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1ab8383db333e9983c03e5802d275b9f3f87e392013daa2e2af80ccb08e30a9e | Text | 2,330 | 57 | [](https://gitter.im/zadorlab/sella)
# Sella
<img width="375" height="353" alt="image" src="https://github.com/user-attachments/assets/8cc92eb6-f1d7-4a94-ab5f-1f448592d653" />
Sella is a utility for finding first order saddle points
An example script
```py... |
d301a20f17779910e32b164caf51acf51e7953d9aa991fdfad707b8952df1412 | Text | 2,334 | 19 | # Arkypallidal neurons in the external globus pallidus can mediate inhibitory control by altering competition in the striatum
#### C. Giossi, J. Bahuguna, J. E. Rubin, T. Verstynen and C. Vich
#### Abstract
Reactive inhibitory control is crucial for survival. Traditionally, this control in mammals was attributed sol... |
2a34db0a9f65542c22b567065c9aa6a0f579bf30d7559a58ceed550ccf09bce7 | Text | 2,335 | 44 | # FP2
This repository contains MATLAB codes for analyzing fiber photometry data. Raw data (.csv files) can be obtained from SYNAPSE SOFTWARE (TDT).
The files '0607_VF4_f_4055.csv', '0607_VF4_f_465.csv', 'Expected output1.mat', and 'Expected output2.mat' are included for the demo.
1. System requirements:
These codes ... |
c01c32ee3ecccc6c78bfb914ac42beb7a114f0b378a6b9fcadf2eb2a518a7404 | Text | 2,338 | 35 | This data repository contains six structures storing the data from the Sonneborn et al.
Communications Biology publication "Divergent Subregional Information Processing in Mouse
Prefrontal Cortex during Working Memory". The six structures contain the raw data used to
make all figures in the paper. Each of the thre... |
f47e4190fc612ed4a2ef36c9bda3c0d5d6e690db84c707cf9de6edf7cd8f15ce | Text | 2,338 | 51 | # Analogous cycles
This repository contains code accompanying the following paper: Yoon et al 2024 "Tracking the topology of neural manifolds across populations".
* One should first download & install <a href="https://julialang.org/downloads/">Julia</a>. The code has been tested on Julia version 1.10.4.
* We recom... |
ad9593bab2231b8bcf57e5c4347ae78564fa8af9a4fa6cd984c8103e1b080dfd | Text | 2,344 | 65 | <div align="center">
<h1>In Vivo Mapping of the Chemical Exchange Relayed Nuclear Overhauser Effect using Deep Magnetic Resonance Fingerprinting (rNOE-MRF) </h1>
</div>
【<a href='https://github.com/InbalPower100' target='_blank'>Inbal Power</a> |
<a href='https://mri-ai.github.io/' target='_blank'>Michal Rivlin</a... |
10774efdeaadffa847889e93c8d586a4780496ded8f939b024080731811a5398 | Text | 2,348 | 72 | # DataPrepCV
# Mosquito Dataset Preparation
This repository contains the necessary tools for creating and organizing the mosquito dataset used in the VectorCam research project. It includes two Jupyter notebooks and associated utility files to handle the dataset.
## Requirements
- Python 3.6+
- Jupyter Notebook
- p... |
9159a06df026c806357b717adfb6f98ccbaac23fac2a69798445594a99b4bda0 | Text | 2,350 | 33 | This package is distributed under the terms of the GNU GPLv3 & Creative Commons Attribution License. Please credit the source and cite the reference below when using the code in any from of publication.
This repository contains MATLAB code for detecting frontloading, together with demos, as described in:
C. Ardin... |
076922ce85a23da2c916a6eb4aefd9eec86b79b2d0035c6954bbdb6775e2dd78 | Text | 2,351 | 39 | # Malaria stage classifier
This is the documentation of a Python package to classify RBCs in microscopy images. It includes:
* a package for the stage-specific classification of RBCs (`Malaria_stage_classifier`) with four folders:
* `Code` which contains four modules and the code file:
* `NN.py` which initi... |
4234912b4e7a68a6588674a0fe2b7c6f32c43e672a8914e67c6064ad96895acc | Text | 2,353 | 46 | <h1> Computation noise promotes cognitive resilience </h1>
Authors: Charles Findling and Valentin Wyart
<h3> Summary of the paper </h3>
We show that adding biologically inspired computation noise promotes cognitive resilience in well-controlled behavioral tasks.
<h3> Summary of the code </h3>
This code provides th... |
6b44fe4eddfe538a73e501cb6a19b15470b2ea0b28f4cc1ad4eb3b3e26af6f49 | Text | 2,355 | 44 | Code accompanying Leupin and Britz, PNAS (2024)
We here provide the code for preprocessing, epoching, and analysis of EEG data in sensor and source space. EEG data can be made available upon request.
# Code organization
Each folder is generally organized with a main, helper and constants script.The base folder contains... |
beda9e174991643d1b20ad266e47eb82e0d81839ca54ba1bfa938f241265ff20 | Text | 2,370 | 37 | # **Multi-Regional Control of Amygdalar Dynamics Reliably Reflects Fear Memory Age**
## Code and Demonstrations
- **Analysis of power, phase-amplitude coupling and instantaneous amplitude correlation**:
- Check the `Correlation_and_Modulation_Analysis` folder for the following demos with expected outputs:
- `PS... |
a64d00aaa9144539e64585e0a6de5006f59aacb621ba0531d92e4a2a33f6a65b | Text | 2,371 | 42 | # EyeNED OCT-ONH: vendor-neutral analysis of optic nerve head OCT
This repository provides a vendor-neutral assessment of the anatomy of the optic nerve head, including the extraction of common features related to optic neuropathy, such as cpRNFL thickness and B... |
ba397ff61502518dca9b3b095ede4e11a093ad3f4190e8a94637fe945dba8098 | Text | 2,371 | 18 | # MPET model of infusion test in the human brain
This directory contains the code and algorithm used to conduct simulations in the article _Modeling CSF circulation and the glymphatic system during infusion using subject specific intracranial pressures and brain geometries_ (DOI tbd).
All simulations performed, with t... |
4b79373a5d67c4f21ac0e9f6a0eebe5fb77ee373a7196633fb3cad7eb73c713e | Text | 2,379 | 41 | Welcome to the GitHub repository for the following publication: [MoCHI: neural networks to fit interpretable models and quantify energies, energetic couplings, epistasis and allostery from deep mutational scanning data (Faure AJ & Lehner B, 2024)](https://www.biorxiv.org/content/10.1101/2024.01.21.575681)
Here you'll ... |
a7c1e90fdc9ddbf0efcee12636a1dfc557d76e88fa553acc13291029c73dfefe | Text | 2,381 | 55 | # How to train and evaluate models
1. Prepare data (converting to grayscale, resizing and fusing the label files). This step assumes that your data is
organized as follows:
```
├──data-root
├── DBdumps
├── ProlificExport
├── ReyFigures
│ ├── data2018
│ │ ├── newupload... |
2b2d229510e54b071521140996000d8051608bcf266cde2887fa96b3a73e100d | Text | 2,392 | 49 |
# CoExpNets brief instructions
CoExpNets is based on the excellent and widely used WGNCA package, but incorporates a refinement we detail in the following paper <https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0420-6>. It provides ways to create, access and exploit networks based on basic WGCNA fea... |
20b83534af9bd9f9c15704b746c49bbf327acf539d0cf7fed552dc0cd30d560d | Text | 2,405 | 27 | # Marigold: Zebrafish pose tracking made easier
Marigold is a free and open source web app for analyzing zebrafish behavior. It is being developed by Gregory Teicher (gteicher at umass dot edu) in the [Downes Laboratory](https://www.downeslab.org/) at University of Massachusetts Amherst.
Marigold is compatible with a... |
357c53eaa103dbe5c30623b6abe544272175ae153e08ee41ce4a0446a9c4c1b0 | Text | 2,430 | 52 | # Cross-ancestry analysis of brain QTLs enhances interpretation of schizophrenia GWAS
This repository contains analysis and ploting code in our paper about constructing brain expression regulation architecture in African American, European, and East Asian populations:<br>
* DNA-seq quality control and imputation<br>... |
799b7e7f812e01df4fd095d4f4301217c26f777c5920bb5e6234a43b63bd6b57 | Text | 2,435 | 67 | <div align="center">
<h1>In Vivo Mapping of the Chemical Exchange Relayed Nuclear Overhauser Effect using Deep Magnetic Resonance Fingerprinting (rNOE-MRF) </h1>
</div>
【<a href='https://github.com/InbalPower100' target='_blank'>Inbal Power</a> |
<a href='https://mri-ai.github.io/' target='_blank'>Michal Rivlin</a... |
9d6a1a6804530981b9b23cd0e6012af7e067a5726f282be6c8b2b33dccc0e44c | Text | 2,438 | 35 |
# Kernel Mean Embbeading Regression (KMER) or Kernel Ridge Regression with EEG frequency spectrum used for Age prediction:
This is the framework used for the paper "Predicting subject traits from brain spectral signatures: a case for brain ageing"
[paper](https://www.biorxiv.org/content/10.1101/2023.11.02.565261v1)
T... |
c4dd38c0176459fd94e3d59c80cc031d2ef0dd0344cb635f3c70e39c48281308 | Text | 2,444 | 40 | # EEG microstate transition cost correlates with task demands
Solving the Schrödinger bridge problem for computing brain transition cost.
See our work: Barzon, G., Ambrosini, E., Vallesi, A., & Suweis, S. (2023). [EEG microstate transition cost correlates with task demands](https://www.biorxiv.org/content/10.110... |
38102f0026cfde9cc8198e0a01bdc6d77d338569aad94687619d335c0e6a1956 | Text | 2,445 | 56 | # Sitetack: A Deep Learning Model that Improves PTM Prediction by Using Known PTMs
## Overview
Post-translational modifications (PTMs) increase the diversity of the proteome and are vital to organismal life and therapeutic strategies. Here we have developed models that use known PTM sites in prediction via sequence-... |
d2e9bf64bde7255f345247f6068a2b2fbcb36dd42ba126af0152dd6a6ecb737a | Text | 2,454 | 65 | # wlBurst v2 Library
## Overview
The wlBurst library provides Matlab scripts for identifying and
characterizing transient oscillations in neural signals ("LFP bursts").
This repository contains version 2 of the library, which is the active
branch as of September 2020.
The wlBurst project is copyright (c) 2018-2020 b... |
7ceaaab52212a3cb2941855ba8907e5caf9499615fda7bce4c26af63d8002420 | Text | 2,471 | 94 | # DeepVID v2: Self-Supervised Denoising with Decoupled Spatiotemporal Enhancement for Low-Photon Voltage Imaging
This repository is the PyTorch implementation of DeepVID v2, as presented in the following preprint:
Liu, C., Lu, J., Wu, Y., Ye, X., Ahrens, A. M., Platisa, J., ... & Tian... |
ee77e5232abf3ed86ce60d40b6d15aa8908e386a7cc8063190f4ae082be47dc0 | Text | 2,491 | 62 | ### README
This readme file was generated on 2024-02-12 by Mariah Kenney
GENERAL INFORMATION
Title of Dataset: Distribution of datasets contributed to the Brain Image Library by technique and species (Figure 5) from The Brain Image Library:
A Community-Contributed Microscopy Resource for Neuroscientists
Name: ... |
888c27ffd98d86a81dbb9d495a15fae9dc316caf31a24daac5f2b444c4140ff4 | Text | 2,507 | 90 | WONAMBI
=======
Package for the analysis of EEG, ECoG and other electrophysiology modalities.
Allows for visualization of the data and sleep stage scoring in a GUI.
Provides automatic detectors for spindles and slow waves.
Features
--------
- Can read files of format:
- Axon (.abf, ABF2 only)
- BCI2000... |
454a3864d6671f19a2d869fb1fe9f53262190ae862972ca2f5aa71c8bdad97cc | Text | 2,515 | 54 | # scPair is a computational framework for boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection
scPair, a deep learning framework for computational analysis of single cell multimodal data. scPair performs automatic, implicit feature selection to infer the features of... |
794c9541cc955fb489a0313b56213c28a5b9f96907d2f541b9ca4d02dfcaadc2 | Text | 2,520 | 75 | # Generative Effective Connectivity (GEC) Framework
**Matlab implementation of the GEC framework** developed for:
> *Kringelbach, Sanz Perl, Tagliazucchi, and Deco.*\
> “Towards a naturalistic neuroscience: mechanisms underlying the flattening of brain hierarchical organisation in movie‑watching compared to rest and ... |
ec2b8f385aad7e01b670df66b91f8e3bbafd4eef5ad65eaf97d0038287dc7732 | Text | 2,526 | 61 |
# HANNA Project
[](https://pubs.rsc.org/en/Content/ArticleLanding/2024/SC/D4SC05115G)
[](./LICENSE)
[.
### Data structure
This toolbox was specifically writte... |
3fed87cd279b1aee087f59828b9239c4f4cde405224b825019e8b444ddd2be99 | Text | 2,532 | 41 | # 7T-neonate-t1-t2-mapping
<img title="" alt="example T1 and T2 maps" src="front_page_image.jpg" width=70%>
Reconstruction of T1 & T2 maps plus analysis code for 7T neonatal quantitative MRI project. This code accompanies a paper submitted to Magnetic Resonance in Medicine, a link will be posted here if/when it i... |
315db392ceb9c1befae9c97504421f7a8b9450fade8cd96e88a97112cbc4657b | Text | 2,533 | 70 | DeMapper: A **De**constructed **Mapper** (TDA) Toolbox for MATLAB
==============
DeMapper is a simple toolbox to run Mapper techniques (from Topological Data Analysis) in MATLAB.
Find the documentation at: https://braindynamicslab.github.io/demapper/
There are many examples on how to use the tool, as tests:
htt... |
8b00cd49bb9ca2fab40d9923c5ae528a04570193a481e5b02c6e3e918c361f21 | Text | 2,536 | 52 | # Predicting chemotherapy-induced thrombotoxicity by NARX neural networks and transfer learning
This repository contains a demonstration for learning an individual
patients time series with NARX networks. It accompanies the puplication
"Predicting chemotherapy-induced thrombotoxicity by NARX neural networks
and tran... |
6ccd376c0ea15deb25652c867fed0efcdd5bcb3c3dc9e341fd931f99af012a2a | Text | 2,543 | 46 | # Bridging Cognitive Maps
This repository contains the code for the experiments and figures used in [Bridging Cognitive Maps: a Hierarchical Active Inference Model of Spatial Alternation Tasks and the Hippocampal-Prefrontal Circuit](https://arxiv.org/abs/2308.11463) by Toon Van de Maele, Bart Dhoedt, Tim Verbelen, and... |
d0f7539c520360081300805c7cbf7441c289f676300dd4c11afc3daffea6ce04 | Text | 2,543 | 70 | 
Repository associated with the paper
**Brain change trajectories in healthy adults correlate with Alzheimer's related genetic variation and memory decline across life**
================
[Preprint](https://www.biorxiv.org/content/10.1101/2023.10.09.559446v1)\
Status: Accepted ... |
6ad17802a3d75403d318a2b85d8fd952438025fb8ddcd20b936e2451c268a5fb | Text | 2,555 | 57 | # smart-comp-sci
Examples and numerical tests for SMART scientific computing paper.
To run the code in this repository, it is necessary to install [SMART (Spatial Modeling Algorithms for Reaction and Transport)](https://github.com/RangamaniLabUCSD/smart.git).
See more info about running the code and reproducing the r... |
c0a6773c73e185eedbd9bd4cac879a676b12d3c41dc673eee05353739744078d | Text | 2,559 | 30 | ### APT: The Animal Part Tracker
APT is a machine-learning based software package that enables tracking the pose or posture of behaving animals in video. APT can work with potentially any animal (or animals), in any settin... |
4e2b58a40a715abff359528d4e4f92cd9d822afee9affae34ac3bb053c7fd076 | Text | 2,571 | 84 |
treem - neuron morphology processing tool
=========================================
Module provides data structure and command-line tools for accessing and
manipulating the digital reconstructions of the neuron morphology in
Stockley-Wheal-Cannon format (SWC).
[](ht... |
cdc5f967f193179f692678699a2b1cc18124b7a2253762d4b517eb51408daa8d | Text | 2,572 | 83 | Ginkgo
=========
#### Ginkgo is a cloud-based single-cell copy-number variation analysis tool.
#### Launch Ginkgo: [qb.cshl.edu/ginkgo](http://qb.cshl.edu/ginkgo)
Usage
=========
* Step 0: Upload .bed files
* Step 1: Choose analysis parameters
* Step 2: Compute Copy Number Profiles, and a Phylogenetic Tree
* Step 3:... |
821b6d68b0023ec8d181f0a645f9d44b441be1520992dbe3ee2b911225387e87 | Text | 2,573 | 51 | # ExplictImplicitDissociation
This script calls every script necessary to analyse the differences between contexts.
PATHS['ScriptsPathRoot'] should correspond to the GitHub folder of the Bayesian Battery.
If not, it can be changed in the first lines of this script.
Data files should be in a folder called 'BayesianBatt... |
57bdacce75dc43ec5f932b96a0a0a9d90e490936ac98d02bd90f5e10eedd9d2d | Text | 2,574 | 39 | ## sc-TWAS [](https://github.com/gamazonlab/SingleCellPrediXcan/blob/main/LICENSE)
# References
Mapping the landscape of lineage-specific dynamic regulation of gene expression using single-cell transcriptomics and application to genetics of complex ... |
d485f1bd59cfe8da73e43bde72dcdb4796e157e89a6d269b076833899089143d | Text | 2,577 | 60 | # Connectome Spatial Smoothing
Here, you may find the Python codes and sample scripts for Connectome Spatial Smoothing (CSS).
For more information you may check our article on **Connectome Spatial Smoothing (CSS): concepts, methods and evaluation**. All resources are provided as complementary to the following article... |
7dcd6664c559f8d0b7d69e99a18a26cd6fff41fbdac2632bbd4f19de6605e7f0 | Text | 2,578 | 90 | Properties of winning Iterated Prisoner's Dilemma strategies. A meta
tournament analysis.
--------------------------------------
**Authors**: [@Nikoleta-v3](https://github.com/Nikoleta-v3) [@drvinceknight](https://github.com/drvinceknight) [@marcharper](https://github.com/marcharper)
This repository contains the sour... |
e4faed277b9a0cb328a92bc004b10860ff9d15cafb9cd9581c28ee7771e5d44d | Text | 2,579 | 84 | <!-- [](https://codecov.io/gh/r-bierman/SRRS) -->
ELife publication: https://elifesciences.org/reviewed-preprints/87517
## SPRAWL: Subcellular Patterning Ranked Analysis With Labels
SPRAWL... |
b6a5466a14ed0116042d8a96f3393da9cb0a131da21ac341c076b2fc0788b605 | Text | 2,589 | 23 | # A Randomization-Based, Model-Free Approach to Functional Neuroimaging: A proof of concept. | [_Entropy_, 2024](https://www.mdpi.com/1099-4300/26/9/751)
## Matan Mazor 🔴 & Roy Mukamel 🟦
A TWISTER experiment is comprised of four experimental runs of equal duration: A1, B1, A2 and B2. The experiment is created in two... |
b5d13f6b1e796c3131d8f7f239bd20c3cb29b292795ec09a875acd03e2b04151 | Text | 2,594 | 29 | # Aysegul_snRNA_AuditoryCortex Project
[](https://www.docker.com/)
[;
* populati... |
bf22ef17825593aab03ecdf32795c4ed66eaebcd7ad80d82a7df5e80dac75e0a | Text | 2,618 | 79 | # chexpert-labeler
CheXpert NLP tool to extract observations from radiology reports.
Read more about our project [here](https://stanfordmlgroup.github.io/competitions/chexpert/) and our AAAI 2019 paper [here](https://arxiv.org/abs/1901.07031).
## Prerequisites
Please install following dependencies or use the Dockeri... |
9f9ff5ba8e7b2c8a08b39536954d0f9c2fb12cc4cc42f86e090b93fe350d99fa | Text | 2,624 | 93 | %%%% TrihexyTrioAllAnalysis
% This contains details on how to replicate the analysis from the paper:
% Grogan et al., 2024. Muscarinic receptors mediate motivation via
% preparatory neural activity in humans.
% Anonymous data are available here (https://osf.io/zuq5c/)
% The paths in the scripts given here will need ... |
d8a83c6cacd7c8c1b7e09628435f6724424652c1ee6b46bd7c6fec05318c4537 | Text | 2,628 | 39 | # npx-analysis
This repository contains the code used for the analysis contained in Palacios et al., bioRxiv, 2024, [Golgi cells regulate timing and variability of information transfer in the cerebellar-behavioural loop]
[Golgi cells regulate timing and variability of information transfer in the cerebellar-behavioura... |
3d58c854fb5d67c4a35b02a1e68a376d7ea8b1fb645e1ebed1618dc1ce02ec18 | Text | 2,631 | 26 | # DeepH-hybrid
This code provides an implementation of the DeepH-hybrid method described in the paper _A deep equivariant neural network approach for efficient hybrid density functional calculations_ ([arXiv:2302.08221](https://arxiv.org/abs/2302.08221)).
DeepH-hybrid is built upon DeepH series of Deep-learning Hamil... |
1e271ae87115e8eb8ea79e3ac570bfc0dca8218cc188e9b70cb024c7681862ca | Text | 2,632 | 39 | # Secondary thalamic dysfunction underlies abnormal large-scale neural dynamics in chronic stroke
## Phillip R. Johnston, John D. Griffiths, Leanne Rokos, Anthony R. McIntosh, Jed A. Meltzer
Repository for code and data supporting Johnston et al. (2024) - Secondary thalamic dysfunction underlies abnormal large-scale ... |
f5a5d782e095a950df2d5d3ec05ec67fd54786b00386a4dbaca5c9ab231a445c | Text | 2,640 | 69 | # RANSynCoders
### Industry-Practical Anomaly Detection and Localization for Asynchronous Multivariate Time Series
RANSynCoders (or RANCoders) is an unsupervised deep learning architecture for real-time anomaly detection and localizaiton within large multivariate time series. The method utilizes synchrony-analysis ... |
d8d99721f3e6c8e2b36d23f6ebb3858b6e64b1ba6069865a3c1c4387649e817d | Text | 2,643 | 44 | # Deep-learning based extraction of circle of Willis topology with anatomical priors
This is the code repository of our paper _Deep-learning based extraction of circle of Willis Topology with anatomical priors_.
We extract a graph representation from the circle of Willis topology from 3D TOF-MRA scans. A complete cir... |
f968b5af36a2c1288f948db8ef8963281ef0c7b38441e8e070147f8609b0988a | Text | 2,653 | 73 | 
[](https://doi.org/10.5281/zenodo.13861219)
Repository associated with the paper
**Brain change trajectories in healthy adults correlate with Alzheimer's related genetic variation and memory decline across life*... |
8dd7540bb76b8ef23ec39ca4bb1dab455bb25ac22752a1eba01e0f0973682857 | Text | 2,655 | 46 | <div align="center">
<img src=https://github.com/Quantum-Accelerators/quacc/blob/main/docs/images/quacc_logo_wide.png width="300"><br>
</div>
# `quacc` – The Quantum Accelerator 🦆
[](https://codecov... |
407f07db983caf4e61355330d0bcf0c6a3c776a33f8bdeb26e1f4c124f72bdf2 | Text | 2,660 | 81 | # Automated segment-level coronary artery calcium scoring on non-contrast CT
This repository is the official implementation of [Automated segment-level coronary artery calcium scoring on non-contrast CT: a multi-task deep-learning approach](https://insightsimaging.springeropen.com/articles/10.1186/s13244-024-01827-0).... |
e4672b5a3c848587d424f5f0050203669d2582490b0b1dfbf15703fc983bc97b | Text | 2,664 | 40 | **Note: as of 2019, PMTK is no longer supported - use at your own risk.**
The new version of my book (which is in progress) now uses the Python code available from
https://github.com/probml/pyprobml/.
PMTK is a collection of Matlab/Octave functions, written by Matt Dunham, Kevin Murphy and
<a href="https://github.c... |
9be0b0fed8cc0ec7cb4b5c0228a90c89dc7bac0f39c41e048a2f0385d3b7c52c | Text | 2,669 | 7 | This experiment implements a realtime R-peak detector to entrain binocular rivalry stimuli to sytolic and diastolic phases of participants' cardiac cycles, followed by a modified heartbeat discrimination task (to meausure interoceptive accuracy as it pertains to the experimental manipulation in the rivalry task). It us... |
bcb04513a7b422c1bd4aa035d0fe47c1e46560c0dca4ead08f172c4c258e822f | Text | 2,673 | 45 | # subunit_grid_model
Functions to fit subunit grid models to spiking data from retinal ganglion cells.
This repository is a supplement to the manuscript ["Nonlinear receptive fields evoke redundant retinal coding of natural scenes"](https://www.nature.com/articles/s41586-024-08212-3).
## Requirements and installatio... |
88e475a7cc20694818009c3f9a5bb79ac810e05caafe61b80c1cdc17c4d38e1e | Text | 2,692 | 43 | # NUPT-FPV
NUPT-FPV: A multimodal dataset based on fingerprint and finger vein <br>
Paper: A Dataset and Benchmark for Multimodal Biometric Recognition Based on Fingerprint and Finger Vein.<br>
Journal: IEEE Transactions on Information Forensics and Security, 2022.
## Short Information
NUPT-FPV obtained 840 finger in... |
b7d0c3ee6215654247f6079f4d584edc4242a0a9471f1cbc0bd376a2e1340dd4 | Text | 2,698 | 30 | msDyNODE - Neural Ordinary Differential Equation-based multi-scale Dynamical modeling
====================================================
This code implements the model from the paper "[Multiscale effective connectivity analysis of brain activity using neural ordinary differential equations](https://www.biorxiv.org/c... |
90d0abc83d9ea8b72b7c065e8bb099698708102083494f9ee482ae5b4caa8f85 | Text | 2,701 | 35 | # FADE_SAME
**FADE and SAME scores for successful aging in memory**
This code belongs to the paper "A comprehensive score reflecting memory-related fMRI activations and deactivations as a potential biomarker for neurocognitive aging" by Soch, Richter et al. (2021), published open access in *Human Brain Mapping*. For ... |
e086a8e364ce203e2946dd4da1e8703c23620dd7f645cf9fd7586226256536c9 | Text | 2,721 | 29 | # Quality of Life after Deep Brain Stimulation in Parkinson’s Disease: is the target a factor?
## Authors
Sandra Murcia Carretero MD[^1], Katrin Petermann MSc[^1], Ines Debove MD[^1], Mário Sousa MD[^1][^3], Julia Waskönig MD[^1], Andreas-Antonios, Diamantaras MD[^1], Gerd Tinkhauser MD PhD[^1], Andreas Nowacki MD[^2]... |
afeb65957d6e0217260c8fd1d6894031b79e780784293ecd86e2e7f8b9a54bc8 | Text | 2,725 | 16 | This repository contains the MATLAB code used in Schretter et al. 2024 ("Social state alters vision using three circuit mechanisms in Drosophila") to analyze visual features during female aggression and male courtship behavior and generate the behavioral timeseries and averages depicted in the figures.
This code was ... |
1d7952393b3bb23e6e305d107c999d90ce1e2dc858e3a8344ed06973405ec362 | Text | 2,726 | 94 | > [!WARNING]
> The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.
> Future development will take place at: https://github.com/openbraininstitute/connectome-analysis
# Connectome Analysis
#### General functions to analyze connectomes from a topological... |
2d3335c3233c12ca3844df0d955848cf0d3f65ed9ed5e9e69f06ceb422130631 | Text | 2,732 | 33 | # mrs
### Updated by Meaghan Perdue 17 Dec 2024
Data contained in this directory was published in:
Perdue et al., 2023, NeuroImage, <https://doi.org/10.1016/j.neuroimage.2023.120087>
Also used as source data for control subjects included in: Perdue et al., 2024, bioRxiv <https://doi.org/10.1101/2024.05.06.592786>
## ... |
f248ed5066fae66768972f2391005d590883af556180433fb019a470aedd8712 | Text | 2,747 | 49 | # ERGO-II
We have previously published [ERGO](https://github.com/louzounlab/ERGO), a deep learning based method
for predicting TCR and epitope peptide binding.
Several evaluation methods were suggested, including Single Peptide Binding (SPB), Multi Peptide Selection (MPS) and
TCR Peptide Pairing (TPP).
ERGO uses only ... |
2da8100682a13e1b339957ac9e91ed04e9c2739dcde6bef0193501a8e61acb18 | Text | 2,758 | 43 | # Anatomy-Aware-Classification-axSpA
This is the accompanying repository for the paper **Anatomy-centred deep learning improves generalisability and progression prediction in radiographic sacroiliitis detection**.
## Background
The assessment of radiographic sacroiliitis on pelvic radiographs plays an important role i... |
6389395df3b1f66f021545591a1ac046ccfd3357e0f8e9ebaf2be265843615d8 | Text | 2,766 | 84 | # RRHO2
Implementation of improved RRHO2, for which all regions in RRHO plots are meaningful.
## Install This Package from github
First you need R `devtools` package installed.
* In R console
```R
library(devtools)
install_github("RRHO2/RRHO2", build_opts = c("--no-resave-data", "--no-manual"))
```
## Citation
*... |
9be978f021e1366b5f112e000aa38b08b0d3e1753286a08fc231758b3252aac9 | Text | 2,780 | 106 | # VEDB Odometry README
## Overview
This repository, is for transforming the t265 data within the Visual Experience Database with the `headCalibrate.py` script. This script is designed to perform the calibration of VEDB T265 odometry data from sensor coordinates to head coordinates. It uses the Pupil Recording Interfa... |
03bf7efd72591be42ad7566a753d5aa64f93da681b8fd00f4361221e4f654f1d | Text | 2,782 | 54 | # Extracting Structured Data from Organic Synthesis Procedures Using a Fine-Tuned Large Language Model
Organic synthesis procedures are traditionally represented by free-form texts.
This project explores how large language models can convert such unstructured
texts to structured data, so they can be used for downstrea... |
169f92d037c571d21790bdc12b8b8078ee9588dc521b393ef8b64677ce7bc49a | Text | 2,792 | 42 | # BrainMorphometry_Inflammation_BEANstudy_2021
This repository houses code (or links to code) used for the following study:
##### *Ted K. Turesky, Laura Pirazzoli, Talat Shama, Shahria Hafiz Kakon, Rashidul Haque, Nazrul Islam, Amala Someshwar, Borjan Gagoski, William A. Petri, Charles A. Nelson, Nadine Gaab (2021) B... |
a0b5f7771bee11b7aa984596e9a68011bca56e3baf5e99058f1904d3c53fe073 | Text | 2,795 | 51 | # Using cluster-based permutation tests to estimate MEG/EEG onsets: how bad is it?
Code and data for simulation project on MEEG onset estimation.
[[Preprint]](https://www.biorxiv.org/content/10.1101/2023.11.13.566864v1)
## R code
| Notebook | html version | Content | Figures |
| ----- | ----- | ----- | ----- |
|`fd... |
a1ce9a57ed8a590f56b4a2d3d4bb064758d4efcd465f304eb33c291caa8aa967 | Text | 2,800 | 57 |
This repository includes the implementation of 'DeepPL: a deep-learning-based tool for the prediction of bacteriophage lifecycle'. Please cite our paper if you use our model or code. The repo is still actively under d... |
2d813bb0bdeb54bcbe09b5def6d02e6652a0dca57ef340f63b7caa2dacd68c89 | Text | 2,803 | 36 | # Codes for paper Zheng et al. 'Hippocampal Theta Phase Precession Supports Memory Formation and Retrieval of Naturalistic Experience in Humans'
This repository contains the code for the following paper:
**Hippocampal Theta Phase Precession Supports Memory Formation and Retrieval of Naturalistic Experience in Humans*... |
9ad381d4c8b34e3b4c307a0237c90ae8f6347d4d6b913af5431d449036d5ff48 | Text | 2,808 | 86 | # Deep neural networks and humans both benefit from compositional language structure
This repository holds the code for the paper:
Galke, L., Ram, Y. & Raviv, L. Deep neural networks and humans both benefit from compositional language structure. Nat Commun 15, 10816 (2024). https://doi.org/10.1038/s41467-024-55158-1
... |
b4df71d5f4a0f109f2f55e2fc421c36072997a7df92931f1f5f62349a060fe7b | Text | 2,828 | 33 | # TDBRAIN
Code used in the paper The Two Decades Brainclinics Research Archive for Insights in Neurophysiology (TDBRAIN) database
# TD-BRAIN-processing-code
This python API can be used for automatic* EEG artifact removal (eye-blink) and detection. as well as processing and producing the figures in the TD-BRAIN manuscr... |
952858a07c4286dcf94e03d41eda29af14c9fc3c8fa92e430feb1a98db424070 | Text | 2,844 | 51 | # An Improved Sample Selection Framework for Learning with Noisy Labels
<h5 align="center">
*Qian Zhang, Yi Zhu, Ming Yang, Ge Jin, Yingwen Zhu, Yanjun Lu, Yu Zou, Qiu Chen*
[[PLOS ONE]](https://doi.org/10.1371/journal.pone.0309841)
[[License: MIT License]](https://github.com/LanXiaoPang613/SOS/blob/main/LICENSE)
<... |
e50fce29a4779c6c513e23b89b2ac105260e94a547945094b9dc2739c4a5b3d9 | Text | 2,848 | 46 | # scHetG
scHetG is a structure-preserved scRNA-seq data integration approach using heterogeneous graph neural network. By establishing a heterogeneous graph that represents the interactions between multiple batches of cells and genes, and combining a heterogeneous graph neural ne... |
ce8d001880750f310448a011e9972bc511b445c31a950eab79ba45edfa5c9456 | Text | 2,849 | 84 | # GarnerKindLai_MeTu
GarnerKindLai_MeTu paper
https://www.nature.com/articles/s41586-024-07967-z
## OS
All EM analyses were performed in MacOS using R and Python. All calcium imaging analyses were performed in Windows using Matlab.
## Required packages
### R
Natverse https://natverse.org
Tidyverse https://www.tidy... |
cf2f8079a286f827fcf3e0da633abdd61c2d5776fb779fa42b5efa888b041a26 | Text | 2,853 | 86 | # LDCNN: A new arrhythmia detection technique with ECG signals using a linear deep convolutional neural network
# Introdction
<p align = "justify">
The Electrocardiogram (ECG) is an essential and widely used instrument for diagnosing cardiovascular diseases. It involves the recording of electrical signals produced ... |
0b73c14d20d3d86dafc1a8608b5de27e11714759f564f775df8dcb112efe706d | Text | 2,854 | 64 | # MMNN_STS
Repository supporting the training and evaluation of a multimodal neural network for prognostic modeling of soft tissue sarcoma patient outcomes
<h2> Installation </h2>
git clone https://github.com/DigITs-AIML/MMNN_STS.git
cd MMNN_STS && pip install -r requirements.txt
<h2> Usage </h2>
1. Modif... |
8f0312513c183a49c38a74ed99ff928fe4ef3e0bbad92e8637816ddf2ace870e | Text | 2,865 | 30 | # scRNAseq_prion_neuronal_vulnerability
This repository contins source code for analysis of single cell RNA sequencing data in the investigation of neuronal vulnerability in prion disease:
Single-cell transcriptomics unveils molecular signatures of neuronal vulnerability in a mouse model of prion disease that overlap ... |
85bc3546cb03a953c86b69c5c193020fb5d34bf9ec4c41eda0f7e1cfdb793fe0 | Text | 2,870 | 24 | # neuronal_dynamics
Code for ["Between-area communication through the lens of within-area neuronal dynamics"](https://www.biorxiv.org/content/10.1101/2022.04.11.487906v3), Gozel and Doiron, *bioRxiv*, 2023.
## simulate
This folder contains all the scripts needed to run the simulations of the three-layer network of ... |
f8bdd836f63f00026101c3f3331b4134b23626132321204ff534bf1bfd939003 | Text | 2,870 | 50 | # EMMA-Ferret
Single stream EMMA framework used for Ferret Stimuli Analysis. For detailed experiments and insights please read our [article](https://www.biorxiv.org/content/biorxiv/early/2024/06/11/2024.05.21.595171.full.pdf)
## Introduction
This repository implements a computational model inspired by the Explicit Mem... |
474bf6cf53d0d0a3f7ecf3d878d4a7e5a7f28431578267547bb991309531abb8 | Text | 2,887 | 43 | # Readily-interpretable deep learning translation of GWAS and multi-omics findings to understand pathobiology and drug repurposing in Alzheimer's disease
Human genome sequencing studies have identified numerous loci associated with complex diseases, including Alzheimer’s disease (AD). However, translating human geneti... |
7df4f87e1d08c12b6b24f56094575f921641589d050c1f9842f743f896aabcc5 | Text | 2,896 | 36 | # Datasets for "Accurate and efficient structure elucidation from routine one-dimensional NMR spectra using multitask machine learning"
## substruct_to_struct_dset.tar.gz
This unzipped tar.gz archive contains the dataset of used for training the substructure-to-structure transformer model and contains the following fo... |
ea5e436def35b631c378704e143d277803ca2288e2a64083891e481dd8e19ec5 | Text | 2,904 | 42 | # BodyCompL3_DLNN_Open_Code
Pre-processing and deep learning network open code for training an L3 CT automatic segmentation of fat and muscle
To train the network, simply run
python run_offline.py
This script will load the params.json config file and take all settings from there. Important are the following settings... |
5c3e41f0cdc59c485f13c8447aa6141092bb926eff423328a142a5920e348e90 | Text | 2,911 | 46 | # Python Toolkit of Statistics for Pairwise Interactions (_pyspi_)
[](https://doi.org/10.5281/zenodo.6541022)
_pyspi_ is a comprehensive python library for computing statistics of pairwise interactions (SPIs) from multivariate tim... |
21022689c151600ccdd08dbb3cb271420111b3b9dfe57440e23d72cc3ec1238c | Text | 2,916 | 57 | # Solo Computational Paper 1
Working title: **Metabolic heterogeneity of human microglia across Alzheimer's disease pathology in SEA-AD**
This repository is for a reproducible, solo-author computational immunology study using public human single-nucleus RNA-seq data. The current dataset choice is SEA-AD because it pr... |
1e7dd80ee3c4ddf571f3754dcbc5c0812d3f71d890c3403d5ed2416e05227d31 | Text | 2,926 | 42 | # LGMF-GNN
Code of paper "An Objective Quantitative Diagnosis of Depression Using a Local-to-global Multi-modal Fusion Graph Neural Network"
## Overview
Content includes source code for the implementation of local-to-global multi-modal fusion graph neural network on large multi-site MDD fMRI datasets for major depress... |
1413cf7e15ad1c0ad774d42a585ca44db33263562bbb839e77528ee7b782689a | Text | 2,933 | 78 | # BiœmuM: Biomimetic Emulation of multicompartments neurons
## Overview
BiœmuM is a biomimetic real-time Spiking Neural Network (SNN) emulating multicompartment Hodgkin & Huxley neurons.
_Maintainers_: Timothée Lévi (timothee.levi@u-bordeaux.fr), Jérémy Cheslet (jeremy.cheslet@u-bordeaux.fr)
_Authors_: Roma... |
d7b89f846be69fdacceed3bffa6c8a60a25dd5e5f816ab7eec7f33476a4da959 | Text | 2,941 | 52 | # scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction
scNODE is a generative model that simulates and predicts realistic *in silico* single-cell gene expressions at any timepoint. scNODE integrates the idea of variational autoencoder (VAE) and neural ordinary differential equation (ODE) to... |
23e25722d6ffeebab73ac211b215445c479ff33fc1878c50892554d42ed2ae9b | Text | 2,952 | 68 | # Cellular uptake of random elliptic particles
## Associated paper
The present code is the supplemental material associated to the paper [1].
## Dependencies
In order to make sure that you are able to run the code, please install the required versions of the libraries by executing the command bellow in your ter... |
50eac6219e5fec8ce179a71352027213326081f6a19253c5d0b271489cf70c39 | Text | 2,957 | 106 | # TOSICA: Transformer for One-Stop Interpretable Cell-type Annotation
## Package: `TOSICA`
We created the python package called `TOSICA` that uses `scanpy` ans `torch` to explainablely annotate cell type on single-cell RNA-seq data.
### Requirements
+ Linux/UNIX/Windows system
+ Python >=... |
952a0fe340f0a44d62413e237ca188898381f8b637cc145fc2db0eabe6e5b872 | Text | 2,968 | 99 | # AxionFileLoader
This repository contains Matlab loaders for Axion BioSystem's AxIS and AxIS Navigator files. It enables extraction of raw voltage, spike times and waveforms, viability, contractility data, and stimulation timing from Axion's .raw and .spk files.
## Example usage
### Voltage data from a raw file
V... |
a43830cb4d7d4c0ae6ebf66ce45342515277d739321c461bedf5501b083cf9df | Text | 2,968 | 27 | # SPComBat
### Superpixel-ComBat Modeling: A Joint Approach for Harmonization and Characterization of Inter-Scanner Variability in T1-Weighted Images
--------
**Maintainer**: Chang-Le Charles Chen, chc348[at]pitt[dot]edu
**Licenses**:
- Matlab code: MIT License
**References**: Please cite our [paper](https://direct... |
581ba42d71bbf552a77c85a32748a860baa89dbcdb9f8de21b75f84ebf04ccfd | Text | 2,972 | 67 | # Deep-prior ODEs Augment Fluorescence Imaging with Chemical Sensors
This code contains the method Deep spatiotemporal priors for Uncoupling Sensors Kinetics (DUSK). The run file estimates the spatiotemporal distribution of a chemical species of interest (CSI) in a simulated case and on one real data.
Paper: https://... |
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