ecb1e882dcc024d079 | Text | 2,346 | 72 | # DDHD2 Proteomics Analysis
This repository contains the full R-based analysis pipeline for label-free quantitative proteomics comparing **DDHD2 knockout (KO)** and various rescue conditions in mouse neurons. The code supports data preprocessing, normalization, imputation, batch correction, differential expression ana... |
6b8ca3244d694701882755be6aed2404628ad0b2e8d8f6e02b417b6c19a9d20e | Text | 2,350 | 28 | ## Code for simulations presented in the manuscript: "Unintended bias in the pursuit of collinearity solutions in fMRI analysis"
This code contains simulations to assess the ability of various models for the Monetary Incentive Delay (MID) task for fMRI data.
Use [uv](https://docs.astral.sh/uv/getting-started/install... |
c6fa43158da763287cba907b509c9d7966f643e781e9d121ac9b9b532a103bde | Text | 2,353 | 39 | # Neural codes of probability
This repository accompanies the paper entitled
*A non-monotonic code for event probability in the human brain*.
by Cedric Foucault (1,2,#,§), Tiffany Bounmy (1,#), Sébastien Demortain (1), Bertrand Thirion (3), Evelyn Eger (1), Florent Meyniel (1,4,§)
1. Cognitive Neuroimaging Unit, Neur... |
3b12d5b75147919b73539033cc64d0ab0eac04467e2b0f428b2ad6b9ed4980a5 | Text | 2,357 | 76 | ***
# Optical Labeling with Artificial Intelligence Using Infrared-Responsive Functional Textiles
## Overview
This repository contains the code and resources for the project described in the paper:
**Optical Labeling with Artificial Intelligence Using Infrared-Responsive Functional Textiles**
Functional textiles in... |
29b9d270d4f6a05ad4b07d6ce1eeb19fe7f3b906253536fa7f65c914c9593293 | Text | 2,361 | 21 | # Competition and Cooperation of Assembly Sequences in Recurrent Neural Networks
**Tristan M. Stöber**<sup>1,2,3,✉️</sup>
**Andrew B. Lehr**<sup>2,4</sup>
**Marianne Fyhn**<sup>2,5</sup>
**Arvind Kumar**<sup>6</sup>
<sup>1</sup>Institute for Neural Computation, Ruhr University Bochum, Germany
<sup>2</sup>Cent... |
9dbe430f1cb25a335cf8ac4131f98683fda0e2138c75d54fc4e4c84399f32f13 | Text | 2,367 | 56 | # DeepT1-WMH
White Matter Hypointensities lesions for **T1-weighted** MRI images.
It relies on a Convolutional Neural Network pre-trained on FLAIR segmentations using the large JPSC-AD cohort.
For background... |
0c0e67af6f25753d645e20ff620c8aff7ea206d3c3ae168b01103000ff0678cf | Text | 2,381 | 44 |
# paO<sub>2</sub> Prediction in Neurosurgical Patients
The repository contains the code (quarto notebooks) for paO<sub>2</sub> prediction in neurosurgical patients. Four notebooks are needed. The first one is used for preprocessing like data cleaning, missing values, scaling the data and feature selection. The second... |
dd3e2c7fbd3e797cc209114fccb82605071a340c5510314708cf35c86b76fcac | Text | 2,392 | 33 | ## Physiological Signal Reconstruction using Deep Learning
### Description
Many studies of the human brain using functional magnetic resonance imaging (fMRI) lack physiological measurements, which substantially impacts the interpretation and richness of fMRI studies. Natural fluctuations in autonomic physiology, such... |
559ae0d32044175b1d87839af3443e9bc456fdd705188196064ac7e3ae7132b5 | Text | 2,395 | 39 | ## General Overview
This dataset contains the five data collections used for the analyses in our study, "Real-time self-supervised denoising for high-speed fluorescence neural imaging". It includes newly generated/collected data as well as publicly available datasets that have been reused. The source of each dataset i... |
4952b165c67f5de1de12b102211d5753899f766825ae24233bbe239e2f57cc5d | Text | 2,411 | 47 | # DBS Therapeutic Window Prediction
[](https://www.python.org/downloads/)
[](LICENSE)
[]()
> Machine learning framework for predict... |
fcc1e9c61f908c75733566969f63c48d62f4bbcf950445370563555ecd800e6e | Text | 2,417 | 43 | # Humans Have a Longer Period of Cortical Maturation Across Depth and Hierarchy Than Macaques
## About
This repository contains the code and data supporting the study *"Humans Have a Longer Period of Cortical Maturation Across Depth and Hierarchy Than Macaques,"* published in *PLOS Biology*.
## Code
**To reproduce F... |
d18a3dd8096b3c543ba717b52ab892ed9003963a0d1c4e7a388d2c16350a5221 | Text | 2,422 | 64 |
# Noninvasive megapixel fluorescence microscopy through scattering layers by a virtual reflection-matrix
This repository contains the implementation of the I-CLASS algorithm for incoherent data, such as fluorescence, as described in "Noninvasive megapixel fluorescence microscopy through scattering layers by a virt... |
b9989baa60d7b432b3ff62c1cd1dfbfff7331fb05e4ca5da5769b7b84a81b55e | Text | 2,427 | 88 | # STR_DA_ACh: Dopamine and Acetylcholine Modulation in the Striatum
This repository contains the full implementation, configuration, and analysis code for the simulations presented in our study on dopaminergic and cholinergic modulation in striatal circuits. The code is bundled in a self-contained Docker environment t... |
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