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c97ac88556d195ddc93c109bb806a351f18e08571ca8708c955bb04d36e6ac46 | Text | 4,955 | 90 | # Synaptic plasticity in the perforant pathway drives inhibitory reorganization in the Dentate Gyrus
> **Software release for the computational models used in the paper**
> _“Synaptic plasticity in the perforant pathway drives inhibitory reorganization in the Dentate Gyrus”_
This repository contains the code to rep... |
57a98b2dac82acd4e19e59345020ec7898f3b164ea1574cfb607b30f9cdb224a | Text | 5,019 | 85 | [](https://travis-ci.org/iskandr/fancyimpute) [](https://coveralls.io/github/iskandr/fancyimpute?branch=master) [ is an initiative of the ISMRM Perfusion Study Group, founded in 2019 after a membership survey, and with a mission to:
>“promote the sharing of perfusion imaging software in order to eliminate the practice of duplicate devel... |
12d01145812e75367491b0bd5285b9b3496d13c8937b8ab4bb8ac223f9465a6d | Text | 5,061 | 112 | 
A **Dynam**ic Programming Approach to Segment **ONT** Signals.
Dynamont is a segmentation/resquiggling tool for ONT signals.
Dynamont was tested on
* RNA002
* RNA004
* DNA R10.4.1 5kHz (I applied the trained transition parameters from the RNA004 model to the DNA R10 models. These should ... |
3783740ea47d81844006800b67481d35df56a77a2f7d62978dde9d1485595f5e | Text | 5,065 | 111 | 
[](
https://anaconda.org/bioconda/syri)
## [Help us in upgrading syri](https://github.com/schneebergerlab/syr... |
0e7e4fd71a34a6b492a6993f3a1e08f139b2f558a60defd110c8ba038be0950c | Text | 5,067 | 89 | # Fiber Photometry Control vs Test Batch Analysis
## Introduction
This repository provides a Python-based batch analysis pipeline for comparing Control and Test groups in long-term fiber photometry experiments. The script is designed for lock-in demodulated CSV files and enables fully automated preprocessing, normaliz... |
adad14865e01217067e876e2ecafdf25bf1e60e2a10b7552ef72a9154eee11cb | Text | 5,097 | 75 | # Hamster.jl
[](https://github.com/mschwade-code/Hamster.jl/actions/workflows/runtests.yaml)
[](https://codecov.io/gh/TheoFEM-TUM/Hamster.... |
0f5b80b5dce7f0f311704188e9c0d9e07d4269981735f3a91737fdab4067b1f0 | Text | 5,118 | 122 | <div align="center">
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
<a href="https://pytorchlightning.ai/"><img alt="Lightning" src="https://img.shields.io/badge/-Lightning-792ee5?logo=pytorchlightning&logoColor=... |
6a1ac03bf8be368287fcd6a2d96077b0418d87254a247c3362dee137db6881e1 | Text | 5,120 | 175 | # eTSC: Epilepsy Temporal-Spatial Classification Network
This repository contains the implementation of eTSC-Net, a deep learning framework for epilepsy classification using multi-modal MRI data (T2W and FLAIR).
## Project Structure
```
etsc/
├── data/ # Data loading modules
│ ├── __init__.py
│ ... |
ea0935ab2554f6d83842fe1d33dbfcdcb56da2f9220466f2314187a95fe4b0cd | Text | 5,152 | 178 | # metaprivBIDS
[](https://metaprivbids.readthedocs.io/en/latest/?badge=latest)
This Python build tool enables a given user to calculate a variety of different data privacy metrics on tabular data from a user interface.
# ... |
177edf3b1bf3ee6e51e7039fd98bbdbbd623219150f9a85075df9b181ebb7ffa | Text | 5,166 | 58 | # tumor_segmentation
This repository contains the build information and automation script for creating the ``tumor_segmentation`` Docker image, distributed using github's container registry. This requires a personal access token (classic not fine-grained) with at least read access for packages. For more information on ... |
740367e274dbcf7794783b9b3c8c3f4790e635ab8662160c96feed6a14914555 | Text | 5,171 | 119 | # GP-WAITER
GP-WAITER (Genome-Phenotype prediction using Weighted self-AttentIon TransformER) is a novel model that integrates GWAS-derived SNP weights into a hybrid CNN-Transformer architecture via an efficient tokenized embedding scheme. The model's design enables dynamic learning ... |
1f24d5e08042ab804063dbca02de8e69a318d10d63b3877248308db1d5c708d7 | Text | 5,173 | 83 | # Real-Time Seizure Detection using Electroencephalogram (EEG)
This is the repository for ["Real-Time Seizure Detection using EEG: A Comprehensive Comparison of Recent Approaches under a Realistic Setting"](https://proceedings.mlr.press/v174/lee22a/lee22a.pdf). You can checkout [pdf file](paper/Real-Time%20Seizure%20D... |
09b4338e3140b5596b68bb169243d01b122adc659b5d2cc80b77bb225137215a | Text | 5,176 | 150 | NOTE: This project is no longer actively maintained.
# gradunwarp
gradunwarp is a Python/Numpy package used to unwarp the distorted
volumes (due to the gradient field іnhomogenities). Currently, it can
unwarp Siemens data (and GE support very soon).
## Installation
### Prerequisites
gradunwarp needs
> - Python ... |
e2f9fb39b74446aa38af022ec5e494bf31dbab4df71d2e20d3d9104a09d33331 | Text | 5,184 | 139 |
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[](https://www.r-project.org/)
[](https://opensource.org/licenses/MIT)
## Overview
This repository contains code for validating multiple publicly available brain-age estimation packages on the Alzheimer's Disease Neuroimaging Initiative (ADNI) datas... |
37006cf397144c1e74fb4b4c07963134b9f52221a045138bd0a4c7d3288c9a6f | Text | 5,220 | 80 | # Pseudo-Healthy Image Synthesis via Location-Guided Diffusion Models for Focal Cortical Dysplasia Lesion Localization
Focal cortical dysplasia (FCD) is a developmental disorder frequently linked to drug-resistant focal epilepsy, where surgical intervention is often the most pro... |
58dc71ba0aae0ddb95c8c83f0e36de3a4fb7d0ef990b0e22bdad341040922c4f | Text | 5,220 | 33 | # Code supplement to the LRRK2 MRI study
[](https://lbesson.mit-license.org/)
[]([https://doi.org/10.1101/2025.03.09.25323610](https://doi.org/10.1101/2025.03.09.25323610))
This rep... |
6286eea9bd209268af2a68a897afc807848f0a9dbe98984909212f5421813f96 | Text | 5,250 | 48 | # Summary
This repository provides the complete dataset associated with Ding, Tran, et al. (2026) published in *Nature Neuroscience*: **Functional bipartite invariance in mouse primary visual cortex receptive fields** (https://doi.org/10.1038/s41593-026-02213-3).
In this study, we leverage the inception loop paradig... |
6f4e1b6c547d3f762c1a4f45019aa60f99ded6a59230050064ff12a7692c612e | Text | 5,260 | 113 | # mc_analysis
A Python package for simulating and fitting pulsatile time-of-flight resolved BFI measurements from MCX `.mch` files, with support for brain sensitivity analysis computations.
This is designed to accompany the paper: "Monte Carlo simulations of time-resolved blood flow index: times-of-flight beyond ~1 n... |
d0b823256dc312e51f2558224e772e6c0c085b4b820505a0b300c0414563e5c4 | Text | 5,278 | 102 | # Sim_Funcky_Pipeline
Sim_Funcky_Pipeline is a pipeline designed to preprocess BOLD Functional MRIs for visualization and further analysis. This tool also calculates the average signal intensity per ROI in a given volumetric atlas and returns a pairwise similarity matrix.
## Overview
The preprocessing pipeline clos... |
4e52c3a92fc5510a61b762ba247488ddf02e659eefcdbdc0937182ba29c41720 | Text | 5,287 | 173 | # 🧠 ConvoReleNet – Hybrid Deep Network for Motor Imagery EEG Classification
This repository contains the official implementation of **ConvoReleNet**, a hybrid deep neural network combining **Convolutional**, **Transformer**, and **Recurrent (BiLSTM)** modules for **Motor Imagery EEG (MI-EEG)** classification.
The co... |
ee3f2fb385d57b612baed572572e82b3b6363207d75ea50cef4319c6d030e8cd | Text | 5,301 | 138 | # Generalized Deep Diffusion-Weighted Imaging (DeepDWI) Reconstruction Framework
## Introduction
DeepDWI implements self-supervised learning image reconstruction techniques for DWI.
<p align="center">
<img alt="Light" src="figures/motion/gif_diff/motion_diff.gif" width="100%">
</p>
<p align="center">
<img alt="... |
245b47068ebf2d65439a20a998a55be8600bdc74697b8b3ea2ac52bac2b5b330 | Text | 5,304 | 100 | # SafetyHelmetWearing-Dataset(安全帽佩戴检测数据集)
Safety helmet (hardhat) wearing detect dataset(安全帽佩戴检测数据集, SHWD). We also provide pretrained models.
## Introduction
SHWD provide the dataset used for both safety helmet wearing and human head detection. It includes 7581 images with 9044 human safety helmet wearing objects(pos... |
ced4ef65113bf9811442efa6770ad2738e61f824918a6a5ccf9b3b57aa20337c | Text | 5,355 | 109 | # BrainAlignNet
BrainAlignNet is a deep neural network that registers neurons in the deforming head of freely-moving C. elegans. This repository contains the source code for data preprocessing, as well as network training and testing.
## citation
To cite this work, please refer to our preprint:
**Deep Neural Networks... |
573bb8f0fa725b28c87f0780997d19796f65879e41fbf74938d471f209d4b33d | Text | 5,377 | 105 | # DeepGO-SE: Protein function prediction as Approximate Semantic Entailment
DeepGO-SE, a novel method which predicts GO functions from protein
sequences using a pretrained large language model combined with a
neuro-symbolic model that exploits GO axioms and performs protein
function prediction as a form of approximate... |
ca0a983c332f7fe814c81b2ccb0c420cb8f7b2183a89aad844580bcb8ebae6ef | Text | 5,437 | 124 | # Hierarchical distribution of reward representation in the cortical and hippocampal regions
This repository contains the Jupyter Notebooks and associated code used for the analysis in the paper "Hierarchical distribution of reward representation in the cortical and hippocampal regions" (Soma, Okamoto et al.).
##... |
d320de6bbcf3980be918e9075e02078a7d11d849bd4a0f7fcdcd73bd7f2d4e48 | Text | 5,443 | 121 | 
[](https://www.python.org/downloads/release/python-390/)
[](https://www.python.org/downloads/release/python-3100/)
[.
## 1. R files
The following R scripts are available
- ... |
5b81bd7b1cb1f7db9aacc1d1f9e85d32b4849cb249953a0bc9af66ca7f836e44 | Text | 5,483 | 106 | [](http://www.brain-score-jenkins.com:8080/job/vision/job/vision_unittests_daily/)
[](https://brain-score.readthedocs.io/en/... |
4752f1db3c0b9037b3321bfc5a2dab3c91e7978f042802da4e2fc88c00efe632 | Text | 5,487 | 61 | # FW-DTI-Beltrami
## Authors
Golub, Marc; Universidade de Lisboa Instituto Superior Tecnico, Institute
for Systems and Robotics, Department of Bioengineering
Henriques, Rafael; Champalimaud Centre for the Unknown,
Champalimaud Neuroscience Programme
Nunes, Rita; Universidade de Lisboa Instituto Superior Tecnico, Ins... |
37fb5dbdf6d6c7beb839c395c16a3c238c4189ef45aad62d642dcec067284bad | Text | 5,492 | 163 | # Visual Search in Virtual Reality (VSVR)
This repository contains the code for the visual search reinforcement learning model described in the paper "A resource-rational account of human eye movements during immersive visual search". The codebase implements a meta-MDP framework for modeling visual search behavior in ... |
c5b243449187a109bab7c3a3ec72d8d3402269bde0ac3bee242a8f8917e95c3e | Text | 5,503 | 81 | ## Multimodal Medical Image Fusion To Detect Brain Tumors
Images are the largest source of data in healthcare and, at the same time, one of the most difficult sources to analyze. Clinicians today must rely largely on medical image analysis performed by overworked radiologists and sometimes analyze scans themselves. C... |
a309cc19711707facce3533e288e9286fbbd1654c2b7119c9656b5e7a9b9bc8b | Text | 5,512 | 83 | # CortexModel-Learning
## Overview
A rate-based circuit model of layer 2/3 mouse V1 incorporating excitatory and inhibitory neuron populations to investigate adaptation during simple forms of learning described in [Reference placeholder]. This repository accompanies the manuscript and provides both a reference implem... |
08bcd2f261fadf809913d56a84d20ec4d14f39317574ae4eb6157c31fc63c507 | Text | 5,534 | 61 | <img width="303" height="102" alt="neuroesc_long" src="https://github.com/user-attachments/assets/e185a933-e27d-4436-ab1f-52a4fe389e38" />
# Tolman_review_data
Data and analysis code for:
>[Duvelle and Grieves (2026) Tolman’s Sunburst Maze 80 years on: A meta-analysis reveals poor replicability and little evidence f... |
70a8ea716fe6feb7bab3528b69f35b43c41853576515c6e42684dcd2d40c806d | Text | 5,539 | 148 |
<!-- README.md is generated from README.Rmd. Please edit that file -->
<p align="center">
<img src="inst/art/logo.png" alt="Logo" style="width: 50%;" />
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[](https://www.r-project.org/)
[. Human Beta Oscillations Reflect Magnitude and Fidelity of Priority Shifts in Working Memory. *Journal of Neuroscience*.
## Overview
This repository contains MATLAB code to reproduce the an... |
b0c45f57fb44168d9a99938afa732005ab99711fbe49babfc349fdb4d8e11201 | Text | 5,550 | 122 | # ADMET-AI
[](https://badge.fury.io/py/admet_ai)
[](https://badge.fury.io/py/admet_ai)
[](https://pepy.tech/project/admet_ai)
[ for more details, including:
- A larger dataset
- Additional contrast phases
# KiTS19
The official [2019 KiTS Challenge](https://kits19.grand-challenge.org) repository.
## Usage
To get the data for this challen... |
f84f757959aae334a796d152c7ffe1ca34b1ebf8e6155e2511107df17304677c | Text | 5,562 | 83 | # WormTracker3000
The ultimate Bryant/Hallem Lab worm tracking software system.
Designed for tracking worms in thermotaxis assays, chemotaxis assays, and custom linear behavioral assays. See `Code Description.m` for a description of the code functionality.
## Table of Contents
1. System requirements
2. Installation
... |
952d0aa8822818146eb8a4fcf52b81664ad2242fcd229a9713ceef688c42ceb2 | Text | 5,576 | 58 | Winnowmap
========================================================================
Winnowmap is a long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences. Winnowmap development began on top of [minimap2](https://github.com/lh3/minimap2/) codebase, and since then we have... |
902990020d0a23ca3c57844d792875567f8b1d455539de8c32c94f5dd4493a44 | Text | 5,580 | 131 | <img alt="Zennit-Logo" src="share/img/zennit.png" width=500>
[](https://zennit.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/chr5tphr/z... |
68b4a1552dfd8fd010b0ca487709718eebed7c451f9390f116bc8f0f54ef31a4 | Text | 5,600 | 43 | # Base_barrier_cells
## About
The choroid plexus (ChP) is a highly understudied structure of the central nervous system (CNS). The structure hangs in the brain ventricles, is composed of an epithelial cell layer, which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. It encapsulates a stromal m... |
2479a61329863a06078eefcb9d196264fff1576c28de0c0f343c69dbbc08f1a1 | Text | 5,604 | 110 | # AirwayDisNetPublic
## 1. Project Overview
**AirwayDisNetPublic** is a deep learning–based research framework for airway management.
It aims to achieve intelligent recognition and decision support for difficult airways through the integration of multi-plane ultrasound imaging models.
The core concept introduces a ... |
248958fe901c41d7ea75df58ed3e4feb6d918ff80d45d86e13657e7d22de14fc | Text | 5,645 | 180 | ============================================================
Feature Extraction and Classification Pipeline
============================================================
OVERVIEW
This repository contains MATLAB code used for feature extraction and
tumor grade classification described in "Qualitative and quantitative... |
de2fbfa7abb20f0dbab941821d2bf9343212919fb93754b803b0042412abdaf6 | Text | 5,652 | 81 | # A 7T fMRI dataset of synthetic images for out-of-distribution modeling of vision
Here we provide the code to reproduce all results from the paper:</br>
"[A 7T fMRI dataset of synthetic images for out-of-distribution modeling of vision](https://doi.org/10.1038/s41467-026-69345-9)".</br>
Alessandro T. Gifford, Radosla... |
146304e2336d243728483f74a092954195a0a6d28cfcc8ffd282e377fa1a6770 | Text | 5,677 | 45 | # Brain morphometry and cognition as predictors of IBS
INITIATED: [Arvid Lundervold](https://www.uib.no/en/persons/Arvid.Lundervold), 2024-10-21
[Code](https://github.com/arvidl/ibs-brain/tree/main/notebooks), [data](./data), and [images](https://github.com/arvidl/ibs-brain/tree/main/data/BGA_046) accompanying the pa... |
99d41dcfbdba2882c5bd6da5166ea775c791eb5ef7bd103eac7e01fe2a3457c5 | Text | 5,707 | 130 | # A comparison of automatic cell identification methods for single-cell RNA-sequencing data
We present a comprehensive evaluation of the performance of state-of-the-art classification methods, in addition to general-purpose classifiers, for automatic cell identification single cell RNA-sequencing datasets. Our goal is ... |
ce1611bc4f06a4110a3a6263246153824187d409378b5460bd67924cdc0395cb | Text | 5,728 | 81 | # Hamster.jl
[](https://github.com/mschwade-code/Hamster.jl/actions/workflows/runtests.yaml)
[](https://codecov.io/gh/TheoFEM-TUM/Hamster.... |
7b7adc548bdf6e111ebb77b9351dfc02e1ea592d5043f244669725b224251c2d | Text | 5,732 | 114 | --- CONGRADS --------------------------------------------------------------------------
Developed at DCCN (Donders Centre for Cognitive Neuroimaging), Donders Institute for
Brain, Cognition and Behaviour. Radboud University, Nijmegen, The Netherlands
Authors: KV Haak, AF Marquand, CF Beckmann
Congrads is a data-dr... |
df245c0cea36f2b97d3bcb07656bd89525b942dd16f1c8d78e9745d020e9d811 | Text | 5,768 | 107 | # wfield - tools to analysis widefield data
This is a python package for visualizing and analysing data collected with a widefield macroscope.
#### Use the graphical interface to [launch analysis on NeuroCAAS](usecases.md)
### These tools are for:
- Motion correction
- Data redu... |
932e6181fe17a02f96ac559663fc49c9fcfcd0012867c0a93d4601b3b496f02a | Text | 5,802 | 106 | # Developmental Brain Age
This repository contains the release of the model developed for predicting brain age in developmental samples, created in:
> Citation: Drobinin, V., Van Gestel, H., Helmick, C. A., Schmidt, M. H., Bowen, C. V., & Uher, R. (2021). The developmental brain age is associated with adversity, depr... |
e0c4e59f77a5f105d1ef996890d89ee2992349a712705c13c24e703d67983e1d | Text | 5,817 | 78 | # pyPET - A Python library for the analysis of positron emission tomography (PET) data
Author:
Samuel Kuttner<sup>1,2</sup>, PhD, Medical Physicist
<sup>1</sup>PET Imaging Center, University Hospital of North Norway
<sup>2</sup>UiT Machine Learning Group, Department of Physics and Technology, UiT The Arctic Univer... |
c44c9e54c3e1e05b7baac3ebb825347a602125ecaf00dfc435dcf6b402a9c5bb | Text | 5,823 | 93 | # EEGpal
EEGpal is open-source, Matlab-based software designed for the automated or semi-automated pre-processing and analysis of EEG data.
It proposes Graphical User Interfaces (GUIs) that allow EEG pre-processing to be batched across participants with a high degree of flexibility in processing parameters.
It include... |
9f03357a658f3656c7a46d56644505f413fb3eb97e50ff0c83546180104a5b94 | Text | 5,857 | 82 | # ``LYN-track-and-trace`` -- A package to analyze yeast microscopy data
This package is designed to analyze microscopy data of yeast cells. It provide algorithms for tracking and lineage tracing of yeast cells. It also provides a graphical user interface to visualize the data, and the performing various lineage tracin... |
c0ea7e5a52abcbb7ab02591cb8f987595e8922e069445703bf38dbf69c29dbd9 | Text | 5,892 | 115 | # SphereGlue: A Graph Neural Network based feature matching for high-resolution spherical images
## Abstract
Traditionally, spherical keypoint matching has been performed using greedy algorithms, such as Nearest Neighbors (NN) search. NN based algorithms often lead to erroneous or insufficient matches as they fail to ... |
49974cba943699e5122af31070011f405a9b3db227521c455b28e1c0bf5a4e3c | Text | 5,917 | 80 | # neuro-static
Static networks for neural population prediction
## Short model explanation
Model has 4 components:
* core: Receives image, passes it through some convolutional layers. Input is H x W, output is H x W x C
* shifter: Receives eye position and computes expected shift for all cells. Input is a tuple, outpu... |
a8d79925136d856907c668460b527bee72b8c30109698c86ce6d033699914628 | Text | 5,941 | 117 | Coronary Plaque Segmentation Using nnU-Net
This repository accompanies the publication and provides the trained nnU-Net model and evaluation notebooks used in our study on automated coronary plaque segmentation in CCTA. The goal is to enable reproducibility and to support researchers who want to apply and finetune our... |
48a33b7fcea99912baf17caf9ee540539bf8cf087ea913f538a359e519ae12ba | Text | 5,958 | 164 | peaks. Copyright (c) 2020. Winfield Chen.
The peaks software repository, implementing the cluster identification methods described in *An expanded set of genome-wide association studies of brain imaging phenotypes in UK Biobank*. Operating on summary statistics for many phenotypes, this work clusters lead associations... |
008202c1184e2830b74f9cc761ffa28206823dcaee781c0458eadd0d3c249687 | Text | 5,972 | 85 | # Fibrosis-Net #
<p align="center">
<img src="assets/fibrosisnet_logo.png" alt="FibrosisNet Logo" width="25%" height="25%">
<br>
</p>
**Note: The Fibrosis-Net model provided here is intended as a reference model that can be built upon and enhanced as new data becomes available. It is currently at a research stage a... |
5d57a1a04e9fe372e31bd6a749e12d34685d94fcc02eb81b89dfad66995554b9 | Text | 5,973 | 131 |
## 1) Where to find the data
`/data` contains two subfolders with the same content in two formats:
data/
geojson/ # spatial + attributes (for the web map / GIS)
csv/ # attributes only (for spreadsheets / scripts)
### Why two formats?
- **GeoJSON** (`.geojson`): self-contained spatial features. Coordinates are **[... |
245341f3bc5537c6785529fe9021ece2a195641c418412e01c6ee810f89cdc43 | Text | 5,977 | 41 | # Synaptome architecture shapes regional dynamics in the mouse brain
This repository contains code and data in support of "Synaptome architecture shapes regional dynamics in the mouse brain", available as a preprint on [bioRxiv](https://doi.org/10.1101/2025.01.24.634803).
Most of the code was written in Python 3.8.10, ... |
bbcbef8439e0cad07bcef7487e926cae35ffa8e142892086ab9862f2743d32b8 | Text | 6,007 | 158 | # Lasagna - Python Volume Visualiser for 3-D data. #
## Concept ##
Lasagna a lightweight platform for visualising for 3D volume data developed for the [OpenSerialSection](https://... |
3c850c240928968be74d84bb0505996615eae64e33bdf09a6338340dbd2be9cb | Text | 6,013 | 74 | <img src="/../../../../bbuchfink/diamond-data/blob/main/diamond_coat_of_arms2.png" height=280>
Introduction
============
DIAMOND is a sequence aligner for protein and translated DNA searches,
designed for high performance analysis of big sequence data. The key
features are:
- Pairwise alignment of proteins and tra... |
c2a23792403be25d7b6e471bd234d6e1723ed9cc4a4b920d3f3397b5cd52b86f | Text | 6,026 | 133 | 
Draw-EM (Developing brain Region Annotation With Expectation-Maximization) is a package of [MIRTK](https://github.com/BioMedIA/MIRTK) developed by Antonios Makropoulos and the [BioMedIA](https://biomedia.doc.ic.ac.uk/) research group.
It provide... |
427659b7d52adbd4fc9f56792508c20ff9148b0e95d681a5102c74a07f102cd8 | Text | 6,117 | 181 | 
Tracer diffusion in the brain
-------------------------------
We model tracer transport in the brain tissue over 72 hours. The total gadolinium concentration, $c(x, t)$ (amount per brain volume in mmol/l) at position $x$, and time $t \in [0, 259200]$ (in s), satisfies
``... |
6680f026abfb488ec6c0de1d5793ae9cdbdea417d2a39203d3b4341f4e2ac5e1 | Text | 6,124 | 132 | # LUPE 2.0 Analysis Package
> 💡 **Looking to use LUPE with a graphical interface instead of coding?:** Check out the [LUPE 2.0 App](https://github.com/justin05423/LUPE-2.0-App).
This companion Streamlit application requires minimal coding experience and allows you to run LUPE through an interactive interface.
<p a... |
371bf658412582460e546574ee92347d1520207fba324baf0e895c4a6c271c75 | Text | 6,126 | 130 | # SMIntegration : Spatial Multi-omics Integration Platform
## Introduction
**SMIntegration** is an innovative open-source platform for integrated analysis of spatial transcriptomics and metabolomics data. It integrates spatial pattern recognition, differential comparison, network construction, and functional annotation... |
ab889aeea82d29bb67d523a08d8398683a72e44c1fa7ffe8213c26a7d4b5535c | Text | 6,130 | 276 | # A Fast Synaptic Parameter Estimation Method
### Fast Calculation Scheme Based on Second-Order Moments
---
## Overview
This repository provides the MATLAB implementation of the fast synaptic parameter estimation method described in:
> **Fast calculation scheme based on second-order moments**
The proj... |
1dc62e27327e7700b2026e53f738aab2b888e996aa3d9aae48303fd38990a209 | Text | 6,153 | 245 | # methylkey: DNA Methylation Analysis from Illumina Arrays
[](https://zenodo.org/badge/latestdoi/139563728)
`methylkey` is a Bioconductor package for comprehensive analysis of DNA methylation data from Illumina methylation arrays. It supports multiple platforms (27k, 450k... |
569b6d331a53aa72fc2f113a29d5c7233224c4f698bcd92d0f33671d654dec34 | Text | 6,153 | 114 | # Freely Moving Animal (FMA) Toolbox
## Introduction
The purpose of the Freely Moving Animal (FMA) Toolbox for Matlab is to help analyze electrophysiological and behavioral data recorded from freely moving animals.
These data typically include broadband brain signals (e.g. local field potentials), spike data (timest... |
43c0bc8dc4e35bfcad24bb4cd74c7a0b9268086829906fe8894198dc46df3193 | Text | 6,155 | 203 | # The-Long-Range-Depth-Estimation
This project is a derivative work based on [Monocular-Depth-Estimation-Toolbox](https://github.com/Ma-Zhuang/DepthFormer),
which is licensed under the Apache License 2.0.
## 📖 Introduction
**Monocular depth estimation**, a cost-effective solution for reconstructing 3D structures f... |
df8d9af3a3f1e5db2e8b002cc4ec9820acc001727c0358cdbef1d77735d7d2c8 | Text | 6,158 | 236 | # H-FNO-MultiPhysics
[](https://opensource.org/licenses/MIT)
[](https://www.python.org/downloads/)
[](https://pytorch... |
8c2f56462dc082026d6dc8b68ab3bd855e1fa2eaf2514c3b4d3766155d9e7ab2 | Text | 6,175 | 76 | # The representation of emotion knowledge in hippocampal-prefrontal systems
It is well established that humans conceptualize emotion concepts in a low-dimensional space that resembles a map. For the most part, this map is organized using two-dimensions that reflect the pleasantness and arousal experienced during events... |
807e9799ead396713701a5aaa0c025fc3f483cbc71dc337448b9225de02eb4e3 | Text | 6,182 | 78 | # Map-like representations of emotion knowledge in hippocampal-prefrontal systems
It is well established that humans conceptualize emotion concepts in a low-dimensional space that resembles a map. For the most part, this map is organized using two dimensions that reflect the pleasantness and arousal experienced during ... |
315c5f2ec89d8f5a0c663db702d218ec6b57ef63610206fdffaad39d8cc43ce3 | Text | 6,196 | 96 |
# ContrastiveLosses
Implementations and examples of use cases of loss functions used in contrastive representation learning. The loss functions are found in contrastive_losses.py.
Implemented in TensorFlow, orginally for use in genetic data, here shown for other applications as well.
### Computational Environment
... |
5a748541184b4eeb19fad97977d792923e3d1946e586d9536f71ac78d32fabcf | Text | 6,200 | 140 | # MMSplice & MTSplice
[](https://circleci.com/gh/gagneurlab/MMSplice_MTSplice)
[](https://pypi.python.org/pypi/mmsplice)
Predict (tissue-specific) splicing variant effect from VCF. MTSplice... |
d1de65ac1ecd55bd67644b14bd6e4d560a192e4dc0f7ef59388e80a18df06d07 | Text | 6,211 | 173 | # SingleCapillaryReporters
A MATLAB tool for detecting and analyzing capillary segments in ultrasound particle tracking data using Hidden Markov Models (HMM).
## Overview
SingleCapillaryReporters (SCaRe) automatically identifies capillary segments from ultrasound particle tracks by analyzing velocity patterns and sp... |
b6e6de2ebae563e26268400c89762522e99326b6c40c556179a4c66906921ebb | Text | 6,259 | 98 | Handwriting Imagery EEG Dataset
1. Dataset Overview
This dataset contains electroencephalogram (EEG) recordings from participants performing handwriting imagery tasks, including two sub-tasks:
CCS: Chinese character strokes imagery (imagining the strokes of writing Chinese characters).
SV: Single vowels imagery... |
3c211c3788c5eb611f5a0dde34da83d87f9b1e758831073f180058e1b97bc3a2 | Text | 6,261 | 96 | # learning-metacontrol
This is code for the publication, "Understanding human meta-control and its pathologies using deep neural networks" (Kai Sandbrink, Laurence Hunt, Christopher Summerfield). Preprint: https://osf.io/preprints/osf/5ezxs
### Instructions
The main and supplementary figures are generated from the "... |
91abc6ac132c9fdb29149aae41db255d475bf6f82b1f1618bdd4d42cbdde300d | Text | 6,262 | 89 | <div align="center">
<h1>cell-seek 🔬</h1>
**_One single-cell pipeline to rule them all!_**
[](https://doi.org/10.5281/zenodo.10181524) [![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/OpenOmic... |
31853254bb8c327d8837535b9218b4f7ad8a4faab6ebbe3845826d92f6779e51 | Text | 6,265 | 199 | # AI-Assisted 3D Segmentation of FIB-SEM Images
*A simple and accessible framework for training and evaluating deep learning models on 3D electron microscopy data.*
This repository provides Python code, pre-trained models and example datasets to help you train and test several neural networks for the 3D segmentati... |
f8ab67b4bfc8e79eb8960c7e4f1587cf11154760885038855670fb8a2b2aaa3f | Text | 6,272 | 90 | #################################################################################################################
# - Readme: Demo code ripple detection is affected by 1/f noise
#################################################################################################################
Author: Frank J. van Sc... |
9e680a789e3fea1bdbcd44924607df0fdace6d2a6e3e884a57be9eb4d7535d60 | Text | 6,276 | 74 | # CNN-Cone-Detection
Please cite this paper if you use any component of this software: D. Cunefare, L. Fang, R.F. Cooper, A. Dubra, J. Carroll, S. Farsiu, "Open source software for automatic detection of cone photoreceptors in adaptive optics ophthalmoscopy using convolutional neural networks," Scientific Reports, 7, 6... |
a88b9de3f8294cdef0fe836581948033dc95d248e98c510304207a96419b82e5 | Text | 6,276 | 167 | # trRosettaX2-Dynamics: **Generating dynamic structures through physics-based sampling of trRosettaX2-predicted inter-residue geometries**
Overview
----
[](https://www.python.org/downloads/) [ and several packages available through Bioconductor and CRAN.
> ## Update (01/15/2024)
> We're e... |
d6deb77fb05111eddbaa331e08a4514a4515694030d7869b49e3dcda73076a8a | Text | 6,335 | 78 | # D-P foundations
Source code, datasets, and instructions for reproducing the results of our paper 'Cell atlases and the Developmental Foundations of the Phenotype'.
### Developmental and phenotypic gene expression matrices
`matrix_creation_codes` folder - Code to create the developmental gene expression matrix (usin... |
ca430a4355f1f67a3296b5030cf60dc1bfef781ed938d6667a444c92e55e2404 | Text | 6,358 | 69 | # <center>CLASTER
## <center> Modeling nascent RNA transcription from chromatin landscape and structure <center>
## Abstract
_Different cell types and their associated functionalities can emerge from a single genomic sequence when certain regions are expressed while others remain silenced. The study of gene regulatio... |
da49149595bb92fd68cf0ef38b0d1872669aa7f0f5bb2347f154528af2dacdf9 | Text | 6,368 | 186 | # S^2potAE
## S²potAE: A Spatial Spot Autoencoder for Robust Spatial Transcriptomic Deconvolution
**Presenting S²potAE, a novel autoencoder framework integrating gene expression, spatial coordinates, and histology images for precise cell-type deconvolution in spatial transcriptomics.**
To address the... |
4791ff7b0f0744fc6c7705e0ecbc6c9dbb5b0dcda03f4fcabdca232d0fa63969 | Text | 6,376 | 170 | # An Electroencephalographic Study of Sleep Spindle and Infraslow Oscillation in Children with Autism Spectrum Disorder
This project provides a structured pipeline for analyzing infraslow oscillations (ISO) in EEG recordings obtained during Non-REM (NREM) sleep. The analysis focuses on characterizing the ISO spectrum,... |
b1e3ea5900d3ceb46fcd90c0e0d17207b68eb64e40df6f66ed84e1d15d82cfee | Text | 6,442 | 210 | # HarveST: Heterogeneous Graph Learning Framework for Revealing Spatial Transcriptomics Patterns
HarveST is a comprehensive Python package for spatial transcriptomics data analysis that combines graph neural networks with attention mechanisms for spatial domain identification and spatial variable gene discovery.
](https://github.com/Olink-Proteomics/OlinkRPackage/actions/workflows/R-CMD-check.yaml)
[](https://github.com/BiomedSciAI/causallib/actions/workflows/build.yml)
[](https://codeclimate.com/github... |
f3b010ea23fd2eaa45d56e104ff9d0f90f5e88f8c7e20d5a040efd7574eacdda | Text | 6,673 | 87 | # CellTalkDB v1.0
### A manually curated database of ligand-receptor interactions in human and mouse
__Note: a backup website can be stably accessed through [https://xomics.com.cn/celltalkdb/](https://xomics.com.cn/celltalkdb/) in case that the [raw website](http://tcm.zju.edu.cn/celltalkdb/) has to be off line for s... |
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