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|---|---|---|---|---|
c4818f86cdfcdb7dd9edf5acb5535f29ecd3bd9d4c4846aba7183c3d39006fa3 | Text | 9,548 | 123 | # PedsBrainAutoSeg tool
This tool can be used to generate AI-predicted brain tumor segmentations for pediatric patients with any available combination of brain MRIs - including 1) multiparametric MRI i.e., T2w-FLAIR, T1w, T1w post-contrast, T2w; 2) either T2w-FLAIR or T2w; and 3) T1w post-contrast and either T2w-FLAI... |
fe0e781d2ecd824762e7f5b964a443dff8ce3998369b90da94a62ca877cabbab | Text | 9,614 | 134 | # IGUANe harmonization
<img align='right' src="iguane.png" width="160">
This repository provides code to use the IGUANe model for harmonization of MR images. The full method as well as validation experiments are detailled in a [peer-reviewed publication](https://doi.org/10.1016/j.media.2024.103388). The model has bee... |
ecc86c3b07ee561ed9ca8b4fd11e34261eebfc2d7acb19e9fa772dd34d70bc2c | Text | 9,655 | 200 | # A Lightweight Deep Convolutional Neural Network for Detecting Artifacts in Continuous EEG Signals
[](LICENSE)
<p align="center">
<img src="DOCS/images/pipeline_overview.png" alt="EE... |
649ad533da7abf7fbc79b61015f45a17c8425f9be70cd114ad30733bca193d36 | Text | 9,657 | 249 | <div align="center" style="">
<br>
<img src="./logo.png"/ style="height: 5em;">
<br>
<svg xmlns="http://www.w3.org/2000/svg" width="" height="80">
<!-- Background with red border -->
<rect x="2" y="2" width="99%" height="76" rx="8" ry="8"
fill="#fffaf8" stroke="#e63946" s... |
a06270daa60978355f7f27e26a9c2e3d4f525b27184681885633c74cfce0d4eb | Text | 9,732 | 188 | Please visit OSF to download the data: https://osf.io/kjynq/?view_only=f10e01eba9c54779b5de469e489a4e5b
### Historical reconstruction of human moralization
This repository contains code and data for replicating the following work: Ramezani, Stellar, Feinberg, and Xu. (submitted) Historical reconstruction of human m... |
176a5f286aac573d731bbae565890deae4e93c0aebdba4c996117e501a31268f | Text | 9,801 | 210 | # kb-python
[](https://pypi.org/project/kb-python/0.30.2/)
![status](https://github.com/pachterlab/kb_python/workflows... |
4428e2c56eff595f2b1f9fa2c5d24f28c673484bcc633060e0eb02fff3e2bf55 | Text | 9,829 | 91 | <div align="center">
# ECGxAI: Explainable AI for the electrocardiogram
[](https://moody-challenge.physionet.org/2020/papers/253.pdf)
[](https://academic.oup.com/ehjdh... |
88e40241029600c9a002909297406342ca5a36f3ad7d71528566dd256add3c02 | Text | 9,830 | 216 | <!-- PROJECT LOGO -->
<br />
<div align="center">
<a href="https://github.com/rivelco/ENCORE">
<img src="https://raw.githubusercontent.com/rivelco/ENCORE/main/src/encore/gui/ENCORE_logo.png" alt="Logo" width="80" height="80">
</a>
<h3 align="center">ENCORE - Ensembles Comparison and Recognition</h3>
<p al... |
ea21b4d2669214a1de76050e01b8a4f103b02a493630a42923228e8b7f33a9e2 | Text | 9,863 | 299 | # DHG-LGB: Disease-Hypergraph Integrated with LightGBM
[](https://doi.org/10.5281/zenodo.17848043)
01... |
7462dcd5939027a3a13f4968e1d2be1d07e11f1ed8d4bcf669aa00ed3c78d497 | Text | 9,918 | 376 | # PhotoFenton-PAH-Remediation-ML
## Machine Learning Framework for Chemical Remediation Prediction
This repository contains a generalized machine learning framework for predicting removal rates in chemical remediation processes, developed for research in Photo-Fenton treatment systems.
## Table of Contents
- [Overvi... |
f318357f1cecf80479211dc2c8181a4b4ad47046864cbf9298c830deac0484e3 | Text | 9,965 | 249 | # Drosophila Whole Brain Activity Fitting
This project implements a two-stage neural network model to simulate and predict the dynamics of the Drosophila (fruit fly) whole brain activity.
## Data
This project requires two main datasets:
- connectome data from the FlyWire project (version 630/783): https://codex.fl... |
d4bf30bd1dd9dceb5d82d0dc1af0aedac5c8d7264a3a36714d50ede536eefbf7 | Text | 10,090 | 130 |
<!-- badges: start -->
[](https://shields.io/)
[
- [Installation & Dependencies](#installation--dependencies)
- [Flags & Options](#flags--options)
- [Output Structure](#output-structure)
- [Downloading a project](#downloading-a-project)
- [Download from NCBI... |
9c1c9c2a88a2dd6637ccc35912a3265be4ad9ed604b6b4ad1e3c863e9d8bcdaa | Text | 10,136 | 141 | #  
[](https://nf-co.re/rnaseq/results)[![Cite with Zenodo... |
ac845edfd6064cb326aecff0b1c8d55713b16fb339571549e843b09300fdfcdc | Text | 10,158 | 178 |
# Rethinking Visual Geo-localization for Large-Scale Applications
This is the official pyTorch implementation of the CVPR 2022 paper "Rethinking Visual Geo-localization for Large-Scale Applications".
The paper presents a new dataset called San Francisco eXtra Large (SF-XL, go [_here_](https://forms.gle/wpyDzhDyoWLQyg... |
40f13061bc0ee51da4a8eaaaa165be6bcded0a4ffd3e6710903f4ac18e664e40 | Text | 10,194 | 184 | FLAMES version 1.1.2. \
Please note that the version found in the FLAMES preprint can be found under release 1.0.0
Thank you for your interest in using FLAMES for GWAS gene prioritization.
The python version of FLAMES is still being optimized.
If you have any problem using/installing FLAMES please open an issue.
# I... |
19dbb3380634bde27d76d6dc0dc6167432a3d2d43082a8653311cbfeee972d43 | Text | 10,217 | 183 | <p align="center">
<h1 align="center"><ins>LightGlue</ins> ⚡️<br>Local Feature Matching at Light Speed</h1>
<p align="center">
<a href="https://www.linkedin.com/in/philipplindenberger/">Philipp Lindenberger</a>
·
<a href="https://psarlin.com/">Paul-Edouard Sarlin</a>
·
<a href="https://www.... |
badd0976d9b53c820c2bac5c4d237c53ef352513a10e8965b0fa46499938d5ba | Text | 10,228 | 198 | <p align="center">
<a href="assets/logo/openplant-mosaic.tiff">
<img src="assets/logo/openplant-mosaic.png" width="100%" alt="OpenPlant lettering formed from a mosaic of plant photographs">
</a>
</p>
<h1 align="center">OpenPlant</h1>
<p align="center">
<strong>A large-scale benchmark for agricultural plant ... |
6806a9f82c54a85bce9f56e4f5061f6fa3763322d51157a870a000cfb1649e68 | Text | 10,285 | 124 | # The Population Spatial Frequency Toolbox
The pSF-Toolbox ([now published in JORS](https://doi.org/10.5334/jors.610)) streamlines the population spatial frequency tuning (pSFT) approach, originally developed by [Aghajari, Vinke, & Ling 2020 (Journal of Neurophysiology)](https://doi.org/10.1152/jn.00291.2019), wit... |
0e911788cb8ad05843a9afe525eaf1742169b0896dab0a4f3e3e7a68ad997304 | Text | 10,403 | 275 | README
================
Rasmus Kirkegaard
22 December, 2023
# R10.4.1 Zymo HMW basecalling
With the release of R10.4.1 I wanted to check the quality of the raw
reads and the consensus accuracy to ensure that we had the right
approach for continuing our nanopore only assemblies from metagenomic
samples ([Mantas et
al.... |
cb0817296f8a573eed2fb34592901248cda6dbf7f260ef22e48988d7390eb373 | Text | 10,475 | 287 | # NEMS ·   
The Neural Encoding Model System (NEMS) is helpful for fitting a
mathematical model to time series data, ... |
11343d8cc568d3d7a82bac523e8ea447adfaa2c2727977aba5c7e8316a7653a6 | Text | 10,487 | 233 | # metaprivBIDS
While sharing neuroimaging data, demographic and clinical information of participants must be associated to provide meaningful analysis for prognosis, diagnosis and biomarker identification. MetaprivBIDS assesses and reduces disclosure risk in such demographic and clinical associated data. It provides r... |
d6873c7cbba66619c8cb9c162354706496e78f5176da051888e7a2919aad4f56 | Text | 10,524 | 131 | # TargetFinder
TargetFinder is a pipeline for identifying and characterizing the gene targets of distal enhancers. In "Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin", Nature Genetics 2015 (to appear), we used TargetFinder to:
- Show that the three-dimensional structure... |
ee34bd13262c42bb99b9428251e235eaf5cc2fc7508f6de0c3844e89d32b1352 | Text | 10,542 | 165 | # Vectorial Reconstruction of an Electric Hearth Vector in Saline Solution
This project implements a minimal analog front-end and software reconstruction algorithm to track a dipole vector immersed in saline solution. Drawing from the **Einthoven triangle** and its bipolar leads, maps electric potential to a real-time ... |
63dfbc2e48ea43dfba91043be269551a56b176aaef458d15e660540bf183edb8 | Text | 10,556 | 270 | # **Normal breast tissue (NBT)-classifiers: advancing compartment classification in normal breast histology**
[Paper](https://www.nature.com/articles/s41523-026-00896-2)
**Abstract:** Cancer research emphasises early detection, yet quantitative methods for normal tissue analysis remain limited. Digitised haematox... |
bd08e13bf1d4afc7e324b4696dee6e1bc62b04b2ec719670670387b08e70dc58 | Text | 10,669 | 200 | # Bioinformatics pipelines, [SLURM](https://slurm.schedmd.com/overview.html) friendly
**.
The repository contains Julia modules, Pluto notebooks, and helper scripts used to generate the results and figures for the article : [Cros... |
f96a58fdc20d1b4fe876813c7f8b55c2a2ffa3178009e9f10942a4ac20206ed1 | Text | 10,758 | 230 | # RapidParc
[](https://github.com/MedVisBonn/RapidParc)
[](https://pypi.org/project/RapidParc/)
[ pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data. MAPS pipeline contains multiple scripts. The run_pipeline.sh is a prototypes of a shell script containing the locations of files needed to ... |
365ad188288f33da22892a3c5fd7d9e145b350dc63e205a3788424fc5690bc16 | Text | 10,878 | 282 | # fastCN
A pipeline for the fast estimation of copy-number based on read depth using
the multi-mapper mrsFAST.
If you are interested in generating paralog specific copy-number estimates
consider QuicK-mer2, accessible at: https://github.com/KiddLab/QuicK-mer2
The basic functionality of fastCN is described in [fastCN... |
37f6b892f87c5f31e386f233647776560d46f347f589dde830648c5c2170d7a4 | Text | 10,897 | 263 | # Effective Connectivity of the Human Insula
## About
This repository contains scripts and data used to generate matrices and brain maps illustrating results from:
**_Effective connectivity of the human insula measured by cortico-cortical evoked potentials_**
Pinheiro et al.
The analysis is based on stereo-EEG (s... |
7f2b6259f4fa0e5f33e7ff5f2f214f06f230255875cd26dcb83b2a0409a72e03 | Text | 10,912 | 232 | # ShinyCell is now succeeded by ShinyCell2 which is available at https://github.com/the-ouyang-lab/ShinyCell2
`ShinyCell` is a R package that allows users to create interactive Shiny-based
web applications to visualise single-cell data via (i) visualising cell
information and/or gene expression on reduced dimension... |
5ea00ec01236bd0f2c685f7a5a8adda4a0f431e76f98eacebe963a893dbecb0c | Text | 10,919 | 406 | # COVID19_GWAS_Analyzer
This package provides SAS scripts that perform differential effect size analysis between two COVID19 GWASs freely available from HGI or GRASP databases. Users need to have an... |
787ca673b81bde2bd370e7b09f130f035584b49444b15d8f755dfb2bb84be888 | Text | 11,059 | 167 | # Complex Principal Component Analysis for fMRI
This repository contains a Python command line script for performing complex principal component analysis (CPCA) of functional MRI (fMRI) time courses, as described in Bolt et al. (2022; Nature Neuroscience). CPCA allows for the extraction of traveling wave patterns via t... |
eb0531b429a31f3d957a39b553b373597704c57322f9a518623d26533edaca15 | Text | 11,082 | 210 | <h1 align="center">
<img src="labelme/icons/icon-256.png" width="200" height="200"><br/>labelme
</h1>
<h4 align="center">
Image annotation with Python.
</h4>
<div align="center">
<a href="https://pypi.python.org/pypi/labelme"><img src="https://img.shields.io/pypi/v/labelme.svg"></a>
<!-- <a href="https://pypi... |
d1ba0b304c431f788ffd423ea6ee33222773aa394da3f6e17323301bcc7af155 | Text | 11,097 | 191 | # HimNet : Learning Molecular Hierarchical Interaction for Accurete Molecular Property Prediction
Discovering molecules with desirable molecular properties, including ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles, is of great importance in drug discovery. Existing approaches typically ... |
b4c5b1782fd98b6c460d16b945f5d7dee23e83b3902d28784dea0b9d56d25271 | Text | 11,161 | 258 | # PSN-IBS: Patient Similarity Networks for Irritable Bowel Syndrome
[](https://colab.research.google.com/github/arvidl/psn-ibs/blob/main/notebooks/patient_similarity_networks_ibs_brain_morphometry_cognition.ipynb)
[](https://pypi.org/project/prsedm/)
[](https://anaconda.org/sethsh7/prsedm)
[](https://doi.org/10.2337/dc25-0142... |
435a12a7a823b87690af7ae72b3981ea28f0046c8b8a32eb2a7061bdc9e37299 | Text | 11,311 | 179 | # Vectorial Reconstruction of an Electric Heart Vector in Saline Solution
This project implements a minimal analog front-end and software reconstruction algorithm to track a dipole vector immersed in saline solution. Drawing from the Einthoven triangle and its bipolar leads, maps electric potential to a real-time vecto... |
d67f98c7fd5a1aab0d8450c9769d82323d1ee2ba0744934a31e76865b7974eb0 | Text | 11,366 | 182 | # Headmodel Individualization
**The presented PCAwarp algorithm estimates individual head anatomies based on a large database of heads when structural MRI/CT scans are unavailable using scalp data from photogrammetry or digitized electrode positions. The final surfaces meshes can be used to construct a BEM volume... |
d620953a30d6a07b66f7536a65dc1141f16ca18079d8cd6612f885862d747b96 | Text | 11,400 | 234 | # Detecting neural assemblies in calcium imaging data
In the following, we give a brief overview over the main functions of the repository, to generate datasets of surrogate calcium imaging data and to analyse such datasets for assembly activity.
Some of functions for preprocessing of the datasets as well as most of t... |
c2fcddc9ec6c6a9cd2038cb94e0b0172b17393dbd8b9df0ea647618bf0722a36 | Text | 11,428 | 171 | # ProtoECGNet
Case-based interpretable deep learning for ECG classification. This code implements ProtoECGNet from the following paper:
> [**ProtoECGNet: Case-Based Interpretable Deep Learning for Multi-Label ECG Classification**](https://proceedings.mlr.press/v298/sethi25a.html)<br/>
Sahil Sethi, David Chen, Thomas... |
5b9bf5bf5e7380276d28099147d6ffd8f539da9e8bb7cc65f312e329931d5e1f | Text | 11,442 | 193 | # README - A dataset of harmonized global air quality monitoring metadata - METAIR
Product Name = METAIR
Version = 1.0
Title = A dataset of harmonized global air quality monitoring metadata
Dataset Location = www.doi.org/10.5281/zenodo.1568086
Created Time = June 2025
Release date = December 2025
Number of R... |
8ea74655514afea3b2337d928eec518d88fbe6ebd88d894ec2eaa68ce1c1a5e5 | Text | 11,443 | 138 | <p align="center">
Pytorch implementation of KerNN<br>
Meuwly Group, University of Basel
</p>
# General
The present repository provides access to a Pytroch implementation of the KerNN codes[1], which can be used to learn the potential energy surface (PES) of molecular systems. Such PESs can be used to drive molecular ... |
da3f7d86c41cfaf01f3edea1a0a7774009f87c11417abd3de8a1b8139fa5c0e1 | Text | 11,476 | 128 | # Detection of RNA Outliers Pipeline
[](https://github.com/gagneurlab/drop/actions?query=workflow%3ABuild)
[](https://github.com/gagneurlab/drop/blob/master/LICENSE... |
4b9e9da871ce6f197e01f7319b02028bc6b94500d9d1c7db1abd41a8d00f0cf7 | Text | 11,490 | 180 | # ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline
[](https://circleci.com/gh/ENCODE-DCC/chip-seq-pipeline2/tree/master)
## Introduction
This ChIP-Seq pipeline is based off the ENCODE (phase-3) transcript... |
1e5f39b3f30311858da2cea892defa38bd7e3c5b42a81da9cb31c56744fdd27f | Text | 11,492 | 233 | # A Lightweight Deep Convolutional Neural Network for Detecting Artifacts in Continuous EEG Signals
[](https://doi.org/10.5281/zenodo.19554506)
[](LICENSE)
](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
Implementation of the paper: **"Generative AI Dr... |
3c159f14cb43ab0284136c61cb0a12bae2a3af6a36d54fd8600042074ad031c4 | Text | 11,649 | 226 | # LyROI – nnU-Net-based Lymphoma Total Metabolic Tumor Volume Delineation
[](https://pypi.org/project/lyroi/)
[](https://doi.org/10.14278/rodare.4160)
[![Software License](https://img.sh... |
8fcaab864092358a7a53d894c9f65aba164a9d91b709d521af656615a13b8dd9 | Text | 11,808 | 161 | <p align="center">
<img src="https://raw.githubusercontent.com/seisbench/seisbench/main/docs/_static/seisbench_logo_subtitle_outlined.svg" />
</p>
---
[](https://github.com/seisbench/seisbench/blob/main/LICENSE)
[![GitHub Workflow Status](https://img.shields... |
b734f35bd114d42b4501879a5acb30cd9875b064a437efb09138e60cdfda63bb | Text | 11,907 | 291 |
# EANMD
<img src="https://github.com/dontkme/PersonalScripts/raw/master/Fig.logo.EANMD-02.png" align="right" height="73" width="221"/>
[](https://github.com/dontkme/EANMD/releases) [](./LICENSE)
[](https://pypi.org/project/QtPy/)
[](https://www.anaconda.com/download/... |
0663c30720af4b53ade3555f7938eacbabb14a46e465674a1e2e11863c7f7a04 | Text | 12,004 | 176 | <p align="center">
<img src="docs/source/_static/img/EIR_logo.svg", width="500">
</p>
<p align="center">
<a href="LICENSE" alt="License">
<img src="https://img.shields.io/badge/License-Apache_2.0-5B2D5B.svg" /></a>
<a href="https://github.com/arnor-sigurdsson/EIR#citation" alt="Citation">
<img... |
7b2b26265f2cea4f87dc34b2974a27560f8f1a0b4c37f475b4ab722d679efab9 | Text | 12,149 | 232 |
<table align="center">
<tbody>
<tr>
<td align="center" width="1182px">
<img src="https://raw.githubusercontent.com/virelay/corelay/refs/heads/main/design/corelay-logo-with-title.png" alt="CoRelAy Logo"/>
# Composing Relevance Analysis
[](https://github.com/virelay/co... |
01cf693324e0f35af59908a98582a240de198af2bc60a9d8ce0ba60b15d8bbfc | Text | 12,165 | 183 | # [scStudio - Web Browser Version](https://compbio.imm.medicina.ulisboa.pt/app/scStudio)
**A User-Friendly Web Application Empowering Non-Computational Users with Intuitive scRNA-seq Data Analysis**
**scStudio** is a user-friendly, web-based application for comprehensive and modular scRNA-seq data analysis. It support... |
47326015ed2b971d31b6fd0cad4a26c2d124e5ad9b48e2818bc8deb3f90be02e | Text | 12,168 | 293 | ## Version 2.0 (stable)
[Welcome to my homepage!](https://WangLibo1995.github.io)
## News
[](https://paperswithcode.com/sota/semantic-segmentation-on-isprs-p... |
136fbbb7b5e8c83e443f1042ba8f2a66b0bdad941700364c60f18988ecd87f22 | Text | 12,251 | 141 |
# MEA Network Analysis Pipeline (MEA-NAP)
[
We are delighted to provide the neuroscience community with a new hierarchical MRI atlas of the human subcortex. This repository provides the new atlas for download and stores the code that was used to map the atlas.
Read the [manuscript](https://rdcu.be/b7N8K) published in *Nature Neur... |
ca0a2ea0e94401b4da3ae1ced5084d7afc8e1a3bd8ffa3b0e05903bbc6397f72 | Text | 12,413 | 343 | [](https://github.com/tseemann/shovill/actions/workflows/CI.yml)
[](https://github.com/tseemann/shovill/releases)
[ of single nucleotide
polymorphism (SNP) data, similar to smartpca from EIGENSOFT
(http://www.hsph.harvard.edu/alkes-price/software/) and shellfish
(https://github.com/dandavison/shellfish). FlashPCA is based on the
[https://github.com/yixuan/spectra... |
ab906bd10423dcae5075e85b9bd1fa6648acd704c90cf679c6ce37cd8374c16c | Text | 12,639 | 364 | # richR <img src="man/figures/logo.png" align="right" height="120" />
[](http://www.repostatus.org/#active)
[](https://github.com/hurlab/richR)
[
* [Table](#Table)
This repository contains a number of useful parcellations, templates, masks, and transforms to (and from) MNI152NLin6 space. The files are named according to the BIDs specification
 [](https://travis-ci.org/numenta/NAB) [](https://doi.org/10.5281/zenodo.1040335)
-----------------------------
Welcome. This repository contains the dat... |
c1a99438140c9f2a670c38929b6e04a5c2d62468257f1414c0ff3b99cb0e7bb7 | Text | 13,080 | 364 | <img src="./enformer.png" width="450px"></img>
## Enformer - Pytorch
Implementation of <a href="https://deepmind.com/blog/article/enformer">Enformer</a>, Deepmind's attention network for predicting gene expression, in Pytorch. This repository also contains the means to fine tune pretrained models for your downstream ... |
180d188d1270eccf783d9ab758b19ba59e078a11e75d6fecd8b45e3c05496057 | Text | 13,264 | 293 | 
# AlphaGenome API
[**Get API key**](https://alphagenome.google/ap... |
30c76320dac979328d5926067ed7da2862ea478797613f4c7eed64296dd78fe1 | Text | 13,461 | 403 | # Feature Selection Pipeline for Neuroimaging Data
> Author: Ayumu
A Python package for identifying features (connections) associated with a target variable using two complementary approaches:
1. **PCA-based method**: Uses Principal Component Analysis for dimensionality reduction
2. **T-test-based method**: Use... |
d80898f06a898b7db93159315b07848437425a49fb263400e195a80f10583006 | Text | 13,489 | 42 | # Equisobrain
Equine brain template and atlas : [](https://doi.org/10.5281/zenodo.10731030)
Equisobrain dataset : [](https://doi.org/10.5281/zenodo.13969827)
## Abstract
We compared neu... |
e8d89560fb3aab269a30a57cb5b5fce3b1db2d576af1416bd91af692ccb15907 | Text | 13,491 | 187 | 
Repository Contributors: Timothy Dunn, Jesse Marshall, Diego Aldarondo, William Wang, Kyle Severson
DANNCE (3-Dimensional Aligned Neural Network for Computational Ethology) is a convolutional neural network (CNN) that calculates the 3D positions of user-defined anatomical landmarks... |
930eaea3d9d6799e4a784057d7dd257a333cce1c0e1ef33fbc628c060ebe9f93 | Text | 13,537 | 222 | # GAMBA-MATLAB
A MATLAB toolbox to study whether the expression of the gene(s) of interest (GOI) and neuroimaging-derived brain phenotypes show overlapped spatial patterns. Different statistical **null models** are available to examine both ***gene specificity*** and ***spatial specificity***. This toolbox is an exten... |
e3fde545bdf09862abdeca399216d7bf6451bc0710a570c6a95f5bb7e1c1b6ab | Text | 13,576 | 374 | # Evaluation of Large Language Models for Diagnostic Impression Generation from Brain MRI Report Findings: A Multicenter Benchmark and Reader Study
[](https://doi.org/10.1038/s41746-026-02380-4)
[ of any orientation, resolution and contrast into 1 mm isotropic MP-RAGE, **while inpainting lesions (which enables easier segmentation, registration, etc)**. You can then r... |
e22531c72a8f74029d7f1a615e06cdf30e4c9f5ba715e955bd6345ba546416b6 | Text | 13,807 | 299 | # ExioML
ExioML is a production-grade, ML-friendly layer on top of Exiobase 3.8.2. It delivers PxP/IxI emission-factor tables across 49 regions and 28 years, bundles ML-ready preprocessing and splits, and ships as the official PyPI package `exioml`.
## Introduction
Repository for paper ExioML: Eco-economic dataset for... |
47459fc4fa8ec6abceb9f219ba5cf0abea9fb14fad45055b12dac1d16324d988 | Text | 13,809 | 252 | # VVDViewer
This is the open-source repository for VVDViewer, an interactive rendering tool for confocal microscopy data visualization. It combines the rendering of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed for... |
ac1a2add6e921c26cd4d97a0b0c055b02567522c17fa1121ad14899824228ac7 | Text | 13,867 | 222 | # HAR/SWR Datasets and Machine Learning experiments
Baseline Machine Learning models for Human Activity Recognition (HAR) and Sleep Wakefulness Recognition (SWR) using the Human Activity Recognition Trondheim (HARTH), the Human Activity Recognition 70+ (HAR70+), the DualSleep, the HARChildren, and the walking speed dat... |
b32c40fa7dba6f587f1bf56fd1c09b98738c8348e508429ad64df7c25df0a4f5 | Text | 13,907 | 196 | # Sprod
Sprod: De-noising Spatially Resolved Transcriptomics Data Based on Position and Image Information
## Introduction
Spatial Resolved Transcriptomics (SRT) techniques provide gene expression close to or even superior to single cell resolution, while retaining the physical locations of sequencing and sometimes als... |
e9916473e91e31f32b59dad40035a7e93ce39f814837d172e70b88c24ea9d56d | Text | 14,044 | 151 | 
# Power Pixels: A turnkey pipeline for processing of Neuropixel recordings ⚡
<img src="https://github.com/user-attachments/assets/37d9003a-788a-43d2-a5a6-ff4d7a29f780" alt="PowerPixels logo" width="30%" align="right" vspace="20"... |
9da075a3cc513b0b3a317d71c2f08479affd9619d74cd8329aa6b0cf866616fb | Text | 14,078 | 213 | <h1 align="center">Metabolic and redox transcriptional signatures after brief psilocin exposure in human iPSC-derived cortical neurons</h1>
<p align="center">
<em>A brief perturbation. A broad transcriptional signature.</em><br>
Reproducibility code and interactive atlas
</p>
<p align="center">
<strong>Independ... |
b273b2d9ebd2e4cc07b67f9256d157531e6a0fe7b11cbcefd50d1ce7e36000e6 | Text | 14,080 | 154 | 
# Power Pixels: A turnkey pipeline for processing of Neuropixel recordings ⚡
<img src="https://github.com/user-attachments/assets/37d9003a-788a-43d2-a5a6-ff4d7a29f780" alt="PowerPixels logo" width="30%" align="right" vspace="20"... |
3764c601ddebb943132c0018d9bbe0c9df1981bdbbfe968de9dcfa48d686be2c | Text | 14,208 | 279 | # ABCD-HCP BIDS fMRI Pipeline
[](https://zenodo.org/badge/latestdoi/171551109)
This software takes a BIDS folder as input and determines parameters
for the DCAN Labs' modified HCP pipeline, calling upon the proper code
to run the subject(s).
### Installation
In order to... |
637c682c2058f4d959be30b7ed46b063b02ebc8cd984e96038b3af1cb003ef70 | Text | 14,222 | 402 | # MEP I/O Curve Analysis - Hierarchical Bayesian Modeling
Bayesian hierarchical sigmoidal model for comparing TMS coil efficacy in motor evoked potential (MEP) recruitment, with explicit handling of equipment-induced missing-not-at-random (MNAR) censoring.
## Overview
Motor Evoked Potentials (MEPs) measure cortical ... |
4237a463860dd61563f9e89fce60c732b4c7ed2a4ee3963b5c4c960293bbd221 | Text | 14,227 | 265 | [](https://app.cvat.ai)
# CVAT: Computer Vision Annotation Tool
[![Release][release-img]][release-url]
[![GitHub stars][stars-img]][stars-url]
[![License][license-img]][license-url]
[![CI][ci-img]][ci-url]
[![server pulls][docker-server-pulls-img]... |
3e533283587bd678c5a5729d404528c0b1dd761578be16069d758498d4b4b42f | Text | 14,325 | 155 | # Learning Evidence of Pairwise Association from Epigenomic and TF binding data
**L**earning **E**vidence of **P**airwise **A**ssociation from **E**pigenomic and TF binding data (LEPAE) quantifies evidence of association for pairs of genomic windows based on large-scale epigenomic and TF binding data while considering... |
ab7a745ca71db9ee573772dcc482c7fc98dace8efc999d68dbe59bb7d42cec5c | Text | 14,415 | 156 | # Learning Evidence of Pairwise Association from Epigenomic and TF binding data
[](https://doi.org/10.5281/zenodo.17403040)
**L**earning **E**vidence of **P**airwise **A**ssociation from **E**pigenomic and TF binding data (LEPAE) quantifies evidence of association for pair... |
1535f4165c51990cf5a02f6be51024e223a621aa295b8bb1d1d42c402a034123 | Text | 14,577 | 162 | # Apollo Implant Parts List and Instructions
For more information on the chronic implant detailed in this repository, please refer to our [eLife paper](https://elifesciences.org/articles/98522).
## Issues and Discussions
* NOTE: On 14/06/2024 the files were updated to allow for larger inter-probe distances (a common... |
a2601325072e50a9f270f3466a56b7fc7c608fa56f764f0d163ad9a33515bf9c | Text | 14,598 | 256 | # Infant Cortical Microstructure 👶🧠
This repository contains the MATLAB scripts used to generate the figures for the manuscript:
"Prenatal and early postnatal periods differentially shape the maturation of human cortical microstructure and myelin"
---
## Repository Structure
- **`code/infant_micro_figures.m`**
M... |
047515dc7a26c3dadcb596a2d0b03b29d23f6a1fa90201337369e77061b0d583 | Text | 14,642 | 267 | <p align="center"><img src="https://imagej.net/media/icons/snt.png" alt="SNT" width="150"></p>
<h2 align="center">The framework for quantification of neuronal anatomy</h2>
<div align="center">
<!-- rdcu.be -->
<a href="https://rdcu.be/c59MD">
<img alt="Publication (Publisher)" src="https://img.shields.io/badge/... |
026b4b6f08a4718930eaf24c66e4b95d87f50fb6aacd6378566f914b7318de26 | Text | 14,724 | 452 | # CATS-Net
Official Code for Article “A neural network for modeling human concept formation, understanding and communication”
... |
90349ff76967fa048a37a2db024c5326559a8ed69ce6a63cf496bd330c55a4af | Text | 14,978 | 532 | # Hyperspectral Plant & Parasite Classification Pipeline
An end-to-end Python toolkit for processing, analyzing, and classifying hyperspectral imagery of plant–parasite interactions. This repository guides users through the entire workflow—from raw data segmentation and combination, through model training and feature ... |
f73ef34896c614e62bcccda530ac0b20b30177f37477352ce217246d686d0a08 | Text | 15,090 | 258 | # MRIsegmentation
### Automatic MRI segmentation pipeline for consistent [FEM](https://en.wikipedia.org/wiki/Finite_element_method) and [BEM](https://en.wikipedia.org/wiki/Boundary_element_method) mesh creation from MRI scans of human heads
**0. <ins>[Install prerequisites](#Prerequisites)</ins>**<br>
**1. <ins>[Transl... |
6390f7c6db12a0c1db021790960f188bb9543f7cc4f0298cbcee3f8b26ab4101 | Text | 15,398 | 261 | Project README — Nanonis_AutoSTM_C-Br_bond_selectivity
===============================================
Overview
--------
This repository is a research-grade Python project for simulating and/or controlling molecular-selective reactions and tip manipulation in atomic-scale Scanning Tunneling Microscopy (STM). The ... |
3a967b1a5c691ace4c2fa330e11358ccea5960d03d84bfc9ab2c52ef7e76ca2b | Text | 15,454 | 228 | <p align="center">
<img height="200" src="images/logo.png">
</p>
Welcome to the Sei framework repository! Sei is a framework for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Sei provides a global map from any sequence to regulatory activities, a... |
26d11a5c348303f786ce30a2458cdf1ecffbba49782d6f1c21da2fcfefeb8a23 | Text | 15,492 | 218 | [](https://img.shields.io/github/stars/BGI-Qingdao/4D-BioReconX)
[](https://4D-bioreconx.readthedocs.io/en/latest/index.html)
## **4D-BioR... |
a63d0354bca24c3644b42bc3ce02fc491bce722705e504feca613caad54e9da1 | Text | 15,556 | 343 | # Semantical and Topological Protein Encoding Toward Enhanced Bioactivity and Thermostability
- [Semantical and Topological Protein Encoding Toward Enhanced Bioactivity and Thermostability](#semantical-and-topological-protein-encoding-toward-enhanced-bioactivity-and-thermostability)
- [🚀 Introduction (ProtSSN)](#-i... |
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