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ec256422aca557b6be5a9259b5054541db65c168de3cb932985d6bbdf529c708 | Text | 298 | 10 |
# loompy v3.0
⭐ Loompy v3.0 was released Sep. 24, 2019!
To get started, head over to [the documentation](http://loompy.org)!
Loom, loompy, and the [loom-viewer](https://github.com/linnarsson-lab/loom-viewer) are being developed by members of the [Linnarsson Lab](http://linnarssonlab.org).
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886553caf6880f079b597f15afdd50f595129ac25f33a016654b6efa229177f2 | Text | 309 | 5 | # WM_intelligence
If you use this code or these findings in the research, please cite:
Dong X, Huang W, Chen H, Zhang Y, Liu B, and Shu N. Shared genomic architecture of the brain white matter structural connectome and intelligence. bioRxiv 2025.04.09.647917; doi: https://doi.org/10.1101/2025.04.09.647917
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28c80f4795bbb750fbed5fda33c1bba4272c5e4f58099645d690f1f3ec17a018 | Text | 311 | 2 | # Ferrigno-Iliakis_SciAdv2026
Analysis code from 'Indirect pathway neurons in the tail of the striatum regulate inhibitory control over sensory driven behavior'. We acknowledge the use of generative AI (ChatGPT 5.2, 5.3, 5.4, 5.5) as an auxiliary tool in the generation and optimization of this analysis code.
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5a8809766342ab81cba3c08f96326429d3cda0a0893b7c946e70380b7cf87cb1 | Text | 311 | 9 | ## AlphaFold3 Modeling
This directory contains all generated AlphaFold3 (AF3) models and relevant confidence metrics outputs.
Two independent AF3 modeling conditions were tested:
1. **NBCn2 monomer, two sodium ions, one carbonate ion, and three water molecules
2. **NBCn2 monomer, two sodium ions |
e8e78771752226f6cba7558ec80fd6ff50a6b3f3da8d2b9ec043195a31c939c8 | Text | 317 | 2 | # Physics-Informed-Liquid-Neural-Network-for-Laser-Engineered-Net-Shaping-LENS-Optimization
This repository contains the official implementation of the Physics-Informed Liquid Neural Network (LNN) framework for multi‑objective optimization of material and process parameters in Laser Engineered Net Shaping (LENS).
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5554726f098f07db29d399bb2aa62ab031116cddbab37a09c4d1f633daad9fe3 | Text | 319 | 6 | # Modular-Stereotaxic-Holders
modular stereotaxic holder for implanting optic fibers, guide cannulas, and GRIN anchors
Designed by Andrew Hardaway (andrewhardaway@uabmc.edu)
This is a collection of 3D print designs for making stereotaxic arms that can be used to place optic fibers, guide cannulas, and GRIN anchors.
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d5eac1940f79310a98fbb066e06aa1ed2e9b3fee26338d8a76f2bc3c65a2c445 | Text | 319 | 11 | # communication-subspace
Code for "Cortical areas interact through a communication subspace", Semedo et al. (Neuron, 2019)
v0.2b
This code pack requires the use of MATLAB version 2012b or newer.
1) Change MATLAB workspace directory to root folder
2) Run startup.m
3) Check example.m to see the code pack in action!
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6c8447102b388359d6f312d897d90ec8c66545bcbe130f40a3dc44b2eda8d7a5 | Text | 330 | 2 | # AE and GMM myelin stained tissue
Code for unsupervised classification of myelin-stained rat brain sections using convolutional autoencoders (AE) and gaussian mixture models (GMM) clustering. Compared against PCA-based feature extraction. Applied also to detect pathological changes in a rat model of mild traumatic bra... |
04cde3c2c49cfe7a1df3faf9238b112cacdb00a47cf9c3824cc24033fcd72b3e | Text | 331 | 5 | # FAA-ASD-Neuroimaging
Code for contrastive and transfer learning based aligned multimodal neuroimaging classification of Autism Spectrum Disorder using sMRI and functional connectivity features.
<img width="1705" height="725" alt="archit" src="https://github.com/user-attachments/assets/ffddcf33-d434-4664-aeb9-3b2d481... |
e5961305be8d7ab799abbefeddb684e99199d222368482653a5a6d82593ae194 | Text | 335 | 5 | Data and Supplementary materials for Dissociable neural substrates of integration and segregation in exogenous attention
Cite:
Chen Yu-Jie, Li Ai-Su, Yu Yang, Hu Su, He Xun, Zhang Yang (2026) Dissociable neural substrates of integration and segregation in exogenous attention eLife 15:RP109842 https://doi.org/10.7554/... |
ebcf1b9a669bd36a8051babba2320d72fc49e1e2d29a46727f88b202652bf09e | Text | 339 | 12 | This folder contains scripts used for the analysis in Resolving thyroid lineage cell trajectories merging
into a dual endocrine gland in mammals
Key packages required are
- scanpy
- scvelo
- palantir
- harmony
- cellrank
- moscot
- celloracle
- and associated libraries according to the guidelines for installation o... |
9c07b5c9f6be0cc81134613d29e4341ae89111806401331dc5fb9a67d1df1a1b | Text | 342 | 2 | # Modelling-of-Memory-in-Unmyelinated-Axons
An efficient model to predict conduction velocity changes in unmyelinated axons, based on "memory" where prior activity modulates subsequent action potential speeds. Incorporating linear long-term and non-linear short-term memory components, it predicts propagation speeds usi... |
11b7eb404f2f98208aa1e69bb72fd56a41ce3b678c8f9a0cc76196b1fb1f48e0 | Text | 345 | 9 | # Traveling-wave-analysis
Python code for analysis of cortical traveling waves
If you use this code for scientific publication, please cite:
https://doi.org/10.1371/journal.pone.0148413
https://doi.org/10.1371/journal.pcbi.1007316
For the estimation of spatial frequency, please cite:
https://elifesciences.org/r... |
97f96585971c43c353f2b57b68bc22d10843a51752aa683f531ba8090f7e947e | Text | 345 | 11 | # IMP1088 Proteomics Analysis
R scripts and processed outputs for DIA proteomics analysis comparing control and IMP-1088 treated cells.
## Structure
- scripts/: analysis pipeline
- results/: differential abundance and enrichment outputs
- figures/: manuscript figures
## Raw data
Raw MS data deposited in MassIVE unde... |
48addfb768805abddcbdf4af1cfce89ac784b5622827e0a481cc8ddaacf92d20 | Text | 355 | 5 | MATLAB code for the paper KH Jaeger, and A Tveito, 'Accurate computation of ionic concentrations in the synaptic cleft requires the full Poisson–Nernst–Planck (PNP) equations', 2026.
The script 'run_simulation_PNP.m' can be used to run a PNP simulation and the script 'run_simulation_D.m' can be used to run a pure diff... |
974b0bde4d54ee3b0e9f7c2eda938c64e4afa32814578b9447d7964cf619b7aa | Text | 356 | 5 | <img width="1280" height="720" alt="Graphical abstract" src="https://github.com/user-attachments/assets/01550b48-8c5d-4dc7-abb5-23a7ed6bc331" />
Link to publication: https://doi.org/10.1016/j.neuroimage.2026.121921
This work was supported by the National Institutes of Health [grant numbers R01 MH125411, P51 OD011... |
ce41b1fd9292dcb396e26e312cf7358d5bf1ebc2b8fa07be0ec087ce94608e69 | Text | 361 | 15 | This is the source code for the paper below.
Yoshiki Ito & Taro Toyoizumi 2026
Modeling flexible behavior with remapping-based hippocampal sequence learning
eLife;14:RP106506
https://doi.org/10.7554/eLife.106506.4
## Environment:
python 3.10
## Requirements:
jupyter, numpy, scipy, matplotlib, col... |
7d143e4956950a0bdc9841e79274e259929c8599dcb9017f97873bc0c9549de1 | Text | 365 | 2 | # T2DComplication
This warehouse has documented a study on biomarkers of T2D and its complications. This project utilized a large cohort from UKB to explore the plasma protein and metabolite components related to T2D complications and estimated the predictive performance of markers for complications. The core code of t... |
6c285367a1d3a0100066053b9944caa48bb372cffe34e5ef7b3eb9bc13e11274 | Text | 373 | 11 | # utils_package
Utility function library used in the manuscript:
**"Tailoring AI and ML Models for Genotype-by-Environment Prediction Leveraging Environmental Covariates: A European Rye Example"**
Authors:
Wera Eckhoff, Florence Parat, Gennady Bracho-Mujica, Clemens Flamm, Daniela Bustos-Korts, Hans-Peter Piepho
Co... |
137b245e1cb77bd97cba67f6bb2d19d5405ea94a32b338253946b726ea0f1822 | Text | 376 | 4 | # Multi-Spectral-Image-Classification
This project is created to share Dataset for research study entitled with Stacked-based ensemble learning for multi-spectral image classification for the purposes of land cover land use analysis.
You can find the google drive url using the following link
https://drive.google.com/fi... |
8d08a52832420783a140e17c89c7698bed77cd6bb5dec9b5eca1224591175946 | Text | 378 | 10 | # ML-Coconut-Fiber-Reinforced-Concrete
Optimized and Explainable Machine Learning for Coconut Fiber Concrete Strength Using SHAP, PDP, and ICE
## 🧩 Reproducibility Guide
To reproduce all results
1. Open [Google Colab](https://colab.research.google.com/).
2. Upload `main.ipynb` and `requirements.txt`.
3. Install depen... |
5a66ea3430b14b3140c1ac46c2842ddc92207c031502dc1627ca4d3da4402e63 | Text | 382 | 2 | # SILA-AD-Biomarker
The sampled iterative local approximation algorithm was developed by Dr. Betthauser at the University of Wisconsin-Madison to model longitudinal amyloid PET data and estimate individual A+ onset age. This algorithm may have applications in other areas where long-term population trajectories can be s... |
c84ac171447354ebe3404480bc6838f65b9a9b4d68317780ad0fee1d590d37c9 | Text | 390 | 19 | Arduino code for controlling the active avoidance behaviour
System requirements:
Arduino2.0.2 on Windows10
Installation guide:
No specific requirements. Follow normal installation guide for Arduino2.0.2.
Install time: few minutes.
Demo:
No Demo applicable.
Run time: Infinite.
Instruction for use:
Upload the Ard... |
9970a3bcfa6064d1616c6ef83a12992780b4ba0897fa730a37e07655dcfe0210 | Text | 396 | 5 | # Pursuit of brain disease biomarkers
This repository contains the code and simulation data for the paper "Brain disease biomarkers" - Pascal Helson and Arvind Kumar, 2025 https://arxiv.org/pdf/2509.10547
The code reproduces the RNN experiments and analyses presented in the paper, demonstrating the limitations of coh... |
ed674034153667e5df706a9d23950d303fa528d1a1e29d71e5efa6f8cef98452 | Text | 396 | 14 |
# Custom code for 'The Brain Imaging and Neurophysiology Database: BINDing multimodal neural data into a large-scale repository':
## Available code:
`ask_llama_open.py`
code used to extract structured information from unstructered reports
`ask_llama_category.py`
code used to select a fitting category for each find... |
8f97a8be335b1b5a8931768e2285071dfd3edfec2952f4e6797f51408e3fc37f | Text | 397 | 9 | # The demodulated band transform (DBT)
This repository contains DBT spectral analysis scripts for matlab
For more information please refer to
Kovach, C. K. & Gander, P. E. The demodulated band transform. Journal of Neuroscience Methods 261, 135-154, doi:http://dx.doi.org/10.1016/j.jneumeth.2015.12.004 (2016).
A pre... |
9c4c1afecbfc06706c6232a1579ba92ac2277b3f59620437f27fec4e1546fb4b | Text | 406 | 1 | SuperDIRECTEUR predicts combinations of small molecules by accounting for dynamic molecular mechanistic changes during direct programming induction. To account for these dynamic changes, the cell conversion process is divided into several stages (e.g., Primal stage, Immature stage, and Mature stage). Combinations of sm... |
7ce6c94fe325c9e39acc567d718aaa5786d8d620287430c2bb541e484cca629f | Text | 408 | 12 | Welcome to Andy's Brain Book! This will be updated as the book is written.
Update 1.19.2022: The e-book now has a DOI:
.. image:: https://zenodo.org/badge/178266491.svg
:target: https://zenodo.org/badge/latestdoi/178266491
You can cite the e-book using this as a template:
::
"We followed the AFNI preprocessi... |
236b07f41f4a1a463bef2d0ba920ec54e521059564207b9bce52fc1bbed56845 | Text | 424 | 7 | # EELSfitter-Core_loss
An extension of the EELSfitter code for background subtraction of Core-loss EELS
Use CrSBrWhiteLines.ipynb as an example of how to use the code and the corresponding paper (arxiv link here) for the explanation of the methodology.
Code is made for dm3 and dm4 files, but it is possible to use r... |
86fb8183f95e128293463375bae29844eec91999e0f0edf8fd1a4b18e6573c93 | Text | 424 | 8 | This github contains analysis pipelines for multiplexed RNA imaging data on brain organoid tissue sections.
## 1. Spot assignment
1. Assign RNA spots to cells using Euclidean distance transform
2. Dilate each segmented nucleus to obtain cell mask using Euclidean distance transform
## 2. Spatial signaling score
Create... |
6f800c4c7a826b121a6ed5250f45d8a0ded606aa116c1f55bb000476488002c4 | Text | 427 | 16 | # ICAS-CSVD related brain structural damage
## Background
Cerebral small vessel disease (CSVD) related covert damage can coexist with intracranial artery stenosis (ICAS).
## Purpose
We aim to explore whether the spatial distributions of CSVD markers are diverse in people with or without ICAS
## Core Datasets
- MRI ... |
8c0215d31ba6e6cb0ef22991679465259cacdd74fadbe1fc7cffdc7c12883a4b | Text | 433 | 8 | # Calcium buffer schematic figure
Panel A: same Kd, different kon/koff
Panel B: different Kd vs EC50 combinations and their effect on Ca2+ transient
- Author of the code: Kerstin Lenk
- Skeleton of the code produced with Perplexity, April 2026
- Related publication: Calcium buffering in astrocytes and its relevance f... |
93d24a753b2e88d5ba68ece1e30883736019f8cdc439ad2872a79bfabe2d3daa | Text | 437 | 7 | Data repository for Sandbote et al 2026 published in frontiers in cellular neuroscience.
Repository provides the data used to create the figures in the publication as well as a model demo and data from the parameter sweep of the study (population data).
Morphologies used in this study are provided as .pkl files and a... |
bd2dd863c45d28082ad7f965d16ec5d6d19972f4072b92bc893840792802fece | Text | 437 | 15 | # Vegetation Trend Prediction in Bani Hasan, Saudi Arabia
Reproducible R workflows for vegetation trend prediction using ANN, ANN-PSO, ANN-GWO, Random Forest, and XGBoost models.
## Repository Contents
- ANN, ANN-PSO, and ANN-GWO optimization workflows
- RF and XGBoost bootstrap uncertainty analysis
- Residual diagn... |
644f4b82616b5da533c7a7bbe72cb4879ca3202e8cc6070c01654742f2d59c69 | Text | 438 | 20 | imageAnalysis_gui
=================
Simple MATLAB Image Analysis Tools and GUI
I will add some documentation soon.
Should be straightforward.
There are some broken UI bits.
Feel free to ask questions.
$$$$$ Basic Workflow $$$$$
Program Flow:
importer -> roiMaker -> extractor -> eventInspector
Goals:
import/regi... |
b62fddb22d1a2b0be172f637237602d6c9b2d11c5c1acd6a25588816b8720aa9 | Text | 451 | 6 | - Source_code is R Shiny code for Web server
- Model is the R and Python code to build Immuno-GNN model.
- Citation: Tao Wu and others, Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy, Database, Volume 2023, 2023, baad041, https://doi.org/10.1093/database/baad041
## Update
Th... |
a2387b49477e2b1bfcb18ea5003a7eb5f08becb477a373fdc553461e8138974f | Text | 457 | 11 | This repo contains code to reproduce the paper: Neural sampling from cognitive maps enables goal-directed imagination and planning
Citation:
@article{lin2025neural,
title={Neural sampling from cognitive maps supports goal-directed planning and imagination},
author={Lin, Hui and Yang, Yukun and Zhao, Rong and Pezzu... |
82f199ea3d8131045a61b70d8ea0cf8cd45c1ea2b4ca4bf8a9163f5c536ae71e | Text | 468 | 27 | # README
### What is this repository for?
* Solving the equivalent circuit using DNA nanopore to perform quasi-intracellular recording.
### Dependence
* numpy
* scipy
### Files
* main\_script.py: example pipeline
* dterministic\_HH: functions solving a HH style single compartment neuron with dual patch conf... |
76a3182902f25629511f9cfd48ec021e1087a5e09a4e3510da2f8b7997eca621 | Text | 473 | 7 | Statistical analyses of report
Discovery_cohort_analysis = analysis in Figure 1 and Extended Data Table 1
Replication_cohort_analysis = analysis in Figure 1
Discovery_cohort_interim_data_analysis = analysis in Extended Data Fig. 2
JAKi_antiTNF_Placebo_cohorts = analyses in Extended Data Fig. 3, Extended Data Table... |
b0f4c383c137de4ac3b921dfc6c779f168e15dddd8c3939ea18fb5288997e3e6 | Text | 486 | 3 | # Nuclear counting in cells
This is open-source [ImageJ](https://imagej.net/ij/index.html) script for counting cell nuclei from a directory containing images obtained with all 10x objectives of widefield or confocal fluorescence microscopes. The cell nuclei can be stained with conventional nuclear dyes (DAPI, Hoechst,... |
513131d5d2e2b3f1e1ddfb556f2ef74b76dc486c44432bfbd39d69fe50f10117 | Text | 493 | 7 | [](https://doi.org/10.5281/zenodo.18746422)
MATLAB toolbox for viewing, aligning Allen CCF mouse atlas, and annotating slice histology images.
### [Installation instructions](https://github.com/petersaj/AP_histology/wiki/Installation)
### [Documentatio... |
d9e3b4113e12d29028180a8de62cd791f734c97b5e13b6b39d5e9203802c0097 | Text | 497 | 8 | # CR-ScorpionVenom-Nav
Code for statistical analysis from Akerman-Sanchez et al., 2026
In this repository, you can find the statistical analyses made by the authors of the cited paper.
In the code, you may find "Var1" and "Var2" variables, which correspond to Activation and Inactivation curves, respectively.
The mul... |
3741b0d6c0936705405e68f28f64294ead1f24e7c026be706aa65341e47c8a80 | Text | 499 | 19 | # bio_nnets
1) loading networks from file
run pkgs_files_setup.jl (load pkgs and function files)
run pre_train_script.jl (load data and genes, activation function selected)
run loading_scripts.jl (load networks)
2) training networks:
setup the nnet_setup.jl file
run pkgs_files_setup.jl (load pkgs and functio... |
a1fec505668fd3a198422121a842c47cebb5b2abc906b790fa66f50f40feed62 | Text | 503 | 11 | This folder contains example data for DANT. The following files are included:
- spikeInfo.mat — Raw data with information on all well-isolated units across sessions
- settings.json — Configuration file with settings for running DANT
- mainDANT.m — Main MATLAB script to execute DANT
- DANT_Output/ ... |
c23d55ba7bd44edd03fbf8c68fb5b3b3308922f006e6a7743bb4313e0c0391f5 | Text | 506 | 7 | # DeepGPO
DeepGPO is a deep learning framework for the prediction of MS/MS spectra of O-/N-glycopeptides.
# User Guide
For detailed step-by-step instructions on how to get started with DeepGPO, please refer to [User_guide.md](https://github.com/lmsac/DeepGPO/blob/main/User_guide.md).
# Software
A compiled standalone v... |
322a55ecc34cd8b7a6377d9cc18c8b1eb4b601d1eb290ea8d514c201e6b10c47 | Text | 510 | 5 | # Non-negative ICA in Python
A python algorithm for non-negative independent component analysis (ICA) as described by [Plumbley, 2003](10.1109/TNN.2003.810616). Non-negative ICA is a matrix decomposition algorithm that given a matrix X finds two matrices A and S such that X = AS, where S is non-negative and describes t... |
aeb38c9c8dd494d5d71fd727a26023449c39b5afcacbff7546476cb2aa93f221 | Text | 520 | 19 | # Project README
## Overview
This repository contains code for analyzing neural population responses under baseline and continuous flash suppression (CFS) conditions.
---
## Citation
If you use this code or data, please cite:
Chen Cai-Xia, Wang Xin, Jiang Dan-Qing, Tang Shi-Ming, Yu Cong (2025) Continuous flashi... |
e47b68b88739e60393ddbb50e99080659063e939a89c9f1e86ce83ead01ac8d2 | Text | 525 | 14 | ## Folder Structure
### code
- `feature extraction pipeline.zip`: Feature extraction pipeline code
- `IED channel localization.zip`: IED channel localization code
### epilepsy
Contains epilepsy patient data (`Data.zip`):
- Pre-processed **1-second samples** of IED and non-IED (including daytime and full-period)
- **C... |
4d58ea2d3e22b47b9093d8373eac797bff9732b9560c75ab2aeade634dd94b48 | Text | 531 | 7 | # QT-NIRS
QT-NIRS (Quality Testing of Near Infrared Scans) performs and presents a post-experimental assessment of quality across time and optical channels of an fNIRS recording in an intuitive and time-effective manner, and it provides actionable information for the optimization of subsequent steps of the fNIRS anal... |
62f0464bf36c68f27028a176c6d75c009bff63c217936f9b8029115a1e6fa20a | Text | 539 | 18 | # Astrocyte-proximity-protects-synapses-in-AD
Analysis for data in Gobbo et al. EJN 2026
Raw image analysis was performed in R and data processing was done in Python and R (statistics)
Python files:
Bleaching analysis: Bleaching_Analysis.ipynb
Single calcium event calculation: Single_event_calculation.ipynb
Event ... |
031b6fa8e1a6e7b27ec71f2c3aceca3f1dfebfb7bbe96beb3e43d20e9abfb078 | Text | 554 | 10 | [](https://pypi.org/project/pcg-skel/)
[](https://doi.org/10.5281/zenodo.7703278)
# pcg_skel
Generate robust neuronal topology directly from PyChunkedGraph dynamic segmentations. Skeletonization is ... |
1b0df8f1ced853a0510ea27157df8b8d93f6c1772fe0d01ab84e85c0ba78e074 | Text | 558 | 22 | # my-paper-code
This project reproduces the results in the paper.
# ML-V2LC-CM: Hybrid Machine Learning Framework for Vehicular VLC
## Overview
This project implements a hybrid machine learning framework for Vehicular Visible Light Communication (V2LC) channel modeling.
## Features
- Hybrid deep learning model (DNN +... |
e942746195bb27a9a981d491d591befe67751d52c5067a6564efba606db97507 | Text | 567 | 5 | # GABA signaling in NG2 glia mediates empathic behavior under observational social defeat
All code was implemented using R version 4.1.1 (Platform: x86_64-w64-mingw32/x64, 64-bit).
The required R packages include: tidyverse, rstatix, xlsx, ggplot2, dplyr, Seurat, patchwork, BiocManager, scater, cowplot, readxl, and gg... |
eb77eff2ebcee5b9d53623c58dfd04d82d0868b5b48a71b1142aae62ea6c397f | Text | 575 | 27 | # CNN-Based Inverse Design for G-HMWG Antenna
This repository contains the raw training code used for the CNN-based inverse design
of the ultra-wideband Grooved Half-Mode Waveguide (G-HMWG) antenna.
## Reproducibility
- Random seed fixed to 42
- Compatible with Python 3.9+
## Requirements
Install dependencies:
... |
4d7df1cd8e6df40302b38de14fc3d06f8198cdf1694d2b4979129ca34b27dc46 | Text | 579 | 20 |
arPLS implements the algorithm for smoothing of Raman spectra from:
Sung-June Baek, Aaron Park, Young-Jin Ahna and Jaebum Choo:
"Baseline correction using asymmetrically reweighted penalized least
squares smoothing", Analyst, 2015,140, 250-257
This is an improved algorithm compared to https://github.com/zmzhang/a... |
09d67d1be7c770f93534141a9a800bf767d5e7d17009e47a6c88f6e680979bfa | Text | 582 | 12 | NOTES:
Texturemapping the models is coded to use the image registrated data (rdata) not the filtered data (fdata).
Changes will need to be made in TM_GK between lines 22 and 51
The majority of the computation time is in the cubeCarvingModReduced_3,
ProcessMaps MontionRemovalRegistrationButtonPushed callback, a... |
a679c425495acfec86acf700f424c7665469b36d4c0ababc98ca7c54089a878d | Text | 584 | 16 | # prospect_transferability
The main R and Python functions, which were used in the analyses of the paper: What affects the transferability of the leaf PROSPECT-D model across plant species? A systematic analysis (Rahimi-Majd et al.).
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=5312487
The tested versions of P... |
c72c1ad12a31414b8e68ddc3bedfdffb06357b048c0b8e69b7dea3194a1272d6 | Text | 591 | 11 | # stress-fs-paper
Code repository for the paper "Linking brain structure to stress reactivity: Cingulate surface area predicts acute cortisol responses."
The repository is organized as follows:
- 00_organize_data: Scripts for preparing data for analysis.
- 01_palm: Scripts for PALM analysis.
- 02_whole-brain: Scripts... |
6468320e495b7dca6fff9e01e90c31517ccb2efe24780462498e3e29e900490e | Text | 594 | 12 | This folder contains:
- AHEAD processed data (microscopy and qMRI) used for computing laminar profiles.
- in-vivo processed data (T2* and resting state fMRI) used for computing laminar profiles.
\source_fMRI contains the raw time series of resting-state fMRI at 0.8 iso. mm and the scanning protocol file.
NO... |
d386427de4ea64755ebdf489028ae6439479100a4874b0191ec2f2306f048bd1 | Text | 607 | 20 | ---
language: de
license: mit
tags:
- sentence_embedding
- search
- pytorch
- xlm-roberta
- roberta
- xlm-r-distilroberta-base-paraphrase-v1
- paraphrase
datasets:
- STSbenchmark
metrics:
- Spearman’s rank correlation
- cosine similarity
---
# German RoBERTa for Sentence Embeddings V2
**The new [T-Systems-onsite/cro... |
8eb881012544737e886b31aefea32d8e32bc3d8068984b112826ade5debf24e8 | Text | 615 | 17 | # Adam-eLife_2026
Analysis Code for Adam et al eLife 2026 Manuscript
## Code from other sources:
### Circular statistics
CircStats MatLab package: https://www.mathworks.com/matlabcentral/fileexchange/10676-circular-statistics-toolbox-directional-statistics
Associated paper: https://www.jstatsoft.org/article/view/v03... |
604a8b055802bf9ba29051f0baeb27f5a783b18ea6ecdbbe888fc2c63f2d9b58 | Text | 617 | 11 | # WGD2celltype_evolution
This website contains scripts used in our paper but not datasets due to the size limitation of Github.
For datasets, please refer to files we uploaded to figshare.
The enviroment files (including installation methods, versions, and dependencies) were written in conda_yml folder.
All instruc... |
86ce42bcae0e0d3c630aa78e152cd99e337fac12461d450e450a2156c8784a3c | Text | 631 | 16 | # SlicerFreeSurfer
This repository contains the SlicerFreeSurfer extension for 3D Slicer.
The extension implements a module for importing models, scalar overlays, and segmentations from FreeSurfer, as well as handling the transformation of models from FreeSurfer to Slicer coordinates.
[10k images, 13GB](https://www.kaggle.com/datasets/chelov... |
8a85badbe99c136415cb283948b142df3ae3c5ece66c2a26a07dfec22eee38b3 | Text | 642 | 6 | # datasets
Este repositorio contiene las fuentes de datos utilizadas por DATADISTA.COM en reportajes y proyectos de investigación y datos. Puedes reutilizarlos para elaborar nuevas historias, análisis, proyectos o visualizaciones siempre y cuando nos cites como fuente.
Si quieres avisarnos de tus reutilizaciones o tie... |
0f11b283e416ed7dab6a6c60661915360d8d75ad905e1db55e196699c363ca42 | Text | 652 | 11 | # PhysioMotion_Artifact
Code for motion artifact collection, preprocessing and labeling
Checking_Labels.py provides the code to generate a signal plot and highlights the artifact signals.
Labeling_System.py provides the tool to annotate the artifact contaminated signals at the channel level.
preprocess.py is the ... |
633a34e739593e0408aba6633e57b87db90cc4b0712022ad2c0ae124ce21b2c2 | Text | 654 | 13 | # Weighted EEG Feature Data
This repository contains feature weight data derived from EEG analysis described in:
**Malaia et al. (2025). From Sampling to Inference: Language Experience Changes Processing.**
These data represent weighted feature vectors selected via multivariate modeling of EEG signal entropy and coh... |
082c9698e73bdb5f2975c8209c50c81e4f118b063a91c4e4673718d00370b825 | Text | 658 | 12 | # DBSsync_GUI
This repository is attached to a manuscript which has been submitted for publication on November, the 28th 2025. A preprint describing the toolbox design and functionnalities is available at: https://www.researchsquare.com/article/rs-8228751/v1
Instructions:
1. Clone this repository
2. Create a virtual... |
5adf5d5d19682f618cc10c3faa839c107b2a4dc9c83c01dd4adc9f5f243f0c38 | Text | 664 | 10 | # Jansson_et_al_Choroid_plexus_circadian_analysis
Code and analysis from Jansson et al manuscript Communications Biology 2026
1) deseq2 feb 2023.Rmd is all the analysis from normalized counts to differential gene expression for Figures 1, 2, and Supplementary Figures 2 and 5.
2) Clusterprofiler.Rmd is the functional ... |
aaa6df53606e21fb2a53b58167a945652fe56f1acf38d9e016486cb4a9790f36 | Text | 665 | 5 | This repo contains all the code and data from **Linear and categorical coding units in the mouse gustatory cortex drive population dynamics and behavior in taste decision-making** (https://doi.org/10.7554/eLife.109313.2).
It uses code from https://github.com/machenslab/dPCA for dPCA and http://github.com/cortex-lab/al... |
eff5914d2de21b0bd165415569423a41160dab9b4a1726ad9424cbf55f524a78 | Text | 667 | 3 | # Counting protein aggregates in cells
This is an open-source [ImageJ](https://imagej.net/ij/index.html) script for counting intracellular protein aggregates/puncta from a directory containing images obtained with 10x objectives of widefield or confocal fluorescence microscopes. The detection is based on using the Ima... |
b4fbb0900e0711b87d6fd551af64dea2fc2492e49629673eae056d97a7ef02c1 | Text | 676 | 14 | # Granger_Geweke_Causality
Granger-Geweke causality: Estimation and interpretation
Mukesh Dhamala, Hualou Liang, Steven L. Bressler, Mingzhou Ding, [Granger-Geweke causality: Estimation and interpretation](https://www.sciencedirect.com/science/article/pii/S1053811918303537), NeuroImage 175, 460-463, 2018.
To create a... |
f5312dda3854d23d7f06689d740e07623f99ca5be66ded0490594432b48695b2 | Text | 684 | 9 | # audiovisual_frontal_organization
This repository contains the code and sample data for the following paper:
Frontal cortex organization supporting audiovisual processing during naturalistic viewing. Faxin Zhou, Amirhossein Khalilian-Gourtani, Patricia Dugan, Andrew Michalak, Orrin Devinsky, Peter Rozman,Werner Doyle... |
0db5efbee939e519d70889f67b78f97ae6211216ad5f01080ae5fd42cd24b4be | Text | 686 | 5 | # LRTC_MusicEEG
This repository has the Matlab (.p codes) and data for one participant (subject 8 in article) related to journal article "Long-range correlations in alpha-band of electroencephalogram: a nonlinear embedding and detrended fluctuation analysis" published in Frontiers in Neuroinformatics 2026.
The data (S... |
a6fd63b022da8fcfba8e44fbcc0dbe0500c654dd29ec93ca6f1099ddebf7e66c | Text | 686 | 26 | # alignment
Spatial registration of calcium imaging datasets to reference images.
## Setup
To create a conda environment using the provided `environment.yml` file, follow these steps:
1. Open a terminal.
2. Navigate to the directory containing the `environment.yml` file:
```sh
cd alignment
```
3. Create ... |
87fbfff5f004f2a7349fc75fa422c149135d8eccb377c87d4e19bbf35bae8a2b | Text | 694 | 19 | # High-Frequency Jumping
# Overview
This repository contains the code for simulating photoreceptor-LMC responses and for analysis tools used in the paper "Synaptic high-frequency jumping synchronises vision to high-speed behaviour".
# Repository Structure
This repository contains the following components: See full d... |
cb5665eafc09e7e6ee809e8f2b5145685b2f9e319f85c45a4a33050d89b8a8c7 | Text | 696 | 23 | # StatisticalAnalysis
A Python toolkit for statistical analysis, integrating common statistical methods and visualization functionalities to help you efficiently process data, perform exploratory analysis, and present results.
## Features
- Core statistical methods: hypothesis testing, ANOVA, correlation analysis, r... |
3f2e9f5b61112d2ed635137a185d7ffbcdadab323485245961f5129cb278dd90 | Text | 697 | 10 | # DRGPatchClampProcessing
This repository contains the scripts used for the analysis of patch clamp data in the preprint:
Nociceptor clock genes control excitability and pain perception in a sex and time-dependent manner
Aurélie Brécier, Courtney A. Bannerman, Yu-Feng Xie, Christopher Dedek, Amanda M. Zacharias, Cia... |
85306b8a3a85a4c604669a29bf165ac38106850704f114973b5a00ddf53330b7 | Text | 700 | 16 | There are 3 folders in this upload:
A. MODELLER files:
- Alignment file, input structures and scripts
B. SILCS simulation files:
- SILCS grid free energy FragMaps for NBCn2 of all probes
C. MD simulation files:
1. Compound38J-bound NBCn2: GROMACS inputs for equilibration and production, example producti... |
4854ac3aa250dee653d1495b1715bc7f139e3d434d6d2bff674f83907e219d7e | Text | 702 | 9 | Codebase for the article: "Simulation-Based Inference at the Theoretical Limit: Fast, Accurate Microstructural MRI with Minimal diffusion MRI Data"
Link to the HCP data used in this study can be found [here](https://www.dropbox.com/scl/fo/ju98vjytfc9770txs5l6x/APVZsLQ_WIHhDhl9PXwJkyU?rlkey=doby7x7snb6tp5is3etvhm8id&st... |
0e8aecd15801bb70acbe84340c7105f4a2d527f73d392117c0c323b94f562308 | Text | 704 | 5 | # Data-for-plots
scRNA-SeqDotPlots.R contains the script to generate the expression dot plots and, if necessary, extract raw data and expression stats from publicly accessible scRNA-Seq datastet published in https://doi.org/10.1186/s12983-024-00529-z. All sequencing data from this paper is available as an R object at h... |
d9d91dfa62efc6dc772ad1d5184aeb9b4e401309258af7c0735742e5321129d4 | Text | 720 | 14 | # ct_sa_across_disorders_and_variants
Code and data for generating Figure panels (and statistics) for the cortical differences across psychiatric disorders and associated common and rare genetic variants.
Fig. 2. Global cortical differences across NPDs and associated genetic variants
Fig. 3. Global cortical differe... |
d53cc3f519c64517032f4b6e5038578933d001ea8bbb23061340bf44027d2c2f | Text | 725 | 29 | # Project Title
> Oneliner about your project
## Abstract
Paste your Abstract in here.
## Publication Links
- [Journal](https://#)
- [Preprint](https://#)
- [OSF](https://#)
- [Zenodo](https://#)
- [Figshare](https://#)
## Repository Structure
### data
You can retrieve the data here ...
### docs
Procedures and cod... |
4b65f5360d50b21a3ba74abc748c9fadfab35f3ea15ea8eec6d5f4ec6225fc40 | Text | 732 | 6 | Program for Analysis of Organoid Stress Relaxation after electrical stimulation. Microscopy files are pre-analysed using Fiji to extract the darker area within the organoid.
The area versus time shows a saw-tooth pattern that represents to contraction due to electrical stimulation, the relaxation thereafter can be ana... |
3f53a7a969d6e617cf1511e44af3441c7d3f904b890be0ca5d921395c9ea8aa6 | Text | 740 | 16 | Release of cortical surfaces for NCBR 3T dataset (anonymized)
The surfaces have been generated using CIVET-Chimp.
These are the registered high-resolution (163842 vertices),
resampled on the NCBR average surface, in native space.
They are presented in MNI-obj and gii formats.
If you are using the surfaces, please ci... |
b9a339873bd97e7591aba2a3617284bc465cd79bc53b95f50f9c5ea19f781a7f | Text | 745 | 10 | # CalciumImaging
Analysis of Calcium Imaging data during different sleep states defined by EEG and EMG measurements.
Please send an email to n.calcini-at-neurophysiology.nl or to antoine.adamantidis-at-dbmr.unibe.ch for the relevant publication to cite for this code or questions.
Start the toolbox (UI) with the "Calc... |
11907bb537579f95f4ce78975799fa34f7cdd5d9fd8c7f84dab8ece467d208f8 | Text | 746 | 14 | ## TGF-β signaling promotes astroglial activation and TDP-43 proteinopathy in organoid models of frontotemporal lobar degeneration (Ramsey et al. 2026)
This repository includes the code used in the analysis of single cell RNASeq (scRNA-seq).
All analysis was performed using **R 4.3** or **Python 3.13**.
Read the ful... |
87c1713319813e45ee352cd38b9f324c2e3f7e4488cd304526c4dc21f9b67783 | Text | 763 | 15 | # Comparative striatum
- The repository includes all the scripts used in paper: https://www.biorxiv.org/content/10.1101/2025.04.20.649707v1
- The numbers indicate order.
- The list of the scripts:
## 01_Generate_NHP_gtf_files
- Folder contains scripts to generate NHP gtf files after liftoff to human gtf.
## 02_Species
... |
ee0a56e004348eca0e678f396582dfdac059600a4f960580180814d4198a456e | Text | 763 | 6 | These codes are designed to run on MATLAB R2021a and Python 3.8.8, and do not require any specialized hardware or install other software. After loading the input data, the above code can be directly clicked to run.
Brain_age_prediction_SHAP_demo.py was designed to predict the brain age and achieve the SHAP value for s... |
f4a3a405c4f0ad48897cfd77751eddae3578c1f7b5ead0c00fe2a01749028ac6 | Text | 765 | 13 | # tmEMD
Tailored Masked Empirical Mode Decomposition
Author: Charlie Clarke-Williams
# Requirements
All figures can be reproduced in the example usage notebook, tmEMD_example.ipynb. All data used to produce figures can be found in the data folder in the main repository. Also included is the iterated EMD module (from... |
725a6b902f746ae33c1764bfbafdda4677072b317053cf36f0f21471b13efdc1 | Text | 768 | 16 | # Project Description
This repository contains the code associated with the publication: ["In-Scanner Thoughts shape Resting-state Functional Connectivity: how
participants 'rest' matters"](https://www.biorxiv.org/content/10.1101/2024.06.05.596482v1).
In this work, we show that resting-state scans that systematically... |
cf7750b2d90fb00c0533207560d6c8afacf69bb7fa9116a6ad3d5bbd14b2e3c0 | Text | 770 | 17 | Copper deficiency impairs oligodendrocyte maturation and social behavior via mitophagy and mTOR suppression in ASD
==========================
This repository contains analysis code for the Copper deficiency project carried out by researchers at the [Shimada Lab, Osaka University](https://www.med.osaka-u.ac.jp/eng/intr... |
ff097d1bf0d0c931d04ab743f8877943a57acb6e4cc818325f56afae898855dd | Text | 772 | 11 | # Takoyaki-imaging
Public repository for Takoyaki imaging scripts and data
## Associated dataset
Dataset can be found via CaltechDATA: [Click here to download](https://data.caltech.edu/records/knnyt-x4762?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImY5YWIyMmJhLTA4NjEtNGMzNS1hNTRiLTRjNzBiNjNmZTI3MCIsImRhdGEiOnt9LCJyYW5kb20iOiJ... |
1f1ac1bdb656b8fecc402d6dd7b746dd583f96b347ac5ed24132a5c3763dec2f | Text | 775 | 9 | ### Behavior analysis scripts for chemotaxis experiments.
This repository contains an R script used for analyzing CSVs containing position information over time for worms tracked over the course of a chemotaxis experiment. Description of how the script is used can be found within the script itself. Script was used to... |
e87202b0c6b40ac3d4691609b1ec3184b17ff73cf04ada8abf4d82b63f4d496e | Text | 776 | 43 | # deepzoom.py: Python Deep Zoom Tools
## Installation
```bash
git clone https://github.com/openzoom/deepzoom.py.git
cd deepzoom.py
python setup.py install
```
## Development
Install for local development:
```
python3 -m pip install -e .
```
## Example
```bash
cd examples/helloworld/
# Single image (DZI)
./hello... |
4dbe1033419617e5d8b74dadf0477fdb8a491366089996de53491b5ff80483f4 | Text | 779 | 17 | This folder contains data to
"How Low-Frequency Neural Activity Structures Language in Time" (Henke, L., Maess, B., & Meyer, L.)
--- Data for Analysis in Matlab
timelock_erf_0.2_30_7_nobaseline.mat Individual ERF for each participant and level
itpc_0.2_4_7.mat Individual ITPC values for each... |
69d0e0b51ddf5f00d7ae82daa652f0f1c44c617ef08ea1514d9465501a9bf743 | Text | 793 | 30 | # sensopro-com-dnn
Repository for the MDPI Sensors 2026 paper: Prediction of Center-of-Mass Kinematics of Sensopro Exercises with Neural Network Models
The open-access paper can be found [here](https://www.mdpi.com/1424-8220/26/10/3051).
## Main Authors
+ Heinz Heigi (@hegih)
+ Michael Single (@simplay)
## Citatio... |
7a67e35dfe4cfe8c043a7b32e8258b99b93fceb777de5b5bb8d78397bae3922f | Text | 795 | 13 | # Sleep reveals dynamics integrating and segregating movement and stimulus representations in V1
This is the github repository with analysis code to replicate the analysis of the accompanying manuscript "Sleep reveals dynamics integrating and segregating movement and stimulus representations in V1".
Sleep reveals dy... |
4a6885c80c2c2a3a45956ed3c9ea1a74911b046c6e0bce63fac3c9a86eb8bd60 | Text | 799 | 8 | # PICRUSt2
Please see the [PICRUSt2 wiki](https://github.com/picrust/picrust2/wiki) for the documentation and tutorials. There is a lot of information within this Wiki about how to install and run PICRUSt2 as well as how it works. *Please* read through this before asking questions.
Note that this repository contains... |
19f159a5662c83b9154b6d93240d2d00666fb15147594fd780faaceb5a443068 | Text | 801 | 16 | # SF Gradient Coupling
This repository is the home to all the code that are used in the paper **Brain Functional-Structural Gradient Coupling Reflects Development, Behavior and Genetic Influences**
## Overview
- `./Gradient-Construction`: Construction of Gradients and Structural-Functional Gradient Coupling (S... |
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