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b9e99e48122ffbd179606c588fd382f4f6ee07103e7d500f6c160b739bc94047 | Text | 2,709 | 31 | # Nipoppy
[](https://doi.org/10.5281/zenodo.8084759)
[](https://pypi.org/project/nipoppy/)
[](https://opensource.org/license/mit)
[. Brought to you by [Bachlab](http://bachlab.org) at ... |
a7d8e76810e26ce150ad78ca5b75f01b56ebc8fb6dde9a4fb8473f9528e6e07b | Text | 2,715 | 82 | # GANsForVirtualEye: Time Series Generation Package
[](https://gansforvirtualeye.readthedocs.io/en/latest/)
[](https://github.com/shailendrabhandari/GANs... |
312b614f9a577c2f864f6d78ecb40eba09a7df575ef94706acdd898d2b2622af | Text | 2,741 | 41 | Code for a scientific paper: "AI-powered remote monitoring of brain responses to clear and incomprehensible speech via speckle pattern analysis"
doi: 10.1117/1.JBO.30.6.067001
https://pmc.ncbi.nlm.nih.gov/articles/PMC12148044/
In order to recreate per subjects results:
1. Clone the repository
3. Run: !python -u Speckl... |
25e2fe684f6bc49b181f873b19034a480b25c188115b1c32e0ac42f321d1fb6c | Text | 2,767 | 59 | # SFGPI Neural Analysis
## Overview
This repository contains code to run neural analyses for:
Hall-McMaster, Tomov, Gershman* & Schuck* (2025). Neural evidence that humans reuse strategies to solve new tasks. *PLOS Biology*.
## Dataset structure
- All code to reproduce the neural figures is in `code/`. The code fol... |
ccbacb8e43e51434209f0e878beae70eeef589e149400536f6a1429bf4b6fa1a | Text | 2,774 | 77 | # Using GNN property predictors as molecule generators (DIDgen)
This is the repository for the paper: [*Using GNN property predictors as molecule generators*](https://doi.org/10.1038/s41467-025-59439-1).
You can use DIDgen (**D**irect **I**nverse **D**esign **gen**erator) to generate diverse molecules with a specific... |
e148bea70e9a29f87d1754dd73e03c30c19bea122726514747a7017a02eb3915 | Text | 2,775 | 73 | ## Explosive Neural Networks via Higher‑Order Interactions in Curved Statistical Manifolds
This repository accompanies the paper by Aguilera et al. (2025), presenting a novel class of associative memory networks with **explosive memory-retrieval transitions**, enabled by **higher-order interactions** and **curved stat... |
16eeef5b2552ab51c4761f7344fb073fc2157016b6b1c3c86e85b180dda1b6a6 | Text | 2,792 | 49 | # Liver CT Segmentation
This project trains an nnUNet model to segment liver from CT scans. The model was trained on a dataset of 1565 CT scans from [TotalSegmentator](https://github.com/wasserth/TotalSegmentator/) (N=1204) and [FLARE21](https://flare.grand-challenge.org/) (N=361) datasets. The model is used to genera... |
8a63d47d3c28e51e6475c8961f454894037b6a7fb155fcde2d714db03a36ab4b | Text | 2,797 | 81 | # Temporal Single-Cell Transcriptomic Analysis of Sex-Dependent Changes in THY-Tau22 Mice
# Table of contents
* [Introduction](#introduction)
* [Content](#content)
* [Data](#data)
* [Requirements](#requirements)
* [License](#license)
* [Instructions](#instructions)
# Introduction
This repository contains the code for... |
6ab02dcef7ebdb1a7afc999833319c2b6e1bc1f0221ce5dd940e32c181e87ca1 | Text | 2,802 | 40 | ### What is this repository for? ###
stratifiedIBDGI is a Neural Network based Genome Interpretation (GI) framework for the exome-based in-silico stratification/discrimination of healthy controls, Crohn's disease (CD) and Ulcerative Colitis (UC) patients, the two main Inflammatory Bowel Disease (IBD) subtypes.
More det... |
4ef7b0028e9a9f9c5b540eb9375b10693d6fb3d6e5d29aa94006baa01e1eceaa | Text | 2,807 | 82 | # MacAulayLab: Age study of the choroid plexus
The work and scripts are done by the MacAulay Lab.\
All programs used are free and open-source.
In the interest of open science and reproducibility, all data and source code used in our research is provided here.\
Feel free to copy and use code, but please cite:\
(coming s... |
d71aa164c3f937c6cfd229edf8df96d690ddee5c1fc2a3fb01d166d99bfd63f9 | Text | 2,829 | 25 | This repository contains the scripts to reproduce the main and supplementary results of the paper:
## Contents
• run01_Behaviour: Reproduces the behavioral results shown in Fig. 1.
• run02_TimeFreqAmygdalaStat: Reproduces the time-frequency results and statistics for patients with electrodes implanted in the amygdala... |
7f96cca2f5e060ef950481523a5ba994c46a72d40694bfc3a064b64ea24a8d0d | Text | 2,852 | 72 | # ICA Segmentation Tool
This tool is designed for segmenting the Internal Carotid Artery (ICA) from Time-of-Flight (TOF) Magnetic Resonance (MR) images and calculating its diameter. It utilizes a 2D region growing algorithm with dynamic intensity thresholding to accurately determine the vessel area.
## Features
- Se... |
f0dcb806d7165f17dd7b183ccd70fb462cdb58875f821b1604cff5225e27aa87 | Text | 2,876 | 75 | # 3D-microglia-netoglitazone
This repository implements an end-to-end 3D light-sheet microscopy analysis pipeline for mouse brain hemispheres, including stack preprocessing, automated microglia candidate detection/segmentation, surface-artifact removal, voxelization/smoothing, and registration into Allen Brain Atlas re... |
057244414522e84cc7bac6cce2f8e6826abbb23bf64be56441f9758e041fee84 | Text | 2,892 | 58 | # SK Channel Trafficking
# In-silico modeling of atrial SK channel trafficking.
<p><strong><span style="color:red;">NOTE: THIS REPOSITORY IS ONLY FOR ARCHIVAL PURPOSES AND IS NOT MAINTAINED. FOR AN UPDATED VERSION PLEASE LOOK AT THE HEIJMANLAB GITHUB PAGE.</span></strong></p>
**Link to HeijmanLab:** [https://github.... |
93d009ec5fdd76f444ebf936dee0576b44598d92f4801098cd595219f1ad19ef | Text | 2,898 | 34 | <!-- badges: start -->
[](https://github.com/mjin1812/SMARTTR/actions/workflows/R-CMD-check.yaml)
<!-- badges: end -->
# SMARTTR: **s**imple **m**ulti-ensemble **a**tlas **r**egistration and statistical **t**esting in ... |
43afbd2c926a53fb42ad1c49cb38a3a8499d6afa584627afcee188f6f8fde991 | Text | 2,952 | 29 | Note - the included license file (Attribution-NonCommercial-ShareAlike 4.0 International) specifically pertains to NetTracer3D_V2. This code is open source and freely available to use/fork for specifically non-commercial purposes, assuming citation is provided. For now, this paper should be cited: https://doi.org/10.11... |
3e701d158768aa68098da1ad086a5b69c2431be51494dc89f1ddd5f73dac9f41 | Text | 2,958 | 25 | # Code supplement to the CNV convergence
[](https://lbesson.mit-license.org/)
[]([https://doi.org/10.1101/862615](https://doi.org/10.1101/2022.04.23.489093))
This repository contains... |
33149968d599449e4c62fc2c3016e47ef25652da420ab227d72cbdd8d67c336d | Text | 2,965 | 95 | [](https://pepy.tech/project/tscv)
[](https://travis-ci.com/WenjieZ/TSCV)
[](https://codecov.io/gh/WenjieZ/TSC... |
588939ce5a3a312090a31b465d0726f8da309f47450b6891a7b3d17af132a71a | Text | 2,974 | 36 | # **Data Use Agreement for Little et al., HBM 2025, Derived Human Connectome Project (HCP) Data**
## **Introduction**
This dataset is derived from the Human Connectome Project (HCP) data. Users of this dataset agree to abide by the original HCP Data Use Terms. By accessing or using this dataset, you confirm your comp... |
e092c0c8f5e8afd55a2ad916c547e4eaba891e95ae316872004c321f37fd1790 | Text | 2,978 | 48 | # The Open Course in Data Science for Neuroscience
These materials are an introduction to the ways in which data is used in order to ask and answer questions about the brain. It cuts across many fields of neuroscience, including cellular, systems, and cognitive neuroscience, and is an introduction to those who are inte... |
bf0f0c881b19f9b2b58ca18d51b35a00d9eb178346ef534d5c8437c84a2c9847 | Text | 2,979 | 32 | [](https://zenodo.org/badge/latestdoi/429406115)
# Neuropixels trajectory explorer
Neuropixels trajectory explorer with the Allen CCF mouse atlas
There is also a Waxholm rat atlas version available, though this is not actively maintained.
The program... |
fd775c23ba171df8fcd404add8480ef4cbece19b87b44add41a6dc1caa713590 | Text | 2,980 | 67 | ## Data
The raw data in FASTA format are located in the following folders:
```
data/fasta
├── benchmark
│ ├── test
│ │ └── test.fasta # test sequences for benchmark
│ └── training
│ ├── negative.fasta # non-PA sequences for benchmark
│ └── positive.fasta # PA-sequences for benchmark
└── lob... |
c96700863be703d9021d7fc12f99eb72b5056186acfc4a50df8e8c40ddf0041e | Text | 2,983 | 33 | # Nipoppy
[](https://discord.gg/2VMKFRpjkm)
[](https://doi.org/10.5281/zenodo.8084759)
[](https://pypi.org/pro... |
55569d81a750e9ca077826204526ccc50c629c68f8a749fdd324f684c474218f | Text | 2,985 | 60 | 
# SleepTrip
* a MATLAB toolbox
* a branch of FieldTrip (https://github.com/fieldtrip/fieldtrip see http://www.fieldtriptoolbox.org for details)
* adds 'FieldTrip-style' functionality to analyse sleep EEG and MEG data such ... |
146f1df863c279c040c4849201e790c524bf0cbbe71d84986b0760fe66f7e45f | Text | 3,001 | 36 | # TBI-Analysis
This repository contains a 3D Slicer-based [https://github.com/Slicer/Slicer] image processing pipeline designed specifically for the analysis of traumatic brain injury in murine models. For more detailed information, please refer to the accompanying publication.
*Placeholder for the citation.*
## Dep... |
985b6dc09144ea14378dd2c543b288e8d2a05cb342a77cbc56b7a39c5170f638 | Text | 3,010 | 56 | 
_Figure: Comparison of OpenFold and AlphaFold2 predictions to the experimental structure of PDB 7KDX, chain B._
# OpenFold
A faithful but trainable PyTorch reproduction of DeepMind's
[AlphaFold 2](https://github.com/deepmind/alphafold).
# Documentation
See our new home for docs at [op... |
ec8046649a15f6cd519342c68f51697cde1e36c8ef341c0fc522b3aa590dcf8c | Text | 3,016 | 42 | # Collection of some convex MINLP test problems
This repository contains a script for generating convex MINLP problems and a collection of MINLP test instances available in both .nl and .gms format.
Please cite this work as
```
@article{JKMINLP2020,
author = {Jan Kronqvist and Ruth Misener},
title = {A disjunct... |
a1e5758043c57e732a0abe8ce4bf1092b413606569246ee2849a20af5f8d4d26 | Text | 3,017 | 43 | # Joint-Transformer-in-AD-MRI-Classification
[](https://opensource.org/licenses/MIT)
Joint Transformer Architecture in Brain 3D MRI Classification: Its Application in Alzheimer’s Disease Classification
## Installation
Clone the repository:
git clone ... |
559a80bca95695126bac1c3768d6ad215665b18dc19b177f8ee461ac32c1eda6 | Text | 3,024 | 26 | # Habenula contributions to negative self-cognitions
The repository contains [de-identified effective connectivity data](/data/) and the codes used to support the main findings in the [Kung et al. manuscript](https://rdcu.be/ek1hW) (DOI : 10.1038/s41467-025-59611-7).
The present study leverages ultra-high field (UFH)... |
9346f9c46d59ce04709c830b7d132972f40a082cb76a1405c4ad3f75652fd5cd | Text | 3,040 | 72 | # REGNN
REGNN (Relation Equivariant Graph Neural Networks) is a graph deep learning framework for spatially resolved transcriptomics data analyses on heterogeneous tissue structures.
### Software Requirements
#### OS Requirements
``` REGNN ``` was tested on on Windows 11 12th Gen Intel(R)... |
9c676bdea0fa511e562190ab702c609af0e868e8966abf091817c5dd3c226806 | Text | 3,046 | 32 | # CMI-based Feature Attribution Validation for Neural Time Series Classifiers
This is the supporting code for the paper "A Comprehensive Analysis of Perturbation Methods in Explainable AI Feature Attribution Validation for Neural Time Series Classifiers" by Simic et al.
This code was used to train the models and evalu... |
58054b39f7e4304a131398191164e0ef173cb7d17683eaba9cfa0c5a7fd8e641 | Text | 3,065 | 64 | <h1 align="center">
Learning Aerodynamics for the Control of Flying Humanoid Robots
</h1>
<div align="center">
_A. Paolino, G. Nava, F. Di Natale, F. Bergonti, P. Reddy Vanteddu, D. Grassi, L. Riccobene, A. Zanotti, R. Tognaccini, G. Iaccarino, D. Pucci_
</div>
<p align="center">
https://github.com/user-attachmen... |
f306939e51f6527a0e45e854e7de79ebaf965c45ccc430ef67fa1cb046f472b9 | Text | 3,077 | 83 | # SFGPI MRIQC
## Overview
This repository contains MRI quality control reports for:
Hall-McMaster, Tomov, Gershman* & Schuck* (2025).
Neural evidence that humans reuse strategies to solve new tasks.
*PLOS Biology*.
## Usage
```bash
$ datalad clone git@gin.g-node.org:/sam.hall-mcmaster/sfgpi-mriqc.git
[INFO ] Scan... |
3971b7e626652a1fff115e6474cc1888a1365695b7b109ee4b5cffb58e104755 | Text | 3,090 | 63 | # TPCCLIB project #
Tpcclib project is to develop and maintain
[command-line](https://www.turkupetcentre.net/petanalysis/analysis_shell.html) tools
to [processing and analysing](https://www.turkupetcentre.net/petanalysis/analysis_process.html)
data collected in [Turku PET Centre](https://www.turkupetcentre.fi) ... |
f8c0b1f00e9790210a237b0d2eb82ddd3612b105954e0dc4f157514945fa3717 | Text | 3,090 | 24 | # TinMEG
## Analysing and preprocessing of MEG + MRI data
Inhibitory mechanisms in sensory gating has been traditionally measured in humans by means of startling blinking responses, being partially suppressed by preceding and weaker lead stimuli. Paradigms such as pre-pulse inhibition (PPI) have been used for near hal... |
6ad65249df4a43a10ce244dbc747929726ce04cd4254d2142b600a459a0eec0e | Text | 3,093 | 87 | # SFGPI masks
## Overview
This repository contains anatomical masks for:
Hall-McMaster, Tomov, Gershman* & Schuck* (2025). Neural evidence that humans reuse strategies to solve new tasks. *PLOS Biology*.
## Usage
```bash
$ datalad clone git@gin.g-node.org:/sam.hall-mcmaster/sfgpi-masks.git
[INFO ] Scanning for un... |
2553be7d179e660f3bfe418c51943a6d280d2899440297c4f99db6a7e1c1c311 | Text | 3,106 | 26 | # SOC_Multiomic_sequencing
# Abstract
Fear, while crucial for survival, is a component of a myriad of psychiatric illnesses in its extreme. Persistent fear memories can form through processes such as second-order conditioning (SOC), during which a second-order conditioned stimulus (CS2) acquires significance by assoc... |
dcd916eb05f2035344fd01e43d31557ab05b17134bffb168c7bde8ac7cc7c0a3 | Text | 3,117 | 33 | # Benchmarking methods for mapping functional connectivity in the brain
This repository contains code and data in support of "Benchmarking methods for mapping functional connectivity in the brain", now up on [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.05.07.593018v1).
Due to the size limit, the raw data fil... |
9ab38493fd76aeb47c950041c58dec3f3360d136399c898561278aff4724e6b0 | Text | 3,124 | 55 | <p align="center">
<img src="https://raw.githubusercontent.com/Project-MONAI/MONAI/dev/docs/images/MONAI-logo-color.png" width="50%" alt='project-monai'>
</p>
# MONAI Generative Models
Prototyping repository for generative models to be integrated into MONAI core, MONAI tutorials, and MONAI model zoo.
## Features
* N... |
95ccf177182bf0454cf9bfc517c736d469f8b9b2564d0314afaf140ccca11077 | Text | 3,130 | 63 | # CLIMATE BRAIN
This repository contains supplementary materials associated with the development of the **CLIMATE BRAIN** dataset. The dataset itself is publicly available on [OpenNeuro](https://openneuro.org), under the accession number [ds005460](https://openneuro.org/datasets/ds005460).
## How to acknowledge
Plea... |
14525f913b62f1f1adaa2ea58ecb837122bce7ffd8e7c30d8b873bc6a6c93672 | Text | 3,131 | 57 | # MultichannelLFPAnalysis
#Contains MATLAB and Python code for working with multichannel LFP data
-----------------------------------------------------------------------
#1 - Stimuli are generated and sent, and behavioural videos recorded by scripts in the StimulusDeliveryAndRecording folder
#2 - Behavioural videos ... |
39220e5bead3920bcb094c77c02cff6bbdf1ffd32d0101f12a9abfe358e4622b | Text | 3,157 | 30 | # OIRDropseq
This repo is associated with the publication below =
Metabolic reprogramming of the neovascular niche promotes regenerative angiogenesis in proliferative retinopathy
Gael Cagnone1,2, Sheetal Pundir2,3, Charlotte Betus1,2, Tapan Agnihotri2,3, Anli Ren2,4, Jin Sung-Kim2,3, Noémie-Rose Harvey5, Emilie Hec... |
cca2fbaf421bd474caa5a00859a25a32c02b94ff3a9ae38c8c0b9e312dedbfea | Text | 3,180 | 64 | # **OHSU-NHT-Bahena_TAL_2024**
Thick ascending limb (TAL) cells play a critical role in monovalent and divalent cation transport. Through clustering, differential expression analysis, and visualization.This project aims to:<br>
- <img src="https://cdn.iconscout.com/icon/free/png-512/free-kidney-icon-download-in-svg-png... |
70bba9ead5a744e896e34fd8a97c4af706eb928eaae7a36e3f3a03154454acab | Text | 3,184 | 63 | # Improving acne image grading with Label Distribution Smoothing
This is a PyTorch implementation of our method that improves acne severity grading from facial images by extending the [previously existing approach](https://github.com/xpwu95/LDL) based on label distribution learning.
We made two improvements: (1) gener... |
d5281ea7bf0ef128d7d49b030890a5ae9331e5c09f215b5f9e5858e4bffc75d6 | Text | 3,190 | 64 | # Santa: Unpaired Image-to-Image Translation With Shortest Path Regularization ([CVPR2023](https://openaccess.thecvf.com/content/CVPR2023/papers/Xie_Unpaired_Image-to-Image_Translation_With_Shortest_Path_Regularization_CVPR_2023_paper.pdf))
### Abstract
Unpaired image-to-image translation aims to learn
proper mappings... |
f22c51149c335c5fed3880e83a2bc430f7b740ee9f0ca5d26c84de98fb9fcca8 | Text | 3,206 | 41 | # Miniscope-LFOV
**[[Miniscope V4 Wiki](https://github.com/Aharoni-Lab/Miniscope-v4/wiki)] [[Miniscope DAQ Software Wiki](https://github.com/Aharoni-Lab/Miniscope-DAQ-QT-Software/wiki)] [[Miniscope DAQ Firmware Wiki](https://github.com/Aharoni-Lab/Miniscope-DAQ-Cypress-firmware/wiki)] [[Miniscope Wire-Free DAQ Wiki](h... |
163c4e54e89bec861c6e0afb2e6e59b08930e03d9d430351d176c01a2ff9e250 | Text | 3,215 | 49 | # Graph neural network to integrate multiomics for Alzheimer's disease study
## directory structure of simplified package for verification:
<!-- -- biodomain \
-->
<pre>
- code-GNN-multi-omics
|- src (code)
|- ROSMAP_data (data in csv format)
... |
00bdca04853e64cef85566d94ae23e2e0d4ea063b2ac071f487d3fcbe2d1c0b9 | Text | 3,235 | 53 | This is the Move4AS dataset. It contains 3D motion capture data and EEG data from two imitation motor tasks (walking and dancing).
Full details presented in the paper "A Multimodal Dataset Addressing Motor Function in Autism" at Springer Nature Scientific Data.
- Folder Organization:
The root folder contains all t... |
6d479a9809e3506bc36fe687f8c37af9d6a43a64b352d391b5af86485dfbbfac | Text | 3,236 | 73 | # Multidimensional RF pulse design using auto-differentiable spin-domain optimization and its application to reduced field-of-view imaging
This repository provides code to simulate RF pulse using the spin-domain representation, and optimize multidimensional RF pulses for MRI.
The simulation function is built using a... |
ec88e24c6d90bf316b9ddc3f9c3d7d62dee09436c2f9afed3c881b70747540b6 | Text | 3,249 | 44 | This replication package supports the results presented int the paper "An Empirical Study of Fault Localisation Techniques
for Deep Neural Networks".
The artefact structure:
Folder 'figures': Contains plots for FL part used in the paper
Folder 'Tool Outputs': Contains raw FL tool output
Folder ‘ALT_GT’: Contains ra... |
8ad6fdd6d0b6ced96aba6d30daba88fd364eb606f832036431f3e1b7959fdd17 | Text | 3,252 | 69 | <h1 align="center">CeyeHao: AI-driven microfluidic flow programming using hierarchically assembled obstacles in microchannel and receptive-field-augmented neural network</h1>
<h4 align="center"><a href="https://doi.org/10.5281/zenodo.13363708"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13363708.svg" alt="DOI... |
af31953e76947503ab4a39810ab03a5e29b2e84cc798b3ab181a76a866c7457d | Text | 3,253 | 45 | Summary Statistics for eQTL analyses reported in O'Brien et al. Expression quantitative trait loci in the developing human brain and their enrichment in neuropsychiatric disorders
Gene Level Analyses:
- expression_gene.bed.gz
- normalised, variance-stabaling transformed count data (29875 genes)
... |
44f2c17fe5182f5c70f64be56ed1f04ba4d1fe6fee07e3f6cf2678fd5192002c | Text | 3,255 | 109 | # BLISAcounts
A Snakemake pipeline for enumerating counts from the BLISA sequencing data.
## Description
With `umi_tools`, do:
- obtaining barcode whitelist
- barcode correction and extraction
With `extract_staggered_seq.py`, do:
- barcode extraction of multiplexed sequences with staggered primers
Subsequently, do... |
859e2e052862695ba72bea8aab085dc8ab2c946c8b16140c98816ae5fe1ec475 | Text | 3,290 | 65 | # interneuron
Codes for the manuscript: Edwards, M. M., Rubin, J. E., & Huang, C. (2024). State modulation in spatial networks with three interneuron subtypes. bioRxiv.
1. System Requirements:
Combination of C through MATLAB and MATLAB R2021b (9.11) and 2023b, MathWorks.
Simulations run and processed on combi... |
0667c6822540c040ba70544e586c01f6495f66cdf9ad6264279d068691ac19e4 | Text | 3,299 | 64 | ## A Deep Learning System for Population-level Silent Brain Infarction Detection and Stroke Risk Prediction from Retinal Photographs
Official repo for [A Deep Learning System for Population-level Silent Brain Infarction Detection and Stroke Risk Prediction from Retinal Photographs]
Please contact **njiang2021@sjtu.e... |
28c542bca6fb345243040ffd08c8eaf9f799d1db321e5cb0108da29d39c5ae53 | Text | 3,305 | 96 | # GRANA
<img src="https://img.shields.io/badge/Python-3.9-blue"/>
<a href="www.chloroplast.pl/GRANA"><img src="https://img.shields.io/badge/GRANA-Website-green" /></a>
<a href="https://huggingface.co/spaces/chloroplast/GRANA"><img src="https://img.shields.io/badge/GRANA-Demo-green" /></a>
<img src="https://img.shields.... |
581a0936841bb20525baf01fb5da0935ae7c9012d0f8495c5946ff7172a90de6 | Text | 3,312 | 48 | # Kidney CT Segmentation
The kidney tumor segmentation model is trained on contrast CT (corticomedullary and nephrogenic phases) to accurately delineate the kidney, tumor, and cysts. The [KiTS 2023](https://kits-challenge.org/kits23/) dataset is employed to train a kidney tumor segmentation model (N=489) using an ense... |
fef7449bdf49a7a0ea2a4146fdd34d65a31882ff2f6cb7249a4aa5f3ebb9ab9b | Text | 3,325 | 78 | # SFGPI Behavioural Analysis
## Overview
This repository contains code to run behavioural analyses for:
Hall-McMaster, Tomov, Gershman* & Schuck* (2025). Neural evidence that humans reuse strategies to solve new tasks. *PLOS Biology*.
## Dataset structure
- Scripts to run the analyses are located in `code/`. 'Gener... |
0b37919a3c98784513fddad35bcfd3dbbbcc1c77c072d71c2bde1721b99b1775 | Text | 3,372 | 60 | # Genome-wide identification and analysis of recurring patterns of epigenetic variation across individuals
The "stacked" ChromHMM model learns recurring patterns of epigenetic variation across individuals and histone marks throughout the genome. This model was trained on LCL histone mark data published <a href="http:/... |
9b0c258edfd05db5dd117163dedeb2916967fd0dc13dbe279837ee6b7302ac12 | Text | 3,378 | 39 | # DL4EOS
Using deep learning tools based on neural networks for predicting EOS surfaces under different data conditions.
Compared with classical deduction based modeling pipeline, data driven models allows more flexibility and more tolerance on the usage of physical priors, as well as their forms.
<img src="htt... |
881ba9452417fc5311768e8544ef84473877c6d28a3dd66140e0f1f0bd995277 | Text | 3,394 | 85 | # SFGPI fMRIPrep
## Overview
This repository contains preprocessed MRI data for:
Hall-McMaster, Tomov, Gershman* & Schuck* (2025). Neural evidence that humans reuse strategies to solve new tasks. *PLOS Biology*.
Preprocessing was performed using fMRIPrep, version 23.0.2.
## Usage
```bash
$ datalad clone git@gin.g... |
75ddd8b3fc5559057ffd9224ee7c81683a96051a342a7f204b8ca136782325af | Text | 3,407 | 122 | flim-ccimbrica
##############
Machine learning analysis on FLIM measurements of Coccomyxa cimbrica exposed to Cu(II).
See associated paper with DOI `10.1021/acsomega.5c04304 <https://doi.org/10.1021/acsomega.5c04304>`_.
Data set
********
The full data set used is in file ``src/flimdf.json``. A sample is
shown in ``s... |
b69441751ddc7efa1ac90576bfed1fcb3b4f97eba2a3e0d9b8887e9b75d1798c | Text | 3,415 | 88 | # Glo-In-One-v2: Holistic Identification of Glomerular Cells, Tissues, and Lesions in Human and Mouse Histopathology
The official implementation of Glo-In-One-v2
<img src='docs/Glo_v2_class.png' align="center" height="450px">
<img src='docs/Toolkit.png' align="center" height="300px">
## Abstract
Segmenting glomeru... |
0e8674b29be8fbcab71373b82d0f42fb67ce49e25fc9d4d723ee52e3140b6b14 | Text | 3,423 | 74 | # Brain Connectivity Toolbox for Python version 0.6.1
Author: Roan LaPlante <rlaplant@nmr.mgh.harvard.edu>
Tested against python 3.7+.
## Copyright information
This program strictly observes the tenets of fundamentalist Theravada Mahasi
style Buddhism. Any use of this program in violation of these aforementioned
t... |
f5209441e11ac2d34b83531724b0d69a30247d79179911e1a52923e1504e688e | Text | 3,433 | 105 | # Fiber Orientation Prediction Project
## Overview
Advanced machine learning project for predicting and analyzing fiber orientations using state-of-the-art image processing and neural network techniques.
## Project Structure
```
fiber-orientation/
│
├── src/
│ └── fiber_predictor/
│ ├── apps/ # Appl... |
2effaaca11075f7381066ff8d8af3eefac1d3e75ceb28667f69eb94941757514 | Text | 3,444 | 77 | # Genome alignment and allele-specific expression (ASE) analysis of scRNA-seq data
[-e30613?logo=doi)](https://doi.org/10.1038/s42003-025-08128-2)
[
[[Journal Publication]](https://www.nature.com/articles/s42003-025-08500-2)
## Abstract
We introduce HLAIIPred, a deep learning model t... |
7c9cb7acb9400fdb4ba6e393e7d70dc67724117a2f93d8904c8bb3abec135ed9 | Text | 3,448 | 43 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% MATLAB code for reproducing key quantitative comparisons presented in manuscript:
% "The amyloid precursor family of proteins in excitatory neurons are essential
% for... |
66675c7ba0bee1580ddd6336bb7ee21b940cc3af442d17b9d056d3b15b293825 | Text | 3,458 | 55 | <img src="http://boutiques.github.io/images/logo.png" width="150" alt="Boutiques logo"/>
# Boutiques
[](https://app.codacy.com/gh/boutiques/boutiques?utm_source=github.com&utm_medium=referral&utm_content=boutiques/boutiques&ut... |
7596a884fbd0f5103736dea9d166752710280a7119f5e402badd0582a69958bd | Text | 3,468 | 69 | # HOPMA [](https://doi.org/10.5281/zenodo.15616795)
**A tool to boost protein functional dynamics with colored contact maps**
<img src="https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/jpcbfk/2021/jpcbfk.2021.125.issue-10/acs.jpcb.0c11633/20210312... |
8f8a55b9b66fe1e147741bbeaf6a23c1b85396d2a47da9339f2f6c86750b5d74 | Text | 3,482 | 59 | # QM-GNNIS
## Publication
```bibtex
@article{Katzberger2025,
title = {Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules},
volume = {21},
ISSN = {1549-9626},
url = {http://dx.doi.org/10.1021/acs.jctc.5c00728},
DOI = {10.1021/acs.jctc.5c00728... |
a08cdf60db408fe739a236a6bcbf34e81a58a17dbcbcb4bf4b2846de14092578 | Text | 3,533 | 47 | # Brain age modelling, prediction, and its application on COVID-19 data
This repository contains scripts for Brain Age prediction to explore the effects of COVID-19 and the pandemic on brain ageing, as described in this paper: [A. R. Mohammadi-Nejad, M. Craig, E. Cox, X. Chen, R. G. Jenkins, S. Francis, S. N. Sotiropo... |
cab7b4cfac997706368748b2d274a88743b14f610a2eee7ab96ab362e9c41a58 | Text | 3,533 | 58 | <img src="imgs/dmsfold_logo.png" width="200" height="200"/>
# DMS-Fold
[](https://huggingface.co/LindertLab/DMS-Fold/tree/main) [](https://huggingface.co/datasets/Lindert... |
b249f6aa5c21ff5ce71932429d5bb45081e7399377bd142527ef4194274bc8b1 | Text | 3,540 | 34 | # An open-access EEG dataset for speech decoding: Exploring the role of articulation and coarticulation
João Pedro Carvalho Moreira<sup> 1,#</sup>, Vinícius Rezende Carvalho<sup> 1</sup>, Eduardo Mazoni Andrade Marçal Mendes<sup> 1</sup>, Ariah Fallah<sup> 2</sup>, Terrence J. Sejnowski<sup> 3,4,5</sup>, Claudia Lain... |
f5bf614d1674951fc25ac658322888eb6f4ff5bf2ab0547f3781597a1ee8b697 | Text | 3,542 | 151 | =====================
Fast Neurite Tracer
=====================
----------------------------------------------------------------
Semi-automatic neurite tracing with tera-bytes of imaging data
----------------------------------------------------------------
:Author: GOU Lingfeng
:Contact: goulf@ion.ac.cn
:Date: 29... |
24bbc94149ed29d0128433afbcf323f50c3dfe6481ade48dae7377618e678552 | Text | 3,558 | 51 | # Multi-atlas bundle segmentation
This data is made to be used with the following script:
https://github.com/scilus/scilpy/blob/master/scripts/scil_recognize_multi_bundles.py
This script is in fact a multi-atlas, multi-parameters version of *Garyfallidis et al. (2018)* with labels fusions. We name this algorithm Reco... |
c52ae35cca68519b8d4e2918c6d092db075b2a99ea709b3fffc6536bc8420572 | Text | 3,564 | 61 | # PET Brain Preprocessing
Robust Nipype workflow for preprocessing PET BIDS brain data. Initially developed for 18F FDG PET brain images acquired by project NEMO at the Department of Neurology, University Medical Center Groningen. https://www.movementdisordersgroningen.com/nl/nemo. This workflow was also successfully t... |
0ff9ed636aa395c75817ed7b036c2c8f1737e4fb23ad5d0b7db99b3b74646802 | Text | 3,636 | 48 | # HOPE_neurodisability
This repository covers diagnostic code list (ICD-10, OPCS codes, birth characteristics) used to identify neurodisability in hospital admission records.
Neurodisability was defined as chronic conditions involving impairment of the brain and/or neuromuscular system and resulting in functional li... |
43b9dd2d7fa0d72a81c23a612f26bcba38ab94a9e41a4d8398c89ac3b86c76ec | Text | 3,646 | 62 | > [!WARNING]
> The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
> Future development will take place at: https://github.com/openbraininstitute/NeuroM
... |
696efa1537d805d50f8a553e383d46b8de6b141fc2ad5f0c1b4a415209c26092 | Text | 3,655 | 72 | # `mtag` (Multi-Trait Analysis of GWAS)
`mtag` is a Python-based command line tool for jointly analyzing multiple sets of GWAS summary statistics as described by [Turley et. al. (2018)](https://www.nature.com/articles/s41588-017-0009-4). It can also be used as a tool to meta-analyze GWAS results.
## Getting Started
... |
461e7dcc652eccd329e43c8768d8fbe2eda6b7da62392587d0a536e10bc2af4c | Text | 3,679 | 69 | [](https://zenodo.org/badge/latestdoi/296102080)
# spynal: Simple Python Neural Analysis Library
Tools for preprocessing and basic analysis of systems/cognitive neurophysiology data in Python
Covers typical preprocessing and basic analysis steps in neural analysis workf... |
0eff32645ae31c9bf2704341a4bb00c5b93cca54c4c654ca1faeb39580da4e48 | Text | 3,718 | 64 | # CARMA
## Novel Bayesian model for fine-mapping in meta-analysis studies
We propose a novel Bayesian model, CARMA (CAusal Robust mapping method in Meta-Analysis studies), for fine-mapping in order to identify putative causal variants at GWAS loci. The main features of CARMA are
> Modeling jointly summary statistics... |
f4999f680424cc9b3e902b671499ed5dcdbe5fa7f15a22e7aef0a5d9f4605e03 | Text | 3,719 | 92 | # GHOST - Global Harmonisation Of Scanner performance Testing
Tools to process data acquired with the UNITY Phantom (Caliber Mini Hybrid Phantom).
## Install
Requires python3 but otherwise no special packages. Easiest way to install is to use `pip` inside a virtual/conda environm... |
584360b7d1eab4785ca0aa6b2cb0d37d70068049dbedcc14d5f556ca31164d52 | Text | 3,730 | 109 | # <center> Anime Popularity Prediction: A Multimodal Approach Using Deep Learning </center>
This repository is for the results reproduction of the paper "Anime Popularity Prediction: A Multimodal Approach Using Deep Learning".
## Reproducibility instructions
<ol>
<li>
You can clone this repo into a local dire... |
69935a8277c713e2c27d541cb92671f7f23af51094f345ed5aa8a556e87a5d5f | Text | 3,747 | 67 | # bci-essentials-python
This repository contains python modules and scripts for the processing of EEG-based BCI.
These modules are specifically designed to be equivalent whether run offline or online.
## Related packages
The front end for this package can be found in [bci-essentials-unity](https://www.github.com/kir... |
aae26068780daf8eb9905e22e064ea5665cf91bc3b56f20a2f2daff462aecc70 | Text | 3,747 | 95 | # Herbify: Deep Learning Framework for Precise Herb Identification
## Overview
Herbify is a comprehensive deep learning project focused on the classification of 91 types of herbs using advanced computer vision techniques. The project includes data preprocessing, augmentation, model training (with various state-of-the... |
0234cbe4ba6eb081590ca7142ba6192eeffc9a214fba315ad6eab0221e9a378e | Text | 3,749 | 80 | .. image:: https://raw.githubusercontent.com/amnsbr/cubnm/main/docs/_static/logo_text.png
:align: center
:width: 350px
.. badges-start
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.12097797.svg
:target: https://zenodo.org/doi/10.5281/zenodo.12097797
.. image:: https://img.shields.io/pypi/v/cubnm
... |
965d968663e9107f553215de53239f6cfd8fb18c6c1e394e7509f8c67c6048d2 | Text | 3,773 | 83 | # Functional analysis within latent states: A novel framework for analysing functional time series data
Code repository accompanying the manuscript "Functional analysis within latent states: A novel framework for analysing functional time series data" by Owen Forbes, Edgar Santos-Fernandez, Paul Pao-Yen Wu, and Kerrie... |
b80c13efc26221835afaf760522816810774b732aaf125cbdd546f3df5629ff7 | Text | 3,774 | 67 |
# Neuropixels-NHP-hardware
<img src="./docs/images/Neuropixels%20NHP%20-%2045mm.png" alt="drawing" width="500"/>
This repository and the associated wiki contain a collection of open-source hardware designs and documentation of methods for using silicon probes like the Neuropixels-NHP in nonhuman primates (NHP) and o... |
b0e66bf6eda3d5a07f61044331f62528c49ee6f656a224b110a4addfa63cb0d3 | Text | 3,797 | 114 |
# Axial localisation using deep learning for SMLM
## Installation
Due to conflicting python dependencies, this module relies on two conda environments to function at this time.
Dependencies can be installed using conda:
```bash
git clone git@github.com:mb1069/smlm_z.git;
cd smlm_z;
conda env create --name ... |
bf3fea33147271b29290476098c605518aaa3501df42d3d7d8b6b645a14ebec6 | Text | 3,805 | 95 | # SCORE
SCalable genetic CORrelation Estimator
We propose a scalable randomized Method-of-Moments (MoM) estimator of genetic correlations in bi-variate LMMs. The method compute genetic correlation in two senerios: the samples of phenotypes are shared and partially shared.
### Citing SCORE
If you find that this sof... |
ae1e29c53a1a6a93cda6fd37601053427ba9b79564bee8b3b731595d85175b1a | Text | 3,844 | 64 | # Assessing workflow impact and clinical utility of AI-assisted brain aneurysm detection: a multi-reader study
<p float="middle">
<img src="https://github.com/connectomicslab/AI-Assisted-Aneurysm-Detection/blob/main/images/AI_assisted_scenario.png" width="700"/>
</p>
This repository contains the code for the paper: ... |
2effe0dfd3b83b1a11b8317e5864e08e46ef0be89216c9065cf73725e50d86fc | Text | 3,858 | 96 | # SFGPI Task
## Overview
This repository contains code to run cognitive tasks for:
Hall-McMaster, Tomov, Gershman* & Schuck* (2025). Neural evidence that humans reuse strategies to solve new tasks. *PLOS Biology*.
The repository includes:
1) code to run an online prescreening task for admission to the study
2) co... |
b8550ebc8b8f2fe06c7e1c442a9e6c1af08b0acb2ea0ed460dad8eb287bb8deb | Text | 3,867 | 97 | # 3D Filament Annotator
[](https://zenodo.org/badge/latestdoi/513980347)
[](https://github.com/amedyukhina/napari-filament-annotator/raw/main/LICENSE)
[ is a shiny-based endocrine genetic web app for tissue cross-talking. Now we have both human data in sex from [GTEx](https://gtexportal.org/home/) and mouse data in diets from [HMDP](https://www.ncbi.nlm.nih.gov... |
bc829d168866e8f934ba4b38a57f3da6e98cabf0ea912731d77e089dbda202c9 | Text | 3,891 | 70 | ### Camformer
Code repository for the paper [Predicting gene expression using millions of yeast promoters reveals *cis*-regulatory logic](https://doi.org/10.1093/bioadv/vbaf130) by Tirtharaj Dash and Susanne Bornelöv.
**Problem**: Let $S = \{A,C,G,T,N\}^{110}$ denote a promoter sequence of length $110$. Here, $A$, $C$... |
4f9d1b9c611211246c4bf5df29bbe17f0b64f1738fa86ce143c534147706e53b | Text | 3,898 | 69 | >📋 Accompanying code for "A U-Net model for Local Brain Age"
# A U-Net model for Local Brain Age
This repository is the official implementation of [A U-Net model for Local Brain Age](https://www.biorxiv.org/content/10.1101/2021.01.26.428243v1).
>📋 
- lookup table must be loaded into ``lookup table`` folder, raw EIS datafiles into ``raw data`` folder
- then when the matlab code ``NOVA_batch... |
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