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ceb6fe4562ee6b257b5555e2128e2f8c09d608181d8654f7dd38698476b0da8d | Text | 825 | 26 | # Fiber Photometry Data Analysis for Ucn
## Introduction
This repository contains the analysis pipeline for fiber photometry experiments conducted to monitor the activity of Urocortin-expressing Edinger Westphal neurons in vivo.
The code includes two parts:
- Z score analysis
- Area under curve calculation
#... |
a4a1a973a7407964729d176fc3be067837343a71d66abf24710ca927dda5b7cd | Text | 831 | 16 | rayshubskiy_elife_102230_secondary_analysis_code
===
Secondary repository with python-based codebase for 'Neural circuit mechanisms for steering control in walking Drosophila' Rayshubskiy A. et al., 2020 eLife
Primary repository with matlab code: https://github.com/SashaRayshubskiy/eLife_102230_analysis_code
See pape... |
b58f87de5b627372b7221139840c73ec18a59cecd0b2b3513e579a5945c27412 | Text | 855 | 25 | # SCAN paper analysis scripts
If you are using this repo please cite:
```
Gordon, E.M., Chauvin, R.J., Van, A.N., Rajesh, A., Nielsen, A., Newbold, D.J., Lynch, C.J., Seider, N.A.,
Krimmel, S.R., Scheidter, K.M., et al. (2023). A somato-cognitive action network alternates with effector regions
in motor cortex. Natu... |
ef87b9fb1e60b08a494fefbfa81f5012ca98f40b8f902cb8f1be22cf2aa4eae1 | Text | 888 | 20 | # Relating natural image statistics to patterns of response covariability in macaque primary visual cortex
**Farzmahdi A, Kohn A, and Coen-Cagli R (2025)**
Nature Communications 16:6757
This repository contains the code and analysis scripts used to generate the main figures of the manuscript.
Each script corresponds... |
da878e46867724dbbe4fd82b455b749fea46d878e7419da892c6c7b14136b655 | Text | 890 | 28 | ## Introduction
The code is implemented based on https://github.com/open-mmlab/mmdetection.
## Change
The main change is located in mmdet/models/dense_heads/rpn_head_nwd.py.
## Train
```
./train.sh
```
## Dataset
The dataset AcneSCU could be accessed via connection to jiangxian@scu.edu.cn
Please note that AcneSCU... |
8768435fd574592d82e642f31b89e28cc112885b8038361a6e611f9a0a6a57c4 | Text | 915 | 17 | # MaxEntNucleotideBiases
[](https://adigioacchino.github.io/MaxEntNucleotideBiases.jl/stable/)
[](https://github.com/adigioacchino/MaxEnt... |
7cdfe5771cf406f8639c13dcba8b0b5eb7a940dede9c5177d04e734cb7300d52 | Text | 920 | 8 | # SpikeNet1.o
This is a general spike detector to identify interictal epileptiform discharges in EEG. This code demo accompanies this manuscript "Development of Expert-Level Automated Detection of Epileptiform Discharges During Electroencephalogram Interpretation”. The paper is included in this repository (SpikeNet_201... |
2802e18baf3c200d68db15f3b5acf71acb50b6b7299f2905554d33d17afe5d77 | Text | 936 | 15 | # WTools
A Matlab® based toolbox for time-frequency analysis.
**IMPORTANT**: This code is outdated and no more maintained: please check [WTools v2.0](https://github.com/cogdevtools/WTools/tree/v2.0)
## Structure
* Folder "sh" contains all the functions to run the toolbox
* Folder "chans_splines" contains the channel... |
ef888f9bc0f28511d1b783cc8ccaa8b461473c9d720af6ed913b1dedc52dbdc8 | Text | 941 | 23 | <!--
SPDX-FileCopyrightText: Copyright 2024 German Cancer Research Center (DKFZ) and Institute of Radiology, Uniklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU).
SPDX-License-Identifier: CC BY-NC 4.0
-->
# Thoracic aorta assessment in (abbreviated) breast MRI
## License & Copyright Notices
... |
6a0981c8b65f1fe3f668a76ceade998f0b59808c6dc532473749e7c651bee640 | Text | 949 | 8 | # InteractiveStimInterface
Accompanying (Matlab) analysis code for the behavioral data that was collected for this publication: https://doi.org/10.1101/2024.03.08.24303392.
In this experiment, 3 human participants with tetraplegia controlled their own brain stimulation parameters to evoke sensations for their digital ... |
2603f329a3a8f590adde5703d17bdf41075b2624816191e4bbb37c0418782fef | Text | 957 | 12 | # ssdi
An implementation of Dynamical Independence computation and optimisation for linear state-space systems, as described in:
L. Barnett and A. K. Seth, _Dynamical independence: Discovering emergent macroscopic processes in complex dynamical systems_, [Phys. Rev. E **108**, 014304](https://journals.aps.org/pre/abst... |
0533386f68ddc9001ca6a20e58c3b66eddd73e40cbc2d151f85801641065e0b0 | Text | 965 | 24 | # The World Atlas of Language Structures Online
[](https://github.com/cldf-datasets/wals/actions?query=workflow%3ACLDF-validation)
## How to cite
If you use these data please cite
- the original source
> Dryer, Matthew S. ... |
450860e6a1291b465b8969ecc5b44c4b3ca9083df3b61313e9b19328efd03896 | Text | 966 | 19 | # eyemap_T4
R code for "Eye structure shapes neuron function in Drosophila motion vision"
Tested with R 4.4.1 and Rstudio 2024.12.1.
R packages are versioned using renv:
https://rstudio.github.io/renv/articles/renv.html
Suggest start with copying this repo and run `renv::restore()`
Estimated installation time: 3... |
08566a63b0b3cc52fffbecd846ece5eb55469d101c4b4a1213230d65002d62c4 | Text | 983 | 17 | Prediction of melting points
This git repository contains the Supplementary Information to the publication “Prediction of melting points of chemicals with a data augmentation-based neural network approach”:
• main.py
• mygraphconvmodel.py
• Data folder containing all datasets used in the study and the corresponding... |
ca2b65f1d556bba498cd7f7e051e167496996e2131f9c52988e2c4758a2bad17 | Text | 983 | 23 | # ARE (AI-based Review Enhancement)
## Development of meta-prompts for Large Language Models to screen titles and abstracts for diagnostic test accuracy reviews
A preprint manuscript.
https://www.medrxiv.org/content/10.1101/2023.10.31.23297818v1
## Preparation
Users have to prepare the API of OpenAI or Microsoft Azure... |
aed9b045be238a6a0c572be02b4add8ee4a5fe21212f54d146782f0e4056b9ce | Text | 984 | 18 | This code is to analyze the rat in vivo electrophysiology data for the acute ethanol manuscript
getDistAndVelBins.m extracts distance traveled (cm) and velocity from AnyMaze AUX channels in ephys recordings.
This then gets used by ratAcuteEthanol.m to generate graphs using getAnimalDist.m to do
some basic transforms a... |
c98b035dca5f9acdae205c882a2250fa7c18e593f0d92266fe2e362b5eb4881a | Text | 997 | 31 | # brainstorm: Personal Utility Functions <img src='man/figures/logo.png' align="right" height="139" />
The `brainstorm` package houses personal utility functions which I reuse in my R scripts. Please note that this package remains under development.
## Installation
`brainstorm` is designed for the [R](https://... |
d877c03abe34a1d29209f6c326aaaa00974d64a2ba64975ee98a4c8acd99e503 | Text | 1,003 | 30 | 1. GA optimization
Main_GA_neuromechanical_collaborative_body_body.m
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Evalutation of optimized results
opt_func_eva_quasiStatic.m
plot_muscle_deformation.m
plot_membrane_potential.m
animation_script... |
636f49925d9d85b003d07c1ec69e43303a544a166b855f6eb6ad6cb32e71e67a | Text | 1,005 | 11 | # Casp1Aldh1l1-scRNAseq
R code and relevant files used for the analysis of hippocampal scRNAseq data from Casp1(fl/fl) Aldh1l1-CreERT2(+/-) mice and littermate controls.
The raw data from the sequencing run are too large to upload here and will be posted elsewhere. These files are necessary to run the code from the ve... |
ebc6120ab17f8a7f28f1436a742ef3353dbc077cceb5a1fb45d134dc9edfe72e | Text | 1,028 | 38 | # Neural Dynamics of Visual Working Memory During Sensory Distraction
This repository contains the complete pipeline to recreate the analysis and plots from the paper:
**"Neural dynamics of visual working memory representation during sensory distraction"**
*J. Karolis Degutis, Simon Weber, Joram Soch, John-Dylan Ha... |
7667649fad0bb8d1ea91328285ea84bab2eea673fd26f47f394ea6b6403caf89 | Text | 1,029 | 19 | # Mini Analysis Code
The mini_analysis code can be used to analyze spontaneous events in voltage clamp recordings in Igor. This code requires "justfilters". To run mini_analysis: `mini_analysis(startwave, endwave, starttime, endtime, level, plotflag)`. This function assumes that your waves are named "sweepX" where X i... |
9ee99a3973ca78c92e65ec43a5cb4d1ce26c698c12c65bfe0d7d0b991092e36c | Text | 1,030 | 13 | # A-neural-field-model-for-cortical-spreading-depression
Editors: Emre Baspinar (emre.baspinar@inria.fr) & Daniele Avitabile (d.avitabile@vu.nl)
Contact: emre.baspinar@inria.fr
Matlab code package for a neural field model for cortical spreading depression v1.0.0
This Matlab code package contains the implementation ... |
e642f4e49662f6c3768684b0537688819460f9458ebc1d020efe657c1420f11f | Text | 1,034 | 30 | 1. GA optimization
Main_GA_neuromechanical_collaborative_head_body.m
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Evalutation of optimized results
opt_func_eva_quasiStatic.m
plot_muscle_deformation.m
plot_membrane_potential.m
animation_script... |
c5886696ac9c37c2bab34a59eb09f920be3e66e40a8c1cda7429cb258f951e69 | Text | 1,055 | 6 | # Chiu2025_Persistence_BehavioralAnalysis
Code associated with "Cell type-specific contributions to a persistent aggressive internal state in female Drosophila" by Hui Chiu, Alice A. Robie, Kristin M. Branson, Tanvi Vippa, Samantha Epstein, Gerald M. Rubin, David J. Anderson, and Catherine E. Schretter. Code was run us... |
24df97fc61d3fb011f7b470ab9c22d968aa2fda75b4434ed5d56e01d245900b2 | Text | 1,101 | 23 | # Multimodal Single Cell-Resolved Spatial Proteomics Reveals Pancreatic Tumor Heterogeneity
## Datasets
- **Spatial Proteomics Dataset**: Provided as `xx.rds` and `xxx.xlsx`.
- **Cell Type Proteomics Dataset**: Included as `xxx.rds`.
- **Source Code for Data Processing**: Available in `xxx.R`.
## Figures and related ... |
95a7e9527272a600928c281f6bbbd02fa3a2b832bbb12eb6e0950ffa82c1f63e | Text | 1,113 | 34 | # TRF-Tools
Tools for data analysis with multivariate temporal response functions (mTRFs).
This repository mostly contains tools that extend Eelbrain but are not deemed stable enough to be included in the main release.
Includes a TRF extension of the Eelbrain `Pipeline`, documented [here](https://trf-tools.readthedocs.... |
3f88283e7dd2f7bfe489aaf749523e80db88175a83135f9f05371417eb4a4de6 | Text | 1,114 | 13 | # PVA-Ca-data-analysis-script
Python scripts and Jupyter notebooks for processing & graphing calcium imaging behavioral results acquired from PVA chronic pain project
## Items in the repository include
- A Jupyter notebook for running calcium trace preprocessing functions. `Calcium imaging - Trace preprocessing.ipyn... |
16491a2efe8db870f746fd34c2251d2aed888b5883c50ec42c5f7381e05db45c | Text | 1,119 | 6 | # VNC_scRNAseq
Analysis of scRNA-seq of the Drosophila melanogaster adult ventral nerve cord from females and males.
These data and analyses were published in "A single-cell transcriptomic atlas of the adult Drosophila ventral nerve cord" (Allen, Neville, et al., 2020), avaible [here](https://elifesciences.org/article... |
94b53fab32c48f7bb6b7bf91193d96a32cc8cb21a81223713936a81792b14ba1 | Text | 1,124 | 26 | # dmPFC_NoL
This code accompanies Levy et al., 2025, "Role for left dorsomedial prefrontal cortex in self-generated, but not externally-cued, language production". Relies on pre-existing VLSM (https://aphasialab.org/vlsm/), MLSM (https://github.com/atdemarco/svrlsmgui), and odds (https://www.mathworks.com/matlabcentral... |
ed0634c107ff74cae993538e9d930c163f9baf98a0fd3a8d2b5af3a4d39916cf | Text | 1,132 | 19 | The supplementary codes contains two parts, ```spiking_simulation``` for Izhikevich simulation on artificial neuronal networks, and ```goal_directed_network``` for spiking neural networks.
## spiking_simulation
The code is developed with MATLAB and can be run with MATLAB R2024b.
Please run the source code in the fo... |
3e3c90c30cf4a71455278cc6bb4da19a010a1a496ba6b38e8e6a1097e69d02c7 | Text | 1,152 | 13 | # Finger-BCI-Decoding
This is a repository of the scripts used for the study: “EEG-based Brain-Computer Interface Enables Real-time Robotic Hand Control at Individual Finger Level”.
Ding, Y., Udompanyawit, C., Zhang, Y., & He, B. (2025). EEG-based brain-computer interface enables real-time robotic hand control at ind... |
3b530728a6312d3b16340d2fdb88081107284480ac005ab504d8e3d4c5c4dbd8 | Text | 1,157 | 27 | # Simple controls exceed best deep learning algorithms and reveal foundation model effectiveness for predicting genetic perturbations
Daniel R. Wong, Abby Hill, Robert Moccia
correspondence: daniel.wong@pfizer.com
Machine Learning and Computational Sciences, Pfizer Worldwide Research Development and Medical, 610 Mai... |
086290996a9dfdd41bed13c1ccff257e28c5154aaa1facf259bacb1e58419d94 | Text | 1,169 | 33 | # Neural Interaction Detection (NID)
[M. Tsang](http://www-scf.usc.edu/~tsangm/), [D. Cheng](http://www-scf.usc.edu/~dehuache/), [Y. Liu](http://www-bcf.usc.edu/~liu32/). Detecting Statistical Interactions from Neural Network Weights, ICLR 2018. [[pdf]](https://openreview.net/pdf... |
adb568b39a4f9ae6b02463b7e8a7f5a900c72a6a45c27b42ee8fceecdde31c8b | Text | 1,199 | 23 | # tensor_regression
Pytorch functions for performing tensor regression. Still under development. Message me if you'd like to help in its development: RichHakim@gmail.com
These methods are very useful for regression of time series data. I use them to classify and predict neural and behavioral time series data.
## St... |
ecd1d574e8d2963be2316ea526aa688a7758edb0881bfa6297a33de2a484cec9 | Text | 1,205 | 15 | This repository contains the code developed for the paper "Light-microscopy based connectomic reconstruction of mammalian brain tissue"
Tavakoli et al., Light-microscopy based dense connectomic reconstruction of mammalian brain tissue, bioRxiv 2024.03.01.582884; doi: https://doi.org/10.1101/2024.03.01.582884
# Struc... |
6624184f31306fd3be102fd4d35fcebf91077e4cef84851c688a3c986589a278 | Text | 1,215 | 16 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Source data to reproduce key quantitative comparisons/analyses presented in manuscript: "The amyloid precursor family of proteins in excitatory neurons are essential
fo... |
11b5c372b2f3a4ea525b56663cec7c1069cf937e2be0254f6fa9f74b7b7d53a9 | Text | 1,258 | 34 |
The aim is to provide inference services for Dynamical Causal Modeling of Event-Related Potentials (ERPs) measured with EEG/MEG, using SATO Probabilistic Programming Languages (PPLs):
Numpyro: https://num.pyro.ai/en/stable/... |
26cb6dfef71612ac95d96a9e8fbf89988c9fb2246da04acabc2d2517fbb85fb6 | Text | 1,275 | 36 | # MR_CT_NW_MJ_2024
This repository contains the code and data to generate figures for manuscript "Computational basis of hierarchical and counterfactual information processing".
Link to paper: place_holder
## How to run
Different parts of the project was implemented with different programming languages.
To generate... |
922e3cfc48cc0e1388168657dec9430e8c3a2d303702a643e69641f4f952dd1c | Text | 1,279 | 3 | # Spiking multicompartment predictive coding network
Predictive coding is a promising theoretical framework for understanding the hierarchical sensory processing in the brain, yet how it is implemented with cortical spiking neurons is still unclear. While most existing works have taken a hand-wiring approach to creati... |
5f0cb3b5a4578c281d213bb63a675e93ac9c52a5f33cd98fbaa586900a2ab87a | Text | 1,281 | 46 | ===============================
GEOparse
===============================
.. image:: https://img.shields.io/pypi/v/GEOparse.svg
:target: https://pypi.python.org/pypi/GEOparse
.. image:: https://img.shields.io/travis/guma44/GEOparse.svg
:target: https://travis-ci.org/guma44/GEOparse
Python library to ... |
3ba0f11a65c35ef9d0852f363744965ffa224c28d465139d127ab3c75aa70e73 | Text | 1,297 | 11 | # Cook et al 2024 - Mind of a Predatory Worm
This repository is associated with the preprint <a href="https://www.biorxiv.org/content/10.1101/2024.06.13.598904v1.abstract">Comparative connectomics of two distantly related nematode species reveals patterns of nervous system evolution. <a> Requirements and input files n... |
9e075326851698c90aaa2abdd4f7431cbfcb2437cf74a67be1adb1ae4446ca8b | Text | 1,301 | 53 | # ChronoPhylogram
This repository is meant to provide the necessary scripts and data to reproduce the figures shown in the manuscript.
The experiments are meant to run on Linux/Unix/MacOS operating systems.
If problems and/or questions are encountered, feel free
to [open issues](https://github.com/ThibaultLatrille/Ch... |
f36d850235139235cccc714ac062509c1b348d3892a63b79af824833442eabb3 | Text | 1,306 | 19 | ## Accuracy and precision in super-resolution MRI: Enabling spherical tensor diffusion encoding at ultra-high b-values and high resolution
Geraline Vis<sup>1</sup>, Markus Nilsson<sup>1</sup>, Carl-Fredrik Westin<sup>2</sup>, Filip Szczepankiewicz<sup>1,2</sup>
1 Department of Diagnostic Radiology, Clinical Sciences L... |
0c24ee938d3fb4da942d4caf6a35cacf1a6e6ba3350481a0b589fcd0bcbc46c2 | Text | 1,319 | 29 | # PhysiCell Studio
[](https://github.com/PhysiCell-Tools/PhysiCell-Studio/actions/workflows/cancer-immune-test.yml)
A graphical tool to create, execute, and visualize a multice... |
f0dbbd3cb6f838335e756561cea98c3da392a80d64772e6a220febd49d90432f | Text | 1,323 | 58 | # Onedcellsim
<img src="https://github.com/miguelatienza/onedcellsim/blob/main/simgui.png" width="700">
**Onedcellsim** is a project designed to simulate one-dimensional cell migration using Julia, based on [a biomechanical model](https://doi.org/10.1016/j.bpj.2023.02.001) as developed by Amiri et al. (2023). Additio... |
41be73794f43a72a7b4bb29c0949fd9b0f7f80f7392ef935badb9c627ead2d27 | Text | 1,325 | 44 | # flagser-count
A program for counting directed cliques in directed graphs, adapted from https://github.com/luetge/flagser.
## Python package (pyflagsercount)
```sh
pip install pyflagsercount # from PyPI (once published)
pip install . # from a local checkout
pip install git+h... |
76ae8be814e022744c50489949708a6aed10dcae5bebcdb8eefda6163f4a0107 | Text | 1,329 | 39 | # sEMG_Gesture_Recognition
#### 介绍
{**以下是 Gitee 平台说明，您可以替换此简介**
Gitee 是 OSCHINA 推出的基于 Git 的代码托管平台（同时支持 SVN）。专为开发者提供稳定、高效、安全的云端软件开发协作平台
无论是个人、团队、或是企业，都能够用 Gitee 实现代码托管、项目管理、协作开发。企业项目请看 [https://gitee.com/enterprises](https://gitee.com/enterprises)}
#### 软件架构
软件架构说明
#### 安装教程
1. xxxx
2. xxxx
3. xxxx
#### 使用说明
1... |
3f6b4acf101bd1cf249fe785d456ffb24f5ac3462d83ef82d16910157145c3a5 | Text | 1,346 | 62 | # LGTM
Code for LGTM: Gaussian Process Modulated Neural Topic Modeling for Longitudinal Microbiome.
Live demo: https://lgtm-web.streamlit.app/
## Installation
Linux is recommended.
- Clone this repository and enter the project folder.
- Install the package with [uv](https://docs.astral.sh/uv/):
```bash
uv... |
3ade02c261648aeb9abc27d8186f5acf8b6617908bbb0ff1b6f94437bc4cb24c | Text | 1,358 | 49 | # QSM.m
QSM.m is a MATLAB toolbox for quantitative susceptibility mapping (QSM).
## Getting started
### Prerequisites
* FSL's bet for automatic brain extraction
* [optional] FSL's prelude for phase unwrapping
### Installation
Download or clone the repository, build mex files, add toolbox to MATLAB path.
```matla... |
040accf2992a86486fa3637a066bc6e23948b3c3b76438b4a104ccb79ee5fa9a | Text | 1,369 | 63 | PASTIS: Poisson-based Algorithm for STable Inference of DNA Structure
=====================================================================
Dependencies
------------
For Pastis:
- python (>= 2.7)
- numpy
- scipy
- scikit-learn
- pandas
- iced
Additional dependencies for new features (diploid inference
multiscale o... |
42dd746ec7d76af16330a9fcd03c9ac805e12a93911a4a4bae11117af1c60378 | Text | 1,375 | 31 | 1. GA optimization
Main_GA_neuromechanical_2_nodes.m
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Run optimization process 10 times
GA_neuromechanical_2_nodes_run_10_times.m
% Optimization with different population size, running each group 10 ti... |
740ddd4876824d4a6801d60ca9881dec734162fce7b87b6f1f6b12dceace7f56 | Text | 1,382 | 18 | # IDConn
Pipeline for studying individual differences in network connectivity and organization in resting-state or task fMRI data
[](https://opensource.org/licenses/MIT)
[](https... |
8744db36ee9f3054022e777c4ef740fdf9716d43db248ef4beee494d34c62dee | Text | 1,382 | 9 | # Glioma polygenic risk scores and linkage disequilibrium reference panel from: Genome-wide Polygenic Risk Scores Predict Risk of Glioma and Molecular Subtypes
This dataset includes single nucleotide polymorphisms (SNPs) and corresponding weights for polygenic risk scores (PRS) of adult diffuse glioma. In addition, we... |
315bc563abd510c98b40e2332d09a76f7b6bbd68d26840efc9e1f96ee775db08 | Text | 1,384 | 39 | # Introduction
The Virtual Imaging Platform is a web portal for pipeline execution on
distributed systems. An instance of this portal using the
European Grid Infrastructure is accessible at
[https://vip.creatis.insa-lyon.fr](https://vip.creatis.insa-lyon.fr).
# Credits
The VIP logo was designed by Max Langer under t... |
474255270382483983bd0668f091f2b28511c50598fe474fb093cb1484f129a9 | Text | 1,385 | 38 | # **eSpatial: a computational framework to decode the spatially divergent combinations of enhancers**
## **Introduction**
eSpatial is a computational framework to decode gene expression regulation by the spatially divergent combinations of enhancers through integrating spatial profiling of gene expression and chromati... |
03fc4b3eb175d06d4cab8fa0ddb14967c38ae610e824fcbc55e325762eb0eaa3 | Text | 1,397 | 53 | 
# Falcon extensions
The extension does not work as standalone and needs to be integrated with [Falcon](https://falcon-core.readthedocs.io)
The full documentation can be found [here](https://falcon-fklab-extensions.readthedocs.io) but below, you can f... |
86039e7b4db960ae2a9fb4b9df72f11e37973884d58ae193693d3f77847f1b8a | Text | 1,402 | 19 | <a href="http://www.kios.ucy.ac.cy"><img src="https://www.kios.ucy.ac.cy/wp-content/uploads/2021/07/Logotype-KIOS.svg" width="200" height="100"/><a>
[](https://doi.org/10.5281/zenodo.1313116)
# LeakDB
LeakDB (Leakage Diagnosis Benchmark) is a realistic ... |
10585bc913d75872dd9364d34e3c47d54cc62362415efef9ca6ec8b44858dda7 | Text | 1,405 | 9 | # assembloid_LFP_Zourrayetal2025
These MATLAB functions perform the analysis of assembloid local field potentials performed for the paper Zourray et al. 2025.
This set of functions perform the LFP analyses shown in Figure 1 of Zourray et al 2025. They are performed on local field potential recordings from >d200 brai... |
bee4c069cee30d4f756bdf1ec3faa7fc52425289b9d5d593e33862f292c528f8 | Text | 1,406 | 27 | # Code for FORCE trained spiking networks do not benefit from faster learning while parameter matched rate networks do
## Requirements
* [python>=3.9](https://www.python.org/)
* [numpy>=1.22](https://numpy.org/)
* [scipy>=1.10](https://www.scipy.org/)
* [matplotlib>=3.5](https://matplotlib.org/)
* [pandas>=1.3](http... |
9eb9ef586660b961eac0d527103c2db908b8f3319b21fa4f00d528136d61dd4c | Text | 1,409 | 26 | 
[](https://github.com/funkey/gunpowder/actions/workflows/test.yml)
A library to facilitate machine learning on large, multi-dimensional images.
`gunpowder` allows you to assemble a pipeline f... |
76b0265822c9496eeeed63e66b18ae5183b52529d6872b998af2bf45feeeff54 | Text | 1,410 | 20 | This repository contains the source codes and data supporting the findings presented in the paper
"Optical Next Generation Reservoir Computing" by H.W, J.H., Y.B., K.T., M.J., Q.L., and S.G..
Below is an overview of the contents:
1. Folder "exp_results": it contains the experimental results in the paper.
2. Figure2.m... |
8964f132dc49f0f5114788c72ca787ae891c6597e24ff354379cc5fda1bb3358 | Text | 1,410 | 34 | ## README ##
Code for the manuscript:
Cassandra J. McGill, Amy Christensen, Wenjie Qian, Max Thorwald, Jose Godoy Lugo, Sara Namvari, Olivia S. White, Caleb Finch, Bérénice A. Benayoun, and Christian J Pike.
"Protection against APOE4-associated aging phenotypes with the longevity-promoting intervention 17a-estradiol"... |
075de6c2891f0f78968ccdb2e636ae11c619f2fef2dd552f9e0c025f69016ed3 | Text | 1,416 | 30 | ## Deep learning predicts onset acceleration of 38 age-associated diseases from blood and body composition biomarkers in the UK Biobank
This repository contains the code for the experiments in the onset acceleration paper, where we use machine learning to predict onset speed of age-associated diseases and analyse dise... |
45b3037eb18c3763cf3dbe8d2cc59a52456e47a62c20125d3e37425a15a0debc | Text | 1,448 | 8 | Code for reproducing results in [Decoding the Cognitive map: Learning place cells and remapping](https://elifesciences.org/reviewed-preprints/99302), published in eLife (2024).
To train models and generate results, first generate a dataset, using the [create_dataset.ipynb](dataset_generator/create_dataset.ipynb) noteb... |
5483ed0a03a72b38e47a0fce799ab659f2b70a20eba57b43765ad508448d3769 | Text | 1,448 | 34 | 1. GA optimization
Main_GA_neuromechanical_proprioception_head
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Evalutation of optimized results
opt_func_eva_quasiStatic.m
plot_muscle_deformation.m
plot_membrane_potential.m
animation_script.m
% ... |
8d839f2c52988ff92f116b6f3054707c7e5f17d49d75c6510244e7f34d129318 | Text | 1,451 | 11 | # Subgrouping autism and ADHD based on structural MRI population modelling centiles
This repository contains an implementation to cluster MRI population modelling centiles using k-medoids. Prior to clustering, the dimensionality of the data is reduced using UMAP (or tSNE).
To use the code, you will need a csv file co... |
5a4aed203577e42b4356f0abe2bf340f7057c3b39e73ba02c09c82422add54bd | Text | 1,452 | 35 | 1. GA optimization
Main_GA_neuromechanical_proprioception_body.m
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Evalutation of optimized results
opt_func_eva_quasiStatic.m
plot_muscle_deformation.m
plot_membrane_potential.m
animation_script.m
... |
8791ad94252d96c883e6cf7ecba7431c779f358dcab104c548ff05ad0dc1c664 | Text | 1,454 | 39 | # Fusing Multisensory Signals Across Channels and Time
This repository contains the code and data associated with our preprint "Fusing Multisensory Signals Across Channels and Time" (Anil, Ghosh & Goodman, 2024). The work investigates how temporal structure in multisensory signals can be leveraged in integration strat... |
07fd01e46c71cc0bb7fd76e4226f4c1d944dfc68d689b66b0a85fb36dfdde085 | Text | 1,457 | 20 | # Calcium-Imaging
Hong Lab MATLAB scripts for analyzing Calcium Imaging data in _Pristionchus pacificus_.
By Marisa Mackie, for Ray Hong Lab at California State University, Northridge (CSUN)
Contributors: Kathleen Quach, Isaiah Martinez
Written with MATLAB versions 2021a - 2024b
Used in the following publications:
... |
85e086365c4303551d81fcdc1424198b834141955d50a43fb3f864d352b22161 | Text | 1,461 | 29 | # Ellipsoid fit python
Find ellipsoid fit for arbitrary data with python/numpy, plot it or write to file.
(Should work on both python 2.7 and python 3)
Used for 3-axis magnetometer calibration.
If you want to fit an ellipse into arbitrary data take a look at issue #11 - I tried t... |
e0335b269b8fc97347573c41bdade7391769e55e86cecdb569830328cb06d753 | Text | 1,470 | 66 | # LGTM
Code for LGTM: Gaussian Process Modulated Neural Topic Modeling for Longitudinal Microbiome.
Live demo: https://lgtm-web.streamlit.app/
R interface: [installation and usage](r/README.md).
Contact: Xiao Yuan ([yuanx749@gmail.com](mailto:yuanx749@gmail.com)).
## Installation
Linux is recommended.
- Clone th... |
b820c7257f2c2209e6b2972f1b9406b16a32e691224de7777ceecf366af7b872 | Text | 1,508 | 22 | 1: LoadData.m
The fuction of this code is to load and preprocess raw EEG data.
Before running it, the path of raw data and the parameters of filter must be set.
This code would extract epoch data by triggers and integrate it in the 4-dimensional matrices (target × channel × sampling point × block).
2: Codes un... |
24e62966e7e98d78a66046cda63c90c895ba086b0ed8fa3b51bd5e655b194073 | Text | 1,514 | 28 | # Code for FORCE trained spiking networks do not benefit from faster learning while parameter matched rate networks do
[](https://doi.org/10.5281/zenodo.13333935)
## Requirements
* [python>=3.9](https://www.python.org/)
* [numpy>=1.22](https://numpy.org... |
64e76028ffec966ac64c0c34a58dbd5bef99b5bc75a787f10ff768aa838a0f0e | Text | 1,542 | 39 | # Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD
This is the source code repository for [Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD](https://www.nature.com/articles/s41586-025-09083-y). The main analyses use both Python and R, with specific packages detai... |
b34b136327aec5463c82846ab0a757ecfd0bc6611b611ec85b2dc8bd7cca7026 | Text | 1,548 | 52 | # NeuralFlow - version 3
## Short description
Computational framework for modeling neural activity with continuous latent Langevin dynamics.
Quick installation: ```pip install git+https://github.com/engellab/neuralflow```
The source code for the following publications:
1) **M Genkin, KV Shenoy, C Chandrasekaran,... |
01350de23439f6ca907318be450089ab04292f1f7da316525a8bf68cff4b78fb | Text | 1,554 | 18 | ###### _For the ones who asked in the COMIA conference for the enhanced results :)
# Anime Project at COMIA, enhanced results!
Here you can find the code for our paper at COMIA2023 (Mexican Conference of Articial Intelligence), but with this changes:
* Instead of using the split described on the paper (who considers... |
e59537148c672ba91f30d44daabd12fadb87d3e7db08fba2fe39adae8b070371 | Text | 1,557 | 31 | # AR-ioECOG-Pose-Estimation
## Overview
This repository contains the inference pipeline for markerless EEG electrode localization using stereo video captured by the Microsoft HoloLens 2. It implements a multi-stage deep learning workflow including bounding box detection, super-resolution enhancement, keypoint detect... |
6c928759a95f04a9028ace9df65b95f43892632388b74b82d1a6efe6652b481f | Text | 1,562 | 57 | # Wave Analysis Toolkit (WAT) for Widefield Brain Imaging
A Python toolkit for analyzing wave propagation patterns in widefield optical imaging data of brain activity.
## Features
What WAT contributes to：
- Phase analysis tools
- Calculation of wave speed and direction
- Visualization of waveform (e.g. flow, arrow,... |
d79b581bf569a7166b63ecc54f28b1979365d30470e4864e0e6b6b925ed133bb | Text | 1,571 | 43 | # acne_detection
acne_detection
ran in python 3.6.8
## Requirements
* tensorflow == 1.13.1
## Training
```shell
export PYTHONPATH=$PYTHONPATH:/PATH_TO_THE_PROJECT/slim/
nohup python3.6 object_detection/model_main.py --pipeline_config_path=faster_rcnn_resnet101_coco.config --model_dir=./saved_models/ --num_train_st... |
e7748d449165ffe32331777201624da457c408547ad3c5885ee66734aa8adc19 | Text | 1,601 | 18 | # Code for the paper "GABAergic neurons can facilitate the propagation of cortical spreading depolarization: experiments in mouse neocortical slices and a novel neural field computational model" by E. Baspinar, M. Simonti, H. Srour, M. Desroches, D. Avitabile, M. Mantegazza
## A neural field model for cortical spre... |
1cdcd13be2a29b6c05dd520186dc484483b20d83e3e8bc2274a910d2498ba1b3 | Text | 1,611 | 23 | # Nanoneedle Lipidomics
## Repository contents
This repository contains a Collection of scripts in R and MATLAB, used to analyse DESI-MS images of glioma tissue sections and nanoneedle biopsies in the paper ["Nondestructive Spatial Lipidomics for Glioma Classification"](https://www.biorxiv.org/content/10.1101/2023.03.... |
ef9423157d79d92bda9a746b0f4407a9209ef22dfd584fd8fdf10d1ace06f2b0 | Text | 1,618 | 37 | # trompy
A collection of tools for plotting and data analysis from McCutcheon Lab based at UiT in Tromsø, Norway (hence *trom-py*). We study ingestive behavior and motivation in rodent neuroscience experiments but code may be useful in other settings.
Highlights include:
- ~~GUI for analyzing lick patterns in roden... |
d81b23a12d458d7e500d174518b0b5acb3bad58cc8779b179ab27d2db2bb2312 | Text | 1,622 | 18 | # MOGONET: Multi-omics Integration via Graph Convolutional Networks for Biomedical Data Classification
Tongxin Wang\*, Wei Shao\*, Zhi Huang, Haixu Tang, Jie Zhang, Zhengming Ding, and Kun Huang
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classifica... |
adc2faeec94290c804a507f96a0cad1d40da42fe2ec9753e2b7497423a84f0d1 | Text | 1,623 | 36 | # Structure Tensor Validation: Functions for validating the accuracy of structure tensor analysis for estimating orientations in 2D and 3D images.
## Features
- Generate 2D and 3D phantoms simulating axons in brain microscopy with parallel and crossing patterns.
- Perform structure tensor analysis to obtain ori... |
d780f1ef3505b89dbdcedbf259859021243ef62ae6a849497bb0048fb37e860f | Text | 1,623 | 49 | # DTEGNN
Implementation of the dynamic training method applied to an equivariant graph neural network
Correspondance to: ```zugec.ivan@gmail.com```
## Installation
Clone this repository
```commandline
git clone https://github.com/IZugec/DTEGNN.git
```
You can then build the environment with Anaconda:
```commandline... |
4098078611460c143ff07abb1f258e01354148112ac7dc74bbe7de1f50b93cde | Text | 1,636 | 45 | # VIP_reversal
Codes for analysis and making figures for the manuscript "Selective engagement of prefrontal VIP neurons in reversal learning".
## Authors
Jee Hyun Yi1,4, Young Ju Yoon1,4, Huijeong Jeong3, Seo Yeon Choe1, Min Whan Jung1,2,5*
1 Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daeje... |
e444e3b8dc74e87450e467d26d4acbb8fa75dee81801147a663de7f2f3d67db8 | Text | 1,642 | 18 | # fmriclean
fMRI outlier detection, and parcellation, and denoising
To be be run AFTER preprocessing. The expected order of operations would be:
1. fmri_save_parcellated_timeseries.py: Save parcellated timeseries with NO denoising, filtering, etc
* Inputs = full NIfTI time series, ROI labeled volume
* Output... |
fa15d0f3225b9730b27d31cde547025248692b8f429bea528f4d340cc5a4abba | Text | 1,645 | 35 | # vRSAb
SPM functions in MATLAB to perform variational representation similarity analysis using bootstrapped nulls
## Data structure
Place a contrast file (contrast.txt) and the vRSAb.m file in a parent directory
Then place subject-specific data in different sub-directories
 for each of the 5 data
modalities of the tonsil atlas: scRNA-seq, scATAC-seq, Multiome, spatial
transcriptomics (Visium), and CITE-seq.
For both scAT... |
d4b226b194c586a3793b67c9c77bf475c99fa6b147f35d6258df387f364a7649 | Text | 1,674 | 13 | # NeuroFreq
NeuroFreq is an open-source MATLAB toolbox for flexible time-frequency analysis of human brain electrophysiological fields recorded using EEG, MEG, and ECoG.
<img src="./nf_logo.png" width="200" height="200">
Time-frequency (TF) analysis is a vital tool for interpreting brain electrophysiological data inc... |
007c09a2071431b81ef1317cb9b053494a8a37d99446123c0293d9984086211c | Text | 1,682 | 34 | # skeleton3D-matlab: Parallel medial axis thinning of a 3D binary volume
This code calculates the 3D medial axis skeleton of an arbitrary 3d binary volume. It is an optimized MATLAB implementation of the homotopic thinning algorithm described in [1]. We developed it to quantify the network of cell processes in bone [2... |
eeb8a7db75fd6dedc1a1b2ed61d66e746837de4a55ac52a8751db9002bceeb48 | Text | 1,689 | 29 | Finds all Peaks and Calculates Areas Under the Curve (AUC) for MALDI mass spectrometry imaging analyses.
Utilized in:
Sarikahya et al. 2025 [https://www.nature.com/articles/s41380-025-03113-x]
Cousineau et al. 2025 [https://www.sciencedirect.com/science/article/pii/S0003267025006919]
Ng et al. 2024 [https://www.nat... |
762e73dba9e6331232070e760eece1397e2caf3071513a07eb40e2036dc95be3 | Text | 1,702 | 17 | # Fluorescent image gradient converter
The purpose of this repository is to take an immunofluorescent picture and convert the intensity of the color to a pre-defined spectrum.
<img src="https://github.com/chaotix1992/IF-Grad/blob/main/examplePictures/GDp.png" width="300" height="300"> <img src="https://github.com/chao... |
3bdf3320cce5c9fb8b11be04a7bff5e1455e3aef1ac17b3563b1709681be5ae2 | Text | 1,708 | 46 | 1. GA optimization
Main_GA_neuromechanical_actual_connectome.m
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Evalutation of optimized results
opt_func_eva_quasiStatic.m
plot_muscle_deformation.m
plot_membrane_potential.m
animation_script.m
% ... |
cb2422395544264af64375ede5f9df01fb578dc0bfc39d080e4e5cb23dd528de | Text | 1,716 | 47 | 1. GA optimization
Main_GA_neuromechanical_simplified_connectome.m
% This file is for GA optimization
% Optimizaiton process could be saved to ./graph/opt_process.fig manually
2. Evalutation of optimized results
opt_func_eva_quasiStatic.m
plot_muscle_deformation.m
plot_membrane_potential.m
animation_script.m... |
84f8cecb5e8acb206e0ad38951ca4c9f46f6dc3119671a0e739382a7695b1ed6 | Text | 1,720 | 34 | Skeleton3D: Parallel medial axis thinning of a 3D binary volume
This code calculates the 3D medial axis skeleton of an arbitrary 3d binary volume. It is an optimized MATLAB implementation of the homotopic thinning algorithm described in [1]. We developed it to quantify the network of cell processes in bone [2], but ... |
82559b7d446ea537858896b2e05681fe25329b9f26f5a8f9b4dc151feccf5a0a | Text | 1,728 | 31 | # Dynamic Athlete Motivation and Performance Network (DAMPN)
## Overview
**Motivation plays a crucial role in athletic performance**, particularly in high-intensity sports like track and field, where both mental drive and physical ability are essential for success. This project proposes a novel approach for evaluatin... |
fba87766920a95e931bbfeba4cfa724979887007cc30f824a3dabf06b3e90173 | Text | 1,728 | 49 | This repository contains annotated aortic centerlines and masks for 101 randomly selected images from [LIDC/IDRI](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=1966254) and aortic centerlines for 41 randomly selected images from [AMOS](https://amos22.grand-challenge.org). Aortic centerlines were an... |
a4330f18e05fa98cfa7f944c8863d046294b708f1254888d0a2b50e8d7c6e6f4 | Text | 1,729 | 25 | # cellScaleFactors
Authors: Sean Maden, Stephanie Hicks
Datasets containing reference tables for cell scale factors.
Citations:
Main cell scale factors data table source:
Maden, Sean K., Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks, and Kristen R. Maynard. 2023. “Challenges and ... |
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