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02fba8ea5bdfbd1b918d9078058dd642460b7db691b45d05e9554d0abc40174a | Text | 347 | 3 | # BrainSpaces
This is the code prepared by Maria Mannone, with the help of ChatGPT for technical details (but with human debugging), to compute brain spaces once having received connectivity matrices as input. It complements the submission "Sketching a Space of Brain States" by Maria Mannone, Patrizia Ribino, Peppino ... |
aa5f07124347b7b8f81adf1b5025a0002e3da1680c18f74d9ffb682430fe6c34 | Text | 347 | 3 | # BrainSpaces
This is the code prepared by Maria Mannone, with the help of ChatGPT for technical details (but with human debugging), to compute brain spaces once having received connectivity matrices as input. It complements the submission "Sketching a Space of Brain States" by Maria Mannone, Patrizia Ribino, Peppino ... |
300ea00da8ab03b498c73c1ce90cd445225188e5e9b7457c087834f1b322a63d | Text | 348 | 9 |
# MediVision
A deep learning-based medical image classification project trained on 10 publicly available datasets using CNN and LSTM with attention. Includes training code, models, and evaluation scripts.
## License
This project is licensed under the [Apache License 2.0](LICENSE).
© 2025 Md. Tanvir Hayat. See the... |
332ccf5f20fae6bb01c005734fae6356de49649afcd1203e90bdc35a79c2b7b1 | Text | 351 | 11 | # KimYang2017_Cell
These files reproduce all results from Figures 4, 5 of the paper
Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and
Subcortical Sexual Dimorphism
Cell 2017
https://www.sciencedirect.com/science/article/pii/S0092867417310693
You can start with main.py.
This code is only te... |
d8daeda27e0a5ccd88b52b9f0e2c69fe9d8d4de359ca37adb7d30db1e330db0f | Text | 352 | 8 | ## README
Repository for Nature communication publication_Integrative brain omics approach highlights sn-1 lysophosphatidylethanolamine in Alzheimer's dementia
#
ROSMAP 3rd revision 09052024.Rmd contains all the code to generate figures.
#
The associated data files are either included as source data within the public... |
28ac04811cc5940e84771da3531c075567c9b73811ce772400f99521dc2544dd | Text | 353 | 4 | # Repository for the publication *Maintenance of neuronal TDP-43 expression requires axonal lysosome transport* by Veronica Ryan et al 2024.
# For publication transparency and reproducability.
explore_and_meta_analyze_screens-Aug_2024.ipynb is the notebook that relates to meta-analyzing screens from Veronica's team wi... |
acc056500146bcc1131e21a19dd5f1454d634f28a4d02736765c4d048bde54e6 | Text | 358 | 2 | # supplementary-of-SCI
Spinal cord injury (SCI) is a devastating condition that not only leads to motor deficits but also results in significant cognitive impairments, including memory dysfunction. Emerging evidence suggests that SCI-induced secondary damage extends to the hippocampus, a brain region critical for memor... |
6bb123919e6aa18026a2d61c6eeb9f1683a66864b0ac2ac4fe220c6dd3b73fa1 | Text | 378 | 6 | # Complement receptor C3ar1 deficiency does not alter brain structure or functional connectivity across early life development
Hanna Lemmik, Eugene Kim, Eilidh MacNicol, Davide Maselli, Michel Bernanos, Zhuoni Li, Dauda Abdullahi, Esther Walters, Maria Elisa Serrano Navacerrada, Wuding Zhou, Aleksandar Ivetic, Diana ... |
8aa61ca8221e5371a5887a4ffb2a1d3054ea6ab9912d7c8985c592f9f160e868 | Text | 382 | 11 | Vizualization fof phagocytosis assay (fluorescence latex beads uptaken) of HMC3 cells treated for 24h with:
1 µg/mL of AgNPs
4 mM of NAC
AgNPs and NAC
1 µg/mL of LPS
AgNPs and LPS
primary Ab: β-actin (cat. sc-47778; dilution 1:100; Santa Cruz Biotechnology)
secondary Ab: AlexaFluor594-conjugated goat anti-m... |
d9e835add8a4419952967272181497eea251696f3f0e238267acbeccc2514d58 | Text | 382 | 7 | # Seq-N-Slide: sequencing data analysis pipelines
[](https://zenodo.org/badge/latestdoi/66501450)
Seq-N-Slide is a set of streamlined analysis workflows for common genomic sequencing assays, such as RNA-seq, ATAC-seq, ChIP-seq, WGS/WES, and WGBS/RRBS.
For more information... |
bacebe2a756e2b99d18afaa37492fa6ba09f03968d0dad24f579cd3d7d846057 | Text | 389 | 7 | Ingression Simulation
Requires Surface Evolver v2.70 available at https://kenbrakke.com/evolver/evolver.html as well as the python packages listed in requirements.txt.
The script "run_sim.py" runs a set of simulations using multiprocessing to call multiple instances of Surface Evolver.
The scrypt "analyse_output.py"... |
32114afdcc8e5f522bc21f277a59f08e031e3a6ced424e4b9d47cff39778e1b6 | Text | 396 | 5 | # A_functional_clock_in_only_two_dorsal_clock_neurons...-Reinhard_et_al_2025
Code to replicate the analyses in Reinhard et al. 2025 https://doi.org/10.1073/pnas.2506164122
Due to size limitations this repository only contains the scripts and only some example data.
To access the complete activity dataset, please down... |
06fd38b5c4bda2749e29db4087c037bf9589825ccee14722890df979f927b6c8 | Text | 400 | 7 | # phd studies in neurodegenerative diseases & neuroimaging
## projects
1. Hemispheric asymmetry of tau pathology is related to asymmetric amyloid deposition in Alzheimer’s Disease
- repository @ [projects/01_tau_asymmetry](https://github.com/teanijarv/phd-neurodegeneration-imaging/tree/main/projects/01_tau_asymmet... |
29b5f9d3ca908a488019fc57035bf732f20fae090f5c4be7e0ca0e5c996a2689 | Text | 401 | 8 | Code for data analysis of calcium imaging data for:
Hawes Sarah, Liang Bo, Oldham Braden, Sullivan Breanna T, Wang Lupeng, Song Bin, Chang Lisa, Lin Da-Ting, Cai Huaibin (2025) Patchy Striatonigral Neurons Modulate Locomotor Vigor in Response to Environmental Valence eLife 14:RP106403
https://doi.org/10.7554/eLife.106... |
c2ce4c04a2a3a7c3a563ac3d402d300409e20aab75c242b4042f81fba9b3db3e | Text | 404 | 20 | # chipseq_cross_species
Link to project [website]
[website]: https://lecook.github.io/chipseq-cross-species/
## Data management
```
chipseq-cross-species/
├── analysis
├── data
│ ├── genomes
│ └── raw_reads
├── docs
├── code
│ ├── dunnart_peak_calling
│ ├── mouse_peak_calling
│ └── whole_genome_alignment
└... |
9c4f5d804e4d1f7e312cdf21ae010b9ae619de5ef374d5b41f42e3101c1c74b6 | Text | 406 | 13 | # positrack
positrack is a software to track the position of small bright blobs in a video. It runs on linux computers and works with firewire cameras compatible with the libdc1394 library.
# Download
To get the source code: `git clone https://github.com/kevin-allen/positrack.git`
# Install
For a more complete se... |
edc751ea1d3d7d79c0ad79e9ccaf7d0cd6bc1ff6d66bf81821ac90fddd442691 | Text | 410 | 9 | # linearRegression
Outputs regression coefficient and p-value from input file containing paired x and y coordinates
Synopsis: return r and p values for linear regression
Usage: vga_linearRegression inFile
Notes: inFifle is a 2-column file with paiwise data. Edit Makefile to point to the BOOST library and preload any... |
4a02377d1e71afb36fe8fba146fb96bcc5e9bac06e5bc15e9744aa2101a5e6bd | Text | 415 | 4 | The data and analysis programs required to reproduce the Ouchi et al., 2025(DOI: https://doi.org/10.7554/eLife.97270) content are included.
The Figure_data content can be output from the mat file analysis code for matlab/Figures_revised.m.
Due to storage limitations, raw data has been omitted. For both in vitro and in... |
756e41e6bedee6a6f9d15ac9fa7e7668cbc49def58584df7bd177bd3462b3c37 | Text | 422 | 6 | # HABITS
Home-cage Assisted Behavioral Innovation and Testing System
Behavioral raw data can be found in https://doi.org/10.6084/m9.figshare.27192897
Reference: Yu et al. 2025. Novel and optimized mouse behavior enabled by fully autonomous HABITS: Home-cage assisted behavioral innovation and testing syAssisted Behavi... |
1d4961c1040243a3483a4862f339ecfdb5241adcf157b7c2e39574d7f73b6797 | Text | 424 | 6 | # PRS-brain-cognition
Scripts for studying age-related links between polygenic risk, brain measures, and cognition in large datasets (e.g., UK Biobank).
Source and citation:
Chen HJ, et al. Polygenic risk for Alzheimer's disease in healthy aging: age-related and APOE-driven effects on brain structures and cognition.
G... |
c1f4046e69c0a7b956ca9f3cab06aa8eb8cc37a6b78415366156d6830d0d9a87 | Text | 432 | 24 | # CLRIA
CLRIA: connectome-constrained ligand-receptor interaction analysis for understanding brain network communication
## Installation
* Install from PyPI: `pip install clria`
* install from source:
```bash
git clone git@github.com:duzc-Repos/CLRIA.git
cd CLRIA
pip install .
```
* [O... |
23451803cd2ed478c3da911edbc2d4e01faed8e24e38d8c2b2759c8796f5c378 | Text | 436 | 4 | # LuciAge
Code Repository for the paper "Targeting Cdc42 Improves Motor Phenotype in Parkinson’s Disease Mice and Reveals Age-Dependent Susceptibility to α-Synuclein"
The raw sequencing data that was generated in this study is available from ArrayExpress with the identifier E-MTAB-14889. Detailed metadata, the process... |
21e64f5f5535e4247da459991d68c254b9aeab46c5359f68f28bbc8794aefcc7 | Text | 445 | 10 | # Citing
If you use this code or derived results, [please cite our manuscript, https://doi.org/10.7554/eLife.92964.3](https://doi.org/10.7554/eLife.92964.3):
Longjun PuLina Zhao, Jing Wang, Clementine Deleuze, Lars Nilsson, Johan Henriksson, Patrick Laurent#, Changchun Chen#, 2023, <b>Avoidance of hydrogen sulfide is... |
5975961ce2133e9f851a15fa14e4dc66e20a1021910005c7800e9f6f8bd4c7da | Text | 445 | 21 | # pubextract
A collection of [pubget](https://neuroquery.github.io/pubget/pubget.html) plugins and utilities for extracting information from **pubget** datasets.
## WIP
Not much to see here for now, the repo is under construction!
## Installing
```
pip install -U pubextract
```
## Participant... |
7ffc07b19c336962f688bcfe8224cb208611642343b6aae896bf2f8af9ff9534 | Text | 445 | 6 | # Incremental_Self-Organization_of_Spatio-Temporal_Spike_Pattern_Detection
This repository contains the codes to implement the model described in the manuscript "Incremental Self-Organization of Spatio-Temporal Spike Pattern Detection".
For the simulations presented in the current version of the paper, refer to the f... |
519cd77f44ad621a5bd39bb85c30048431df3734e0521a6e504dfa3dfe4cef0c | Text | 446 | 6 | # White-Matter-DES-Brain-Maps
White matter brain maps derived from DES and MRI, both rsfMRI and DWI.
Accompanying code for the publication "Integrating direct electrical stimulation with brain connectivity predicts lesion-induced language impairment and recovery [INSERT LINK HERE]. Data can be downloaded from Zenodo:... |
f4358d4297e873dc59122a96ddde6f99ccf3aac9bfbc3cc78377355953adae56 | Text | 449 | 20 | # Photobleacher Simulator
Tools to simulate a photobleacher.
Relevant paper:
> Murakami et al. Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues. (2025)
### Software prerequisites
Tested on Ubuntu 20.04 LST with the following versions of software.
- Python 3.9.19
- Scipy 1.13.1
- Num... |
27f5e742a813b704cf292dbae2f3e62faaa5a3860ed9524c94f5760697c557a4 | Text | 453 | 10 |
- dataset: goodscent and leffingwell
- experiments: GAT, GCN and NNCONV models trained with goodscent or leffingwell dataset
- gat_goodscent (for example)
- config:
- best_config.json: the best model configuration
- grid_search_config.yaml: the grid search configuration
- models: baseline and GNN-bas... |
d07db5b46c3eb7bba7955d1fdde9432178137ccffac0e87b9a35d863cf43b153 | Text | 454 | 5 | # Functional Summary-based Imputation
FUSION is a suite of tools for performing transcriptome-wide and regulome-wide association studies (TWAS and RWAS). FUSION builds predictive models of the genetic component of a functional/molecular phenotype and predicts and tests that component for association with disease using... |
9db583167771e8a8de793630f3e2f1f24f3a438636822c90b2a5c7450c65bab5 | Text | 466 | 5 | # Comparing and Scaling fMRI Features for Behavior Prediction
This repository contains the code for the paper Comparing and Scaling fMRI Features for Behavior Prediction.
The scripts to run the main analyses are in the folder `scripts`. They are numbered according to the order they need to be run in. The `src` folder... |
edad8df999767df442e168e0ef086e898530bb2cd8ef1de49256ab99c5ca1217 | Text | 467 | 11 | # labelbuddy-annotations
Annotations of academic papers.
The papers were gathered using [pubget](https://github.com/neuroquery/pubget), and the annotations made with [labelbuddy](https://jeromedockes.github.io/labelbuddy).
See more details in the repository's [website](https://litmining.github.io/labelbuddy-annotatio... |
f52a9391700935fad3a63bd9e482a2c4ae6e44b20aef3573599b45a1cb220639 | Text | 470 | 3 | # NeurixAI
NeurixAI is a deep learning framework for **predicting tumor drug responses** from transcriptomic data and drug features. It processes tumor gene expression profiles and drug representations through neural networks, then models their interaction to predict sensitivity or resistance. Using explainable AI (La... |
97c25736ac55e949b826e0cc13ec94f58e42680d63f0d895fb0ccd3ebc35655e | Text | 474 | 9 | # SST-IN_development
Code for "Delayed integration of somatostatin interneurons into visual circuits", Wang, Ferguson, et al. (bioRxiv, 2024)
This code was developed on MATLAB version 2022b with Ubuntu 20.04 LTS, and has also been tested on macOS Sonoma (Version 14.5). The code is compatible with MATLAB 2022b or lat... |
432e8fdea4f42e582dd41ed010280b1f911faf998e0c6cf91b5176e4ea83f672 | Text | 476 | 7 |
## Welcome to the PAWS package!
PAWS is a processing pipeline using pose-estimation software to score paw withdrawal behavior. Based on Jones et al. (2020) A machine-vision approach for automated pain measurement at millisecond timescales.
To learn how to install the package, navigate to [Installation](https://osimo... |
0b92b9da2a1538a45a30140c360d23fe6b034b31018099bbc9378aa277002330 | Text | 490 | 13 | # GM-CB-AD
Shield: [![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa]
This work is licensed under a
[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa].
[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa]
[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0... |
068b9257f072d8a4a5428cbdea54a4a98fbd76052392b73749d56165553f49b3 | Text | 503 | 16 | # Bayesian-hierarchical-model-for-PI
Code repository for the model used in "Path integration impairments reveal early cognitive changes in Subjective Cognitive Decline".
## Installing dependencies
To install the dependencies please use any of the following:
### pip
```bash
python3 -m venv numpyro_env
source numpyro_e... |
d5ab3a1eb0669be3da5dfa1073cc459ba8bc9297fe9b39f267923a85f89ad71e | Text | 522 | 14 | # amygdala_7T
Code repository for primary analyses and figures for Ojha et al., 2025 in Cell Reports
## directory organization
'fmri' contains general processing scripts for the neuroimaging data to compute functional connectivity.
'psych_decoding' contains scripts specific to the psychological domain decoding analy... |
b1554ad842be65e3a40d35930e38f79f66f2bcf5db0c1c1bfa8d773ab7b2c982 | Text | 526 | 22 | # CoRTE - Web Service (WS)
This reporisory contains source code and additional material related to "CoRTE: a web-service for constructing temporal networks from genotype-tissue expression data".
### USAGE
(1) Installing a web-server, we suggest "uvicorn" (https://www.uvicorn.org):
> pip3 install "uvicorn[standard]"... |
abed2cc657c0ed713b45492c630f3b3a404a2bfb588aee53fb532b6d07a0e7a8 | Text | 531 | 20 | # Visualization-of-3D-network-map
### 1. Introduction
Python code for visualization of 3D network map.
### 2. Requirements
- Python 3.*
- Packages: jupyter notebook, community, networkx
```shell
pip install notebook
pip install python-louvain
pip install networkx
```
#### 3. Demo
- Run the ... |
b5aa2f4d880e053f8e32845850c9f48578308bfaf4f480f4b2a542fc5dc9158f | Text | 558 | 27 | # Aisenberg2025
## Juptyer notebook to generate Extended Figure 15 b-g
## software dependencies:
see requirements.txt
operating systems: Windows11Pro 24H2
## Installation guide
download the repository
install keypoint-moseq
https://keypoint-moseq.readthedocs.io/en/latest/install.html
typical install time: 20 mi... |
ce9f622656fb1ebc4279d6c9e2fc7fee4029595702412e3e9637196ae53dc46c | Text | 560 | 22 |
# Building the ASL models
The current version of the ASL models are designed to build with the latest
version of Fabber from FSL. Although it may be possible to build them against older FSL
releases this is not guaranteed.
Build instructions for Fabber core and model libraries can be found here:
https://fabber-c... |
6905c2b57570c1ce80c4ed34eee2774eee6f9013dec3bc65b790b81f1966919c | Text | 563 | 18 | # amygdala_7T
Code repository for primary analyses and figures for Ojha et al., 2025 in Cell Reports
## directory organization
'fmri' contains general processing scripts for the neuroimaging data to compute functional connectivity.
'psych_decoding' contains scripts specific to the psychological domain decoding analy... |
fa37537f71f1627a392aeb0368002cc6075b0f869ad8de2ca3568ac547f118c1 | Text | 566 | 11 | [](https://travis-ci.org/satra/mapalign)
This repo implements diffusion map based embedding [1] and alignment [2] algorithms.
[1] http://dx.doi.org/10.1016/j.acha.2006.04.006
[2] Langs, Golland and Ghosh (2015) Predicting Activation Across ... |
57ffdda9ef232dc84ae0c2c57dc9ea9371873e1188e08875bdb714e19f6ffbd6 | Text | 572 | 7 | 1. Utilize 2D interaction from RIC-seq and RNAstructure package to predict the secondary structure of SARS-CoV-2 genome RNA
2. Once SHAPE or DMS data are publically available, the predicted structure could be further improved.
3. All the commands are recorded in a shell script named 'run.sh' or 'work.sh' in each fold... |
e51860b179fb13e4d303af5e11855c22723d57f323d876e63ce45be9d333b47d | Text | 578 | 21 | # cbm
Contains matlab scripts for "computational and brain/behavior modeling".
## Requirements
MATLAB and its optimization toolbox
(tested with matlab2014b and higher)
## Installation
Download and add it to your matlab path.
## Manual
See manual.pdf or manual.html
## Python version
There is a python version of the ... |
42ea4a65bc8660e30e612887d2303f00b16c4a674d6b8d71988b2df04ae44322 | Text | 581 | 13 | # autopipy
This is a python package to analyze the data we collected on the AutoPI task.
It relies on several python packages (opencv, deeplabcut, etc).
The aim is to have all our code to anayse our autopy data sets within a single development environment (python/jupyter lab).
The variables extracted from each tri... |
ed9c05d1a4c4716546ad722f2310c50fc6db486f6b3e9f0ed8204d219c9dc56f | Text | 585 | 6 | # Chappel-Farley_2025_Sleep-NetworkArchitectureSleepConsolidation
This repository contains the scripts used to generate network metrics from resting-state fMRI data
If you use this code in your research, please cite our paper:
Chappel-Farley MG, Adams JN, Betzel RF, Sattari NS, Berisha DE, Meza NJ, Janecek JT, Niknaz... |
32affea3b6f02e22e2f9150bd73b63111a2a5fc2007de5df40e2badecc1dcbe2 | Text | 586 | 12 | # StochasticAgingClock
The repository contains the custom code for our paper:
Accurate aging clocks based on accumulating stochastic variation
https://www.researchsquare.com/article/rs-2351315/v1
Meta information for RNA-seq samples used in the paper can be found in SupplementaryTable1.csv
DNA methylation samples c... |
0eb37514dfcabe81242b5e85700743f6d21f80addde93d2f8eda61efdaba24c3 | Text | 590 | 7 | # neuropsychiatric_risk_gene_isoforms
Companion data and scripts to our risk gene isoform manuscript (2025), pre-print available: https://www.medrxiv.org/content/10.1101/2024.02.22.24303189v2
The data files contain the results presented in our paper for 31 risk and 2 non-risk genes and can be uploaded to IsoVis to vi... |
6da15f84243f4218c25daec46ee96cf8fe7879dc09344d763e1bc71d9c3b34e8 | Text | 591 | 10 | ==============================================
BrainSpan: Atlas of the Developing Human Brain
==============================================
This data set contains RNA-Seq RPKM (reads per kilobase per million; see the whitepaper at
www.brainspan.org) values averaged to genes.
expression_matrix.csv -- the rows ... |
2c78f2df786ca0e6756a347ab1d48eba35867d1d59246de634af2e3b0f72afa4 | Text | 611 | 21 | # This repository contains the code to replicate some of the results from:
[Breyton, M.et al. Spatiotemporal brain complexity quantifies consciousness outside of perturbation paradigms. eLife13 , (2024).](https://doi.org/10.7554/eLife.98920.1)
To generate the resting-state simulations run:
```
snakemake -s snakefil... |
d15ce5726ddc97b50610637f4228f557cf0e850bc9381142db751c8a664bbc3c | Text | 616 | 12 | # PyPARRM
A Python signal processing package for identifying and removing stimulation
artefacts from electrophysiological data using the Period-based Artefact
Reconstruction and Removal Method (PARRM) of Dastin-van Rijn *et al.* (2021;
DOI: [10.1016/j.crmeth.2021.100010](https://doi.org/10.1016/j.crmeth.2021.100010)).... |
12b6ef84cffdf5d8e51e5a680814b9b6c691780a39975db3ba362a84129f831f | Text | 621 | 21 | PD control Simulink robot arm
Continue to optimize PD parameters based on PD control
1. Three files required for the robot model:
RUDF % robot model folder
DOF6_xArm.slx % Simulink modeling
loadrobot.m % load the robot into the workspace
Only with the above can the robot model in Simulink be called
2. PD p... |
778949dee44612974bf28b0f2bbafe2b072ad7381e400e408a78b5c85b5f1681 | Text | 649 | 18 | # CPC: A cerebellar population coding model for sensorimotor learning
See https://doi.org/10.1101/2023.07.04.547720 for the description of the model.
Contact: tianhewang@berkeley.edu
Required package:
circstat-matlab: https://github.com/circstat/circstat-matlab/blob/master/circ_vmpdf.m
This is a MATLAB code that was... |
8708234e802cb8d50f0893a8ccf3b6392aad4eb1611fd2ebceee6d628fa932ae | Text | 651 | 20 | # Code to replicate analysis of Schmidt et al., 2025
This repository contains code to replicate the study presented in Schmidt et al., (2025)
Unraveling the mesoscale functional connectivity of the human primary visual cortex using high-resolution functional MRI. bioRxiv. DOI: https://doi.org/10.1101/2025.03.27.645795... |
1782a7ae162ed0c93d832cf4b5369a4292786d8a8c13cd7631d826070e4b08f6 | Text | 653 | 11 | The repository contains data and analysis script used in the research article "GPT-4V shows human-like social perceptual capabilities at phenomenological and neural levels" published in Imaging Neuroscience in 2025, (https://doi.org/10.1162/IMAG.a.134).
Code by Severi Santavirta, Yuhang Wu & Lauri Suominen
Detailed d... |
da9cf6e6aba9bd3303f0808e94dc66fabc8dfaaf889f7d8762e1343454b72bf9 | Text | 657 | 18 | ### Beware: this is alpha code at best
This is an attempt to implement the core functionality of [The Virtual Brain](https://www.thevirtualbrain.org/tvb/zwei/brainsimulator-software) brain simulator [root](https://github.com/the-virtual-brain/tvb-root) project in C++.
### Dependencies:
* [Eigen](https://eigen.tuxfam... |
70f70f2b2e457600b234c695005c4eca0e7acde5b16d4cc3719dfeb4d3d2831c | Text | 667 | 21 | # SpikesPy
A graphical user interface (GUI) designed for annotating stimulus-locked electrophysiology data, specifically tailored for microneurography research.
## Getting started
### Installation
To install SpikeSpy, we recommend using `uv`, modern Python application managers.Learn more about `uv` and how to inst... |
2f42a661aff10f15395c47aeb239f085af0d8c468717548cb747773485967a08 | Text | 675 | 12 | # decision_dynamics_commitment
Code and data accompanying: Luo*, Kim*, et al. (2025). Transitions in dynamical regime and neural mode underlie perceptual decision-making. PMID: 37904994
The repository is organized into three main directories:
* `code/`: Analysis scripts and figure generation code, organized by figure... |
8445ee5644c9fe8cca5a98aa47d3e943809366a369b65d70cda180e13ba26ba5 | Text | 682 | 19 | # Contents
This repository contain all analysis code and scripts used in Kozlova A et al., 2015.
## Directory structure
This repository merged code and scripts generated by both the Duan lab at RI, NSUHS and He lab at UofC.
Code generated by Duan lab are placed under [SZHANG_code] (./SZHANG_code).
Cod... |
852d57ad9491845886fd1096c77d0d925e47da9f4bd659970bffcbbde89eb421 | Text | 688 | 10 | # Data and scripts for the METL manuscript
[](https://zenodo.org/doi/10.5281/zenodo.10819536)
This repository contains supplementary datasets and scripts for the METL manuscript.
For more information, please see the [metl](https://github.com/gitter-lab/me... |
8869b199fc8fe6941071ce613642d720c51d95bf300d0efc5ba1954feb94e6ee | Text | 688 | 16 | # SSI-stacked-ensemble-predictive-algorithmic-model
The code delineates the development of stacked ensemble algorithmic model that predicts SSI after posterior lumbar surgery (laminectomy and/or discectomy) without fusion for spinal degenertive diseases.
We welcome the model to be explored by the scientific communit... |
cd6112de098adf46fbce63c53cc774b26ca65743652a55eea6edb0e0fdeeef1a | Text | 701 | 14 | The unedited (non-colored) and merged (colored) images show HMC3 cells treated with:
1 µg/mL of AgNPs
10 µM of JSH-23
AgNPs and JSH-23
4 mM of NAC
AgNPs and NAC
Immunostaining details:
Primary antibody: anti-TLR4 (cat. 30400-1-AP, dilution: 1:100; Proteintech)
Secondary antibody: FITC Goat Anti-Rabbit IgG (... |
93d318f0b261b0e7c2fb70bfdda16a7b4cb17f1100acee21a9cea7ab1d149d17 | Text | 703 | 6 | # Demonstration of various ML-based XC functionals
This repository contains the .ptc model files for the NNLDA, NNGGA, and NNGGA-UEG XC functionals (see `models/` directory). It also contains straightforward demonstration on how to use the files. The `demo/demo_NNLDA.py` provides the demonstration on how to use the NNL... |
f6bc9e75d6075634d3954e2438776f31f21833bdb5a4c4e214b0a4c0d4192352 | Text | 707 | 18 | [](https://alleninstitute.org/legal/terms-use/)
# All-active-Manuscript
Codes for generating figures presented in the All-active manuscript.
## Instructions
To run the notebo... |
b06e661af94d9bb8717f5d07a45ead5771ade5eaff31d45a41c44e3fd289e32c | Text | 708 | 11 | # neuropsychiatric_risk_gene_isoforms
<a href="https://doi.org/10.5281/zenodo.16416952"><img src="https://zenodo.org/badge/782291396.svg" alt="DOI"></a>
Companion data and scripts to our risk gene isoform manuscript (2025), pre-print available: https://www.medrxiv.org/content/10.1101/2024.02.22.24303189v2
The data... |
ca47cafb30c0cf82dd81eb9e010b8cea6b3a38fcebf3b61143304c07ba8c6f49 | Text | 722 | 17 | FMRI dataset acquired for the Trapeau et al. (2025) Open Research Europe article on complex sounds mapping in anesthetized macaques.
Trial-types, onsets and durations are in the 'sourcedata' folder in the '.mat' files that correspond to each run. Each '.mat' file contains one 'ScanLog' variable. In this variable, even... |
0880bb9574a999bca45502c370adeab51ce723f989d36504cbf6a28d4af99938 | Text | 729 | 9 | An active learning method that integrates Finite Element Method (FEM), Convolutional Neural Network (CNN) and Monte Carlo Tree Search (MCTS), aiming at high-efficient designs and optimizations for 3D mechanical metamaterials.
# MCTS-AL
Main code of model training and sampling processes of the workflow
# Automatically F... |
ce6ffe6e61d0a97519c935ae6a3a63318b86d67d74d115b78dcf982390bf28d6 | Text | 743 | 9 | # BLAKJac_share
Julia language script examples for the use of BLAKJac sequence-optimization.
More specifically, two scripts are provided:
* SequenceGenerationScript: for the generation of RF-pulse sequences as shown in figure 1 of a manuscript on the benefits of applying an optimized phase to RF pulses. This script use... |
a571ce6a7da0c5b04497b99e2e888bc2ea5daa1505a1928e6d96c1ea6ca4b105 | Text | 745 | 15 | Codes for the following manuscript:
-----
Online reinforcement learning of state representation in recurrent network: the power of random feedback and biological constraints
Takayuki Tsurumi, Ayaka Kato, Arvind Kumar, & Kenji Morita
https://elifesciences.org/reviewed-preprints/104101
2025 eLife
Corresponding auth... |
66430f8a8e028bfdf5816f8563d84a5a4c450a5a166d252d44d9992f05d2fcf7 | Text | 749 | 10 | # Comparative transcriptomics reveals human-specific cortical features
Analysis for a manuscript focused on comparative analysis of single nucleus RNA-seq data derived from post-mortem cortical tissue from humans and four non-human primate species: chimpanzees, gorillas, rhesus macaques, and common marmosets.
* Citat... |
b95b6b9e9984e9630de529c757353afd4a993639acace3cbb55400c78b0f6ab6 | Text | 754 | 16 | # CBCT2CT_cDDPM
Official repo of CBCT-Based synthetic CT image generation using conditional denoising diffusion probabilistic model. Med Phys. 2023; 1-13. https://doi.org/10.1002/mp.16704
It is also a general framework for any image-to-image translation task using a conditional denoising diffusion probabilistic model.... |
851f91293dadf9d6ad84f55ae71296c399d2ebb04e8bed796d0b278b6f1839d6 | Text | 768 | 10 | # Publication Resources
This repository contains supplementary materials for the publication titled "Comparison of machine learning and thresholding-based image analysis pipelines for high-throughput phenotyping of walnut kernels from staged images" It includes the scripts used for the analysis presented in the articl... |
5f0eafac0f07a555a30bc3dcbc94defd8582840d30c4acb5b2a5554849b2e43d | Text | 771 | 8 | # splitBrainNetworks
Preprocessing and analysis code for 'Full interhemispheric integration sustained by a fraction of posterior callosal fibers'.
Callosotomy patient imaging data (raw and/or various derivatives) can be made available upon reasonable request.
The code is provided 'as is', without any warranty. To rep... |
78e321afb791ba8a17d2d9bcc73b720a4c679daf9aae28e94988c8a62661bfa5 | Text | 781 | 22 | # Va3DE
Va3DE: Variational 3D Embedding for Single-Cell Hi-C Clustering
To run Va3DE download and install the package:
```
git clone https://github.com/JinLabBioinfo/Va3DE.git;
cd Va3DE;
pip install .
```
Then you just n... |
d8091acdedf270e21bdb2822b383e07231114621346418fd43c918c5ca5e2992 | Text | 782 | 17 | # meningeal_neut
## neutrophilstress01.Rmd
Meningeal single cell analysis: cell cycle, ribosomal genes, view differential expression results
Code continues from https://github.com/maryellenlynall/2019_bcell_stress/blob/master/bcellstress24.Rmd and https://github.com/maryellenlynall/2019_bcell_stress/blob/master/bcel... |
7410673d2b545d59aee11edfe43668c18a249de86ba9656ceada8c685d9b6818 | Text | 793 | 16 | # Model of the circuit for generating song and vibration in _Drosophila_
Code for
_A neural circuit for context-dependent multimodal signaling in Drosophila_
Elsa Steinfath, Afshin Khalili, Melanie Stenger, Bjarne L. Schultze, Sarath Nair Ravindran, Kimia Alizadeh, Jan Clemens
[preprint](https://doi.org/10.1101/2... |
650e801b5b25225ff3cfa33a43117338df9bb4d3433c0d0fddad7c41b98366cb | Text | 797 | 18 | # RL_models
reinforcement learning
X matrix as N x 5 (N = trials)
1st column: Choices for option A
2nd column: Choices for option B
3nd column: Choices for option C
4th column: Reward/Feedback Received
5th column: Non-presented option (A, B or C)
6th column: Start of new block
References:
1) Determining a role for ... |
1b1822ac5f89f43228918a4bcd8bfef55031d4dcefc3401f8655cab1acac4a9f | Text | 798 | 16 | # SWISC
Pipeline for sleep-wake, seizures and post-ictal state classification in mice
Brandon J. Harvey, 2023-2025
Please see BioRxiv publication: https://www.biorxiv.org/content/10.1101/2023.04.07.536063v2
Pending review after submission to eNeuro.
Input files were recorded with Spike2 and saved in .smrx format. ... |
3c778d0bf3b873015dcba491e898a99b7cd19f315debbfca7fb77d53b5661d44 | Text | 808 | 14 | # Data-driven elucidation of flavor chemistry
Datasets generated from the review paper, Data-Driven Elucidation of Flavor Chemistry, https://doi.org/10.1021/acs.jafc.3c00909
We collected 65,417 data records, containing the molecule names, CAS registry numbers, SMILES, and flavor descriptions, from publicly available... |
c7b6f7fa09258c18277152b2dc307ee39c51f8f55b581837ffdaf7c5787555d4 | Text | 815 | 15 | This repository includes code for simulation and analysis of optically evoked postsynaptic neuronal responses following sequential and patterned optical stimulation of presynaptic neurons.
The results of this repository have been reported in details in the following paper
Compressive sensing of functional connecti... |
3226941349b16bd7d597816e4eaf1b17a473f94445df62f57e6168c9613d3969 | Text | 818 | 9 | # Pulvinar-Gradients-Multimodal
This repository contains codes to reconstruct multimodal pulvinar gradients and related volumetric maps.
Further details can be found in the reference paper:
Gianpaolo Antonio Basile, Augusto Ielo, Lilla Bonanno, Antonio Cerasa, Giuseppe Santoro, Demetrio Milardi, Giuseppe Pio Anasta... |
4ff372feea7a6c07b53a887a13b87e5515fefa84598174c32ef9eb2e2df29a1b | Text | 819 | 8 | # In vivo differentiation of embryonic cells devoid of key reprogramming factors.
<img width="1800" height="1800" alt="graphical-draft-4" src="https://github.com/user-attachments/assets/435cc1f2-422f-46f0-bd05-47f6125c6fd1" />
This repository details the analyses presented in _In vivo differentiation of embryonic cel... |
78ad55555aa47bb9b3e462301513deaac6a4419f50db9c8fec3b2926a4344c84 | Text | 823 | 18 | # Code and Data for "Inter- and Intrahemispheric Sources of Vestibular Signals to V1"
By Guy Bouvier, Alessandro Sanzeni, Elizabeth Hamada, Nicolas Brunel, and Massimo Scanziani
---
## Overview
This repository provides the Jupyter notebooks and full dataset accompanying the paper:
> Bouvier G.*, Sanzeni A.*, Hama... |
6ce6f78ba8bdab2756693be105b72107c0d1bd9d5f9b04844f794f2c909b34f7 | Text | 825 | 15 | # PyPARRM
A Python signal processing package for identifying and removing stimulation
artefacts from electrophysiological data using the Period-based Artefact
Reconstruction and Removal Method (PARRM) of Dastin-van Rijn *et al.* (2021;
DOI: [10.1016/j.crmeth.2021.100010](https://doi.org/10.1016/j.crmeth.2021.100010)).... |
6ae440040cc04aae55c0291455bbd808fe5eead01be145c182277596922ddf0a | Text | 840 | 31 | # DNAm_Atlas
Pre-install software and R packages
This repository contains code and data for the paper:
**"A ternary-code DNA methylome atlas of mouse tissues"**
## 📄 License
This repository uses dual licensing depending on content type:
- 🧪 **Code** (`script/` folder): Licensed under the [MIT License](LICENSE)
- ... |
b114584775c54d2f7afccdaaad1f6458599316a19dd4ea008607bb98ce402b62 | Text | 869 | 19 | Data from: Microsaccades strongly modulate but do not directly cause the EEG N2pc marker of spatial attention
contact: Baiwei liu (b.liu@vu.nl) and Freek van Ede (freek.van.ede@vu.nl)
The EEG data is collected in Biosemi system and the eye data is collected in eyelink system
To analyse the raw data, here is the trigg... |
7172952c72d9fa0d04cd8bff4d47e0dfeb6c9d4ee9164519235281b43e3f2c15 | Text | 895 | 17 | ## From HoloBrain to HoloGraph: A Very First Step to Explore Machine Intelligence for Connecting Dots on Graphs
```plaintext
HoloBrain_HoloGraph/
├─ Holobrain.py # Script for computing Holobrain (CFC)
├─ source/
│ ├─ data/
│ │ ├─ create_dataset.py
│ │ └─ dataset.py # Data... |
8d928ea451b2496fd3987dcb06e48b89adf2b4cc1c77a47e55a175fe78b1dcaa | Text | 897 | 28 | # Photobleacher
Photobleacher is an open-source photobleaching device designed to bleach autofluorescence and pigments in biological materials. For more details about the project, please refer to our [publication](https://doi.org/10.1101/2025.02.24.639965).
## About This Repository
This repository contains the foll... |
a6e51e31108708b6d030faba8bad25a467a3049d0f05e16c46ad8d3f99fdb65b | Text | 901 | 39 | # Saraiva_2025
## Introduction
This is the code repository for the "Parkinson's disease mutant Miro1 causes mitochondrial dysfunction and dopaminergic neuron loss" project.
Please check our manuscript at [doi: XXXXX](https://doi.org/10.1101/2024.09.30.615801).
## Authors:
Project team:
Claudia Saraiva
Please ci... |
878088dc352ba4fa090fee55f9f93c8670c59f32d0476137b211dabdba293a32 | Text | 911 | 38 | # AI-Sleep
AISleep: Automated and interpretable sleep staging from single-channel EEG data
Sleep EEG analysis
## Dependencies
* Python 3.8+
* lspopt==1.3.0
* matplotlib==3.5.0
* mne==1.6.0
* numpy==1.26.2
* pandas==2.1.3
* scikit-learn==1.3.2
* scipy==1.11.4
* seaborn==0.13.0
* scikit-image==0.22.0
... |
05b1090964d84ff114cafe6ec0409fad9279903fc2cebe8c2cdfb092282803ef | Text | 919 | 15 | This dataset contains tablular data and code for paper "IVF and Thermal Manipulation at the First Cleavage Stage Alter Offspring Circadian Phenotype, Sleep, and Brain Epigenetics"
contents:
* data_src/ -- data directory
* data_src/mass_glucose_itog2.csv -- scalar measurements for the animals (mass, glucose tolerance, ... |
16dd42a9cf8c03111c5305bc38fe2b04e70722fa39c1865559a4d675b6321e12 | Text | 921 | 23 |
Authors: Mallia Geiger, Victoria Meslier, Mathieu Almeida
The html document contains the code and figures presented in the paper titled "Exploring the Relationship Between GBA1 Host Genotype and Gut Microbiome in the GBA1L444P/WT Mouse Model: Implications for Parkinson’s Disease Pathogenesis."
The analysis focus... |
baba8a34a44dc3a03e9ad97b20bd05fafc7c3e27ca6b7d17fa07857360143189 | Text | 926 | 9 | # Cell_Type_Evolution
Code used to study evolution of cell types. Each subfolder contains a README to describe the code therein.
First, we used Convert_RDS_h5ad.R to convert the RDS files to h5ad files for use with scanpy.
Next, we used the code in Pseudobulk_FilterOrthos to downsample cells across 100 iterations, ps... |
846a3371853601f762af41dcc2e3596c4452a5cd87a0fab1edcc0d7e44501ae7 | Text | 936 | 18 | # Initialisation and topology effects in decentralised federated learning system
For running a simulation, generate a network in form of an edge file, using,
e.g., Reticula or NetworkX, and pass it to federated.py. To see all parameters and
options, simply run `python federated.py --help`.
```python
import networkx a... |
6e5858cf2543d9a0c4f5f50f5a78755aeb3ec6b715a93c3d3e21c967f3d56180 | Text | 941 | 16 | ## This project is developed by Lab of Functional MRI Technology (LOFT, www.loft-lab.org)
### Work can be cited as:
Shou, Q., Cen, S., Chen, N., Ringman, J. M., Kim, H., Jack, C. R., Borowski, B., Senjem, M. L., Arani, A., Wang, D. J. J., & for the Alzheimer’s Disease Neuroimaging Initiative. (under revision). Generat... |
5d45efa2ba9f23de83191dca72b7e64aa5e3141d536ff86bc5ebf8aaef673f9e | Text | 953 | 9 | # FLIMvivo
"FLIMvivo.py" fits CSV data from FLIM measurements either by convolution or tail fitting. "FLIMseg.py" is a helper script that takes segmentation TIF files and PicoQuant PTU files, extracts the decay data, saves in CSV format by segment, and attemps to call FLIMvivo for them with the appropriate options. Bo... |
991647088c0c22483d4f7c7f764fbdf77c875a21603b38e2d2387073ccbb8bdf | Text | 963 | 18 | ## Recurrent Mechanistic Models (RMMs)
The main branch of this repository contains the code used to produce the results in the paper:
*"Rapid, interpretable, data-driven models of neural dynamics using Recurrent Mechanistic Models"*
Proceedings of the National Academy of Sciences of the U.S.A. 122 (32) e2426916122... |
52d827650b7c8a89dc649049e555b42c7a4b3189e30a755c8d6d1aeca46d9dad | Text | 965 | 30 | # Welcome to this readme
"Many measures reside in here. Pass a 3D matrix, and grab a beer"
This package is a package of measures to calculate "consciousness". That is,
it will include measures that have been used in previous research to give a single
value to characterize a whole state of consciousness such as awake, ... |
da8af1e23fca19128740a60dc7c6b77f0852713c0303909792816e318b6dfd98 | Text | 969 | 39 | # AI-Sleep
AISleep: Automated and interpretable sleep staging from single-channel EEG data
Sleep EEG analysis
## Dependencies
* Python 3.8+
* lspopt==1.3.0
* matplotlib==3.5.0
* mne==1.6.0
* numpy==1.26.2
* pandas==2.1.3
* scikit-learn==1.3.2
* scipy==1.11.4
* seaborn==0.13.0
* scikit-image==0.22.0
... |
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