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c89020ec9edd86e3021b5967ba329bc857470e1474f2d3632d0086b15bee89af | Text | 2,748 | 49 | # Dinosaur: Differentiable Dynamics for Global Atmospheric Modeling 🦖
Authors: Jamie A. Smith, Dmitrii Kochkov, Peter Norgaard, Janni Yuval, Stephan Hoyer
Dinosaur is an old-fashioned (some might say prehistoric) dynamical core for global atmospheric modeling, re-written in [JAX](https://github.com/jax-ml/jax) to me... |
19169f91f0cb90cdd9637397c4476805643ce92f14e1468fe30a831d903b552d | Text | 2,757 | 52 | # Stimulus type shapes the topology of cellular functional networks in mouse visual cortex
[](LICENSE)
[](https://www.nature.com/articles/s41467-024-49704-0)
## Introduction
This reposit... |
6daacf2d57856e3de3ab6316cc80d87335a3375d53d84c7b424002f882865d62 | Text | 2,775 | 63 | # miniC
A LSTM deep learning for predicting if a *Pyricularia* strain carries supernumerary chromosomes (or mini-chromosomes)
# Installation
Python3.9 was tested. A virtual environment can be set up by using the software list in [requirements.txt](installation/requirements.txt).
```
pip install -r installation/require... |
089ee9895e48a3257a932d1e38e2fa470c2456db484bb1715ff4eae582577830 | Text | 2,786 | 36 | # Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in randomly packed cylinders or spheres of permeable membrane (CUDA C++)
The code implements 3d Monte Carlo simulations originally developed in [Lee, et al., Journal of Neuroscience Methods, 2021](https://doi.org/10.1016/j.jneumeth.2020.1... |
1f2798a9184b39181422c53be307aecb46962b33ce6a28ab35d948172e557702 | Text | 2,787 | 83 | # Quick Start Guide for TOF Segmentation with Docker
## Prerequisites:
Ensure Docker is installed and properly configured on your system.
## Step 1: Build the Docker Image
Run the following command to build the Docker image for TOF segmentation:
```bash
docker build -t tofsegmentation:latest .
```
## Step 2: Run the ... |
d8c35665dccbe8be02e77723e5d798aff3b7a0ba25817a11d9b9fe311d3504dc | Text | 2,801 | 60 | # Real-Time Intermediate Flow Estimation for 3D tomography
## Introduction
This project is a modified implementation of [Real-Time Intermediate Flow Estimation for Video Frame Interpolation](https://arxiv.org/abs/2011.06294), developed within a paper that is currently under review.
More details will be added once the p... |
de1158d64474f35e466ec7f21ad1123e32e440e1f1df412fb4e4362d108bc1e8 | Text | 2,812 | 63 | <div align="center">
<img src="https://raw.githubusercontent.com/Matteo-Valerio/pyBioPortal/master/docs/logo/pbp_light.svg"><br>
</div>
-----------------
# pybioportal: a Python package to easily retrieve data from cBioPortal
| | |
| --- | --- |
| Package | [ Classification of molecularly-defined glutamatergic neuron types in mouse BLA with distinct spatial ... |
54642783b65b7651f011a284608ae210ab733239d9c5247e47185ae0aa1372bf | Text | 2,894 | 37 | # Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in randomly packed cylinders or spheres of permeable membrane (CUDA C++)
[](https://doi.org/10.5281/zenodo.10651812)
The code implements 3d Monte Carlo simulations originally... |
2f42e777521b6b65daa6b7c080107102bbd765219c860f7842ca14bb62dc9709 | Text | 2,901 | 25 | # Transcriptome sequencing of rTg4510 AD mouse model
This directory is a repository of scripts pertaining to whole transcriptome profiling and targeted sequencing of rTg4510 mice, and form the source of the paper: [Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a... |
6fd896d2b9e73ba5ba3eb6b57aaea9ad5588ab812a2a14cecfe47d9fab4087ba | Text | 2,907 | 45 | # Electrocardiogram based electrolyte concentration prediction
Codebase for the paper "ECG-Based Electrolyte Prediction: Evaluating
Regression and Probabilistic Methods".
# Overview
Here is a quick overview of the paper
<p style="text-align:center;">
<img src="additional/ECG_regression_poster.jpg">
<p>
# Dataset
Unfo... |
ee8cd46cc97a1a28cd759ad641a77c702d676c09b4b6696a9b878e90ef9cfd3f | Text | 2,920 | 17 | # Great Ape Aging & Expansion Comparison
Utilizing a comparative framework employing both inter- and intra-species similarities we investigated the relationship between cross-species expansion and age-mediated gray matter changes in two great ape species, chimpanzees and humans. The [NCBR](https://www.chimpanzeebrain... |
4014c4178f7ec90306ce149561f6fcfa831e1edd8f32e2cc122992daaa9a896a | Text | 2,933 | 73 |
# RestHoldMove preprocessing
This repository has been made to help searcher to have a quick start on analysing the RestHoldMove dataset available here in openneuro:
[RestHoldMove dataset](https://openneuro.org/datasets/ds004907/versions/1.2.1).
## Introduction
This dataset contains data from externalized DBS patient... |
ab288b03c26c329f888716c6d89ae2baedaab85d683272791e06a7bd8d0b429b | Text | 2,940 | 48 | 2/21/2017
-added 'sad' face trials to face matching task
* 6 more trials for each block in each run (18 more trials each for runs A and B)
-change 'percentage' calculator on terminal feed for face_matching and conflict. now includes skipped trials
12/7/2016
-Starting prompt changes:
* Auto-fill participant ID... |
d2df1d0d84661d6484502334220ff3ab079a0ab06e7b910e29c43157854414cb | Text | 2,969 | 49 | # Ridge counting code for fingerprint images
This function package is designed to count ridge lines intersection between two GUI chosen points and ridge line intersection to two lines with 90 degree angle to each other. The package was designed for images that have been binarized and thereafter skeletonized. The locati... |
806aeb69e0a85c8f02c7b8970ce0391b3e9ae22e8f7fd82b5852bc342e91df7d | Text | 2,989 | 19 | # The engagement of the cerebellum and basal ganglia enhances expertise in a sensorimotor adaptation task
This repository contains the code used in my project *"The engagement of the cerebellum and basal ganglia enhances expertise in a sensorimotor adaptation task"* (https://doi.org/10.1162/imag_a_00271).
**Code** wa... |
b853bf34dd586c2e7777d830c8cf3ea65db0882901a8ae5b8b9202296455d623 | Text | 3,000 | 67 | # Modularized Neural Network Incorporating Physical Priors for Future Building Energy Modeling
This repository proposed a modularized neural network incorporating physical priors (ModNN) for Future Building Energy Modeling, wh... |
8bc658cce6dde40d500e5177d744bf1abea0d798fbf70164fa82e124cd066d1b | Text | 3,005 | 37 | # ASCENT: Automated Simulations to Characterize Electrical Nerve Thresholds
[](https://github.com/wmglab-duke/ascent/blob/master/LICENSE) [](https://github.com/wmglab-duke/ascent/r... |
ebf5f3e8e31afd1889f13e36d3b8316a1d807cb302f75013d60d75a8ae7bb6c3 | Text | 3,008 | 58 | # Zebrafish Angle Analysis
Analysis of zebrafish larvae bending angle during free swimming. Based on WormRuler (https://github.com/dvettkoe/wormruler).
## Overview
This is an open-source python based video analysis tool to analyze the bending angle of _Danio Rerio_ larvae, developed by Marius Seidenthal as part of his... |
703a52a0057f7f33e2240c981e1f582419b5aa7aecfb353b22a4342f41630a39 | Text | 3,013 | 58 |
<div align="center">
# MetisFL: The Open Federated Learning Framework for Scalable, Efficient, and Secure Federated Learning Workflows
MetisFL - The First Open Federated Learning Framework implemented in C++ and Python3.
[](https... |
6e8e58c084d352b983b27ffe09f17b7a05b88fb409b44c8f7fd442370a1c077c | Text | 3,033 | 38 | # DendriteArborAnalyzer
DendriteArborAnalyzer is an ImageJ plugin for the collection of data from images of neuronal dendritic arbors. Data collected include branch lengths, path distances, and Strahler analyses of branching structure.
This plugin extends the functionality of the (Strahler Analysis plugin)[https://im... |
d531a00b7600c88599a92126e8ea87b28ae469b1534496379cdf482513cdeaf6 | Text | 3,047 | 91 | # AMPd-Up
_De novo_ antimicrobial peptide sequence generation with a recurrent neural network
<p align="center">
<img src="AMPd-Up.png">
</p>
### Dependencies
* Python 3.6
* PyTorch 1.7.1
* Numpy
* Pandas
* Biopython
### Installation
1. Create a new `conda` environment:
```
conda create -n ampd-up python=3.6
```... |
b66f9646bacde88cb7374136bedfb1ec077547a0643e7ab1f1abbab7344e0c02 | Text | 3,057 | 59 | # IRnet
Immunotherapy response prediction using pathway knowledge-informed graph neural network
## Overview
Immunotherapy, specifically, immune checkpoint inhibitors (ICIs) are powerful and precise therapies for many cancer types and have improved the survival of patients who positively respondse to them. However, only... |
732c6f1290063e23979e7966396c249c42d9a9dbf0aa3cc55adac147c4d5e5ce | Text | 3,060 | 50 | # Cho2024_MouseEscapeData
🔗 Mouse Escape Behaviors and mPFC-BLA Activity Dataset: Understanding Flexible Defensive Strategies Under Threat (DOI: [10.1038/s41597-024-03688-0](https://doi.org/10.1038/s41597-024-03688-0))
💡 Please email Jee Hyun Choi at jeechoi@kist.re.kr or SungJun Cho at sungjun.cho@ndcn.ox.ac.uk wi... |
62bc648629c4e69dcca11acec03b9b9821a15a591ad593c823f344da9a582140 | Text | 3,076 | 78 | # LCNet-meta-modeling
This is the repo for the following paper:
Lu, Q., Nguyen, T. T., Zhang, Q., Hasson, U., Griffiths, T. L., Zacks, J. M., Gershman, S. J., & Norman, K. A. (2023). **Reconciling Shared versus Context-Specific Information in a Neural Network Model of Latent Causes.** In arXiv [q-bio.NC]. arXiv. http:... |
5728b9e71da44c4087fbcac8ae12239675e117505f98c2f171f66d7a03b9dd98 | Text | 3,083 | 71 | # RIPPLELAB
[](https://www.repostatus.org/#inactive)
![Licence](https://img.shields.io/github... |
6a2bcda5861dd82616da1a21103d0d123c8b9f6b3e2ca0e4011acccab315632b | Text | 3,092 | 68 | <img src="docs/img/figure0_v0.png">
# pySTED
<a target="_blank" href="https://colab.research.google.com/drive/128pOe4KwnZ7MH6HFcd-mG1HjwDWvohnq?usp=sharing">
<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
</a>
We have built a realistic STED simulation platform within the ... |
25416dde2c69681ff3df922bb951e9dc602a98f4cca4f333f37e87788c3e69b4 | Text | 3,108 | 33 | # Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in 3D cells of permeable membrane (CUDA C++)
The code implements 3d Monte Carlo simulations originally developed in [Lee, et al., Journal of Neuroscience Methods, 2021](https://doi.org/10.1016/j.jneumeth.2020.109018), demonstrating the ef... |
3859b72f43291336062252b0427c3c857b868d08f9e1d18523a5b310d6eef9b7 | Text | 3,112 | 58 | # High-performance deep spiking neural networks with 0.3 spikes per neuron
This repository contains code material for the publication: Stanojevic, A., Woźniak, S., Bellec, G., Cherubini, G., Pantazi, A., & Gerstner, W. (2024). High-performance deep spiking neural networks with 0.3 spikes per neuron (arXiv preprint... |
846211eb7d3a6cde913389c714ab02225bc69d6fd124e006c74af6fefade1cf0 | Text | 3,115 | 68 |
# AnaMorph
Framework for creating 3d neuronal morphologies from point/diameter descriptions.
## Build Status ##
[](https://app.codacy.com/gh/NeuroBox3D/AnaMorph?utm_source=github.com&utm_medium=referral&utm_content=NeuroBox3D/... |
7eae62cb3d539771fecdd092ec83fbc4b7a36533d0c2fa3984dc9085fb51dba9 | Text | 3,116 | 49 | # nii_deface
Defacing removes facial features from MRI scans to protect participant identity.
This script masks facial structures and crops away non-brain signal to reduce the field of view.
---
## Installation
This script requires Python 3.9+ and the following packages:
- [ANTsP... |
c76db10fa5ae1cfacac4d6872199eeb20400304e645068f4d671362a2ec3c0e7 | Text | 3,116 | 73 | # `reval`: stability-based relative clustering validation method to determine the best number of clusters
Determining the number of clusters that best partitions a dataset can be a challenging task because of 1) the lack of a
priori information within an unsupervised learning framework; and 2) the absence of a unique... |
16c43f4518278f07beb8925919499662cd2c1fffddf778cc55ba37a5ca6e698e | Text | 3,124 | 55 | # "CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs"
## Organization of this Repository
### The Data:
contains the genomic coordinates of all the back-splicing (BS), and linear-splicing (LS) exon pairs used in this study. Due to the file size limitation in GitH... |
8d6146afca6f494f2fe2ed792feb506118e3fab83c3930b403f31463671be68b | Text | 3,146 | 59 | # High-performance deep spiking neural networks with 0.3 spikes per neuron
This repository contains code material for the publication: Stanojevic, A., Woźniak, S., Bellec, G., Cherubini, G., Pantazi, A., & Gerstner, W., High-performance deep spiking neural networks with 0.3 spikes per neuron,
Nature Communication... |
a0456eef33d23f9475fa0ec3a5015116d54bf3ecb075b9b7a679cf4ac28bb7ee | Text | 3,188 | 42 | This repository provides processed data, stimuli and intermediate results as well as source data to the publication "FMRI speech tracking in primary and non-primary auditory cortex while listening to noisy scenes" by Lars Hausfeld, Iris M.H. Hamers, and Elia Formisano (Communications Biology, 2024)
Anatomical and fu... |
1a33d68b5c72fdcbbe1f38aa17047399ab4a8fa7aedf0973887e6b2c9794c2d1 | Text | 3,202 | 51 | # NeuroMotion
NeuroMotion is an open-source python package for simulating surface EMG signals during voluntary hand, wrist, and forearm movements.
## Overview
NeuroMotion is comprised of three key modules, including part of the Open... |
9fd8caa5c26bc7d84bc2ff28906c9e8264b44df9177a26f797a0ba571b532a2c | Text | 3,209 | 101 | # MEEGLET
> Morlet wavelets for M/EEG analysis, [ˈmiːglɪt]
This package provides a lean implementation of Morlet wavelets *designed for power-spectral analysis of M/EEG resting-state signals*.
- Distinct __frequency-domain parametrization of Morlet wavelets__
- Established __spectral M/EEG metrics__ share same wavele... |
a6e9c646383f51571aeb19be1aaa4f4f675e2612ec9c88863565bb04b08389ab | Text | 3,221 | 79 | # EFMT_Norm_Models
Code to run the Normative Models for the emotional face matching task as detailed in the following manuscript:
**Dissecting task-based fMRI activity using normative modelling: an application to the Emotional Face Matching Task**
Hannah S. Savage (1,2), Peter C. R. Mulders (1,3), Philip F. P. van E... |
2c90add7c60157342bfe670df94781d57999c796dff83609e108fbfccd487d2c | Text | 3,223 | 37 | # Characterizing Robustness of Deep Neural Networks in Semantic Segmentation of Fluorescence Microscopy Images
This repos provides an assay for quantitative evaluation of DNN models in segmentation of fluorescence microscopy images.
## Framework of our robustness evaluation
- **Dataset preparation:**
We propose a ... |
0b0bc99531c5cd29fafcc3b89041766cdf62b528ef77d9175d70823c1c689ddf | Text | 3,237 | 34 | # Realistic Microstructure Simulator (RMS): Monte Carlo simulations of diffusion in 3D cells of permeable membrane (CUDA C++)
[](https://doi.org/10.5281/zenodo.10651814)
The code implements 3d Monte Carlo simulations originally developed in [Lee, et al., ... |
0b420e8b81c339af1b6dfb0ef944342e50b930ba200a7659d4456fd6999016d0 | Text | 3,252 | 85 | cworld-dekker
The README is used to introduce the module and provide instructions on
how to install the module, any machine dependencies it may have (for
example C compilers and installed libraries) and any other information
that should be provided before the module is installed.
A README file is required for CPAN mo... |
824eb1c1183b46e52d3dd0a41bc04087a4b81d19174508040da7a866a6c106e6 | Text | 3,261 | 84 |
# Enhancing Molecular Property Prediction with Auxiliary Learning and Task-Specific Adaptation
[](https://doi.org/10.5281/zenodo.11894598)
## Installation
Follow the [instructions](https://python-poetry.org/docs/#installation) to install poetry. Use `po... |
a61f92e001d755ce405c7e52a015054730eda60db72d1c8d3528cc83e1bcdb2c | Text | 3,283 | 81 | # Joint Decorrelation for Phase-locked Artifact Attenuation
[](https://doi.org/10.1162/imag_a_00272)
This repository provides ... |
ec897bd6e7da3583d33ab3f664b80f73b98a306f6bb9696ab5660a539ef63b5a | Text | 3,284 | 74 | scTab
=======
De novo cell type prediction model for single-cell RNA-seq data that can be trained across a large-scale collection of
curated datasets.
Model checkpoints and traning data
-----
* Training data (compatible with Merlin Dataloader infrastructure): https://pklab.med.harvard.edu/felix/data/merlin_cxg_2023_0... |
28120a0626da79fea37f7c9d7b862bb4d71f43fbe9de9423268b7c444c2c90e4 | Text | 3,305 | 72 | # LaGNA: Network-SDE Inference Framework
Codes and data for paper: Learning interpretable dynamics of stochastic complex systems from experimental data
Authors: Ting-Ting Gao, Baruch Barzel, and Gang Yan*
## GNN-based Stochastic Network Dynamics Inference Framework
This repository contains a ... |
d5445c60aa9e16efd68e5a01d1f7ca98ee6eb13dfc1a24d4ec0ec568d7a105e4 | Text | 3,320 | 75 | # Companion code for Insanally, Albanna, et al., Nat. Comm., 2024. "Contributions of cortical neuron firing patterns, synaptic connectivity, and plasticity to task performance"
This is the code acccompanying "Contributions and synaptic basis of diverse cortical neuron responses to task performance" [currently availabl... |
5e5912760f6a86e062bd3dad524d932abe9043b6a16b77eb4d1b0fae43e4de85 | Text | 3,331 | 88 | ====================
BrainSpace
====================
BrainSpace is a lightweight cross-platform toolbox primarily intended
for macroscale gradient mapping and analysis of
neuroimaging and connectome level data. The current version
of BrainSpace is available in Python and MATLAB, programming
languages widely used b... |
a62a50946e29f90e84f3ab8ef4ca943f87333cc2829dfc0ffd9364096737ca84 | Text | 3,332 | 73 | # SMTRI
A deep learning based approach for predicting Small Molecules Targeting miRNA-mRNA Interactions (SMTRI).
## Requirements
* Python 3.8
* tensorflow 2.11
* e3fp
* matplotlib
* numpy
* pandas
* rdkit
* scikit_learn
* scipy
* xgboost
You can install the dependencies with the versioins specifie... |
1dcdf851c019a6fad806650ff525564a2c3cdcafab5dc5bda5b5ec3c1fc3ec35 | Text | 3,359 | 59 | # olfactionGLM
This is the repository for the MATLAB code used to fit GLM models in the paper by [Federman et al., 2024](https://www.nature.com/articles/s41467-024-49897-4).
Created and mantained by [Sebastián A. Romano](https://github.com/sebromano)
## Acknowledgements
The code is an adaptation of the [neuroGLM](h... |
7af7e8d89fb9e8741366306c50a9048d30aeffe475e4368c85d8e3e04c04f206 | Text | 3,379 | 70 | <img src="docs/img/figure0_v0.png">
# pySTED
<a target="_blank" href="https://colab.research.google.com/drive/128pOe4KwnZ7MH6HFcd-mG1HjwDWvohnq?usp=sharing">
<img src="https://colab.research.google.com/assets/colab-badge.svg" alt="Open In Colab"/>
</a>
We have built a realistic STED simulation platform within the ... |
8f7cf2e1f174abb836f79963618614880cd3596da16e7c76f2ba3a544b056e53 | Text | 3,381 | 43 | # Deep Embedding based Spike Sorting
## Prerequisites
You will need the following to run our code:
* Python 3
* Conda
* Weights and Biases (recommended, optional)
## Getting started
### Launch the virtual environment
1. We recommend launching a virtual environment to install all the necessary Python packages. Multipl... |
21f69daf40b1879beabb5573522e1d1fd0b07a091851bcb6da30c94410a0d077 | Text | 3,384 | 90 | [](https://github.com/brain-life/abcd-spec)
[](https://doi.org/10.25663/brainlife.app.292)
# FSL DTIFIT
This app will fit the diffusion tensor model (DT... |
f25170a585b9a26d7ce28e1021054e00483dd8ad8abdf0d8f5ca2f498044ce7b | Text | 3,397 | 68 | # Ithildin C++ Framework
## Anisotropic reaction-diffusion solver
This is the Ithildin framework for parallellized simulations of excitable
media, using C++ and MPI.
## Citation
Please cite these papers when using the implementation:
- M Cloet, L Arno, D Kabus, J Van der Veken, AV Panfilov, H Dierckx (2023)
"Scr... |
689bc546c2416676aa051bdf038c93aa65480925e33272c3eace1e68ad97b86a | Text | 3,401 | 71 | # Practical Bayesian Inference in Neuroscience: Or How I Learned To Stop Worrying and Embrace the Distribution
This repository is a supplement to Coventry and Bartlett's tutorial on using Bayesian methods in neuroscience studies using PyMC.
![alt text](https://github.com/bscoventry/BayesianNeuralAnalysis/blob/main/Baye... |
7f48a6ef99ff022c7cd809b2d83ef1140e750e214816316c1ee539aa64ea2e57 | Text | 3,433 | 22 | # NANO.PTML-project
*NANO.PTML Model for read-across prediction of nanosystems in neurosciences*
Shan He1,2,3, Karam Nader2, Julen Segura Abarrategi2, Harbil Bediaga3, Deyani Nocedo-Mena,4
Estefania Ascencio1,2,3 , Gerardo M. Casanola-Martin1, Idoia Castellanos-Rubio2*,
Maite Insausti2,5, Bakhtiyor Rasulev1, Sonia ... |
69a9f034f0847b22f2c36cc21586653984220e6e85f2fd364879f75be4533e7f | Text | 3,451 | 65 | # transferGWAS
transferGWAS is a method for performing genome-wide association studies on whole images. This repository provides code to run your own transferGWAS on UK Biobank or your own data. transferGWAS has 3 steps: 1. pretraining, 2. feature condensation, and 3. LMM association analysis. Since the three steps re... |
efc0351db5d91c3bacd9d67bdfaf63063f750d36efda33cfc45d72e41538e61c | Text | 3,473 | 80 | # AP-Net
AP-Net is a python package for modeling intermolecular interactions with atomic-pairwise neural networks.
The AP-Net architecture provides smooth and asymptotically correct interaction potentials.
## Getting Started
#### Environment
It is strongly recommended that you install this package in some kind of v... |
85e6233667e226a9b4f8ceef35af9b6458635e479fd9bbe39ff14eac5ecf5b1e | Text | 3,478 | 53 | # BOLD Moments Dataset
<p align="center">
<img src="images/BOLDMoments_mosaic.gif" width="50%" height="auto">
</p>
This GitHub repository contains starter code for the BOLD Moments dataset (BMD) as described in
the publication, ["Modeling short visual events through the BOLD Moments video fMRI dataset and metadata... |
39447602c33bb47b7be6f5ce11e525cad863a811693694695d6734f81068b16c | Text | 3,479 | 69 | <img src="https://raw.githubusercontent.com/wiki/SainsburyWellcomeCentre/StitchIt/images/rgb_brain_example.jpg" />
# StitchIt
*StitchIt* is a MATLAB package for stitching data acquired via our [ScanImage](https://www.mbfbioscience.com/products/scanimage/)-based acquisition system (BakingTray).
To get started, please ... |
21d8feccda56a5a0b816e5ca844d7aab5d495e8f570342b750c433fd4e5ddc96 | Text | 3,514 | 64 | <div align="center">
<p align="center">
<img src="https://images.squarespace-cdn.com/content/v1/57f6d51c9f74566f55ecf271/6f3943a1-b76d-4674-9df9-87aebd33e517/cebralogo.png?format=2500w" width="95%">
</p>
[📚Documentation](https://cebra.ai/docs/) |
[💡DEMOS](https://cebra.ai/docs/demos.html) |
[🛠️ Installation](ht... |
ed259abf7ec0b1eef1752bb703049159c7f541eef96ce68b619c3a4aefc134b5 | Text | 3,518 | 48 | [](https://github.com/eippertlab/pain-reliability-spinalcord/releases/tag/v1.1)
[](https://zenodo.org/doi/10.5281/zenodo.10518643)
[
This repository open sources code and model weights for automated optimum compression of brain transcriptomic data using deep autoencoding, as detailed in our [article](https://doi.org/10.1002/hbm.26795).
## Table of Contents
- [What is this repo... |
3d18603f9516ee2b400fc1dce4972c1b5ef268f5f4cb8d81beabd343f87d29bd | Text | 3,543 | 54 | BAMClipper
==========
Remove gene-specific primer sequences from SAM/BAM alignments of PCR amplicons by soft-clipping
[Download latest version in a ZIP package](https://github.com/tommyau/bamclipper/zipball/master)
### Dependencies, as tested on 64-bit CentOS 5.5
* [SAMtools](http://www.htslib.org/download/) (at leas... |
9b97b1bd920700f209b556cf43633c61e938924f829a04f908d7dc6e0496b070 | Text | 3,551 | 42 | # ms2_numerosity:
## Code and Data for [Crowding, redundancy masking and the radial-tangential anisotropy of numerosity estimation]
This repository contains the code and data used in [Crowding, redundancy masking and the radial-tangential anisotropy of numerosity estimation].
## Paper Abstract
Humans can estimate t... |
efbdb0c727bf4d42b17f09dc9089903057843b08ddb9292f6fd8928c222bd2dc | Text | 3,551 | 82 | # gym-STED-pfrl
This repository contains the experiments used to train a reinforcement learning (RL) agent in the `gym-sted` environment. Please refer to the `gym-sted` repository to obtain specific information.
## Description
This repository relies heavily on the [PFRL](https://github.com/pfnet/pfrl) deep learning ... |
6944c259bf86e97c625d9b4b684bbf15101a1565d64524ed26db3724123c7b42 | Text | 3,560 | 73 | # Machine Learning-Based Extreme Event Attribution
Supporting code for Trok et al. (2024) "Machine Learning-Based Extreme Event Attribution"
To cite paper:
Trok, J. T., Barnes, E. A., Davenport, F. V., & Diffenbaugh, N. S. (2024). Machine Learning-Based Extreme Event Attribution. Science Advances. [DOI]
To cite cod... |
1c0530aecad0600c2340c2593758b502c0529690bb55d49b8abe55632454eae0 | Text | 3,578 | 90 | # MetaboLiteLearner: Python port of the metabolic rewiring GC/MS workflow
This repository now includes a Python implementation of the original MATLAB-based MetaboLiteLearner workflow. The Python code mirrors the same top-level stages:
1. convert Agilent sample directories into the repository's matrix CSV format,
2. e... |
3c93c9e5b462b4d78ada89ee5504f05b45481f20fd9cef2aeeceb1433ac1085d | Text | 3,579 | 47 | # Percolation on spatial networks with triadic regulations
Codes for triadic percolation on spatial networks generated by the Waxman model. Written by Hanlin Sun (<hanlinsun.work@gmail.com>) and Ana P Millán (<ana@onsager.ugr.es>).
This repository contains codes for generating the time series of spatial patterns and ... |
67ae1e558ca3650f5e7a0384151f4277b5e8ec27b7101c4c6446a61c3bfedc5d | Text | 3,581 | 73 | # gym-sted
OpenAI gym implementation of the [pySTED simulation tool](https://github.com/FLClab/pySTED).
## Installation
### Gym
We recommend using a dedicated `python` environment.
```bash
conda create -n gym-sted python=3.10
conda activate gym-sted
```
Then you can install `gym-sted`.
```bash
pip install -e gym-s... |
ca41e5854472779b1d2d741ff52e11b6ef2b3baaf748fbc43825a1f5a9704d69 | Text | 3,597 | 31 | # Clustering Pipeline
Original code used in "Potter, Bassi, & Runyan: Simultaneous interneuron labeling reveals cell-type-specific population-level interactions in cortex, https://doi.org/10.1101/2023.01.09.523298" to classify mCherry and TdTomato fluorophores. The approach could be used to distinguish any two fluoro... |
fa561d30c0ee6863211ca9be2a042a43749fdd679a435d0f0f7cbc399167a4ce | Text | 3,601 | 47 | ### Important Update: New Repository Available! 🚀
We are excited to announce that a new version of our codebase is now available! The new repository features improved readability, better code structure, and enhanced adherence to best practices. We highly recommend using the new version for a better development experi... |
437b8325f21c6cc25d3f44db309742fd00147ee19b201f366a8aace690df76c6 | Text | 3,608 | 84 | # gym-STED-pfrl
This repository contains the experiments used to train a reinforcement learning (RL) agent in the `gym-sted` environment. Please refer to the `gym-sted` repository to obtain specific information.
## Description
This repository relies heavily on the [PFRL](https://github.com/pfnet/pfrl) deep learning ... |
9ebd802a5639de196e691a35661a8a0f2eb6bac59cb2f0c67ff9b3869d4d535b | Text | 3,618 | 78 | # Spine Generic Public Database (Single Subject)
[](https://doi.org/10.5281/zenodo.4299148)
[](https://github.com/spine-generic/data-single-subject/a... |
cefaa179dca968ebb78ba395b6b5d24589ca79bcb13eb3546890c9cf7884e1a9 | Text | 3,622 | 90 | # INTREPPPID
[](https://zenodo.org/doi/10.5281/zenodo.10652231)  
***IN**corporating **TR**iplet **E**rror for **P**redicting **... |
ae2d725e3ae127c9c08b1f43987918e93b2bafb5f024945e84840b2113084773 | Text | 3,638 | 50 | # APPROX-CR (A Passable Proxy of Residual-like Outcomes via Xgboost for Cognitive Reserve)
*Note: This scoring is done entirely on the user's local computer. In other words, it does not upload the data to any internet-based service for scoring.*
## Compiling Data
To generate APPROX-CR scores, users must have correct... |
ddf0a2b97ee08e04efa2457f02382a25bbbd7a66332391734ee10f429d097fd2 | Text | 3,679 | 56 | # Failure-Dataset-OpenStack
This failure dataset contains information on the events collected in the **OpenStack** cloud computing platform during three different campaigns of **fault-injection** experiments performed with three different workloads (**DEPL**, **NET**, and **STO**).
The dataset contains three folders ... |
8109fe9254c1a744c6ba2cfb07a2b5aea43a1d3ee917b9a1150fd7abeefa1c55 | Text | 3,691 | 77 | # Planameterization
### (Planarian Parameterization)
================================
Scripts for the segmentation and parametrization of worm behavior. Released in conjuction with the publication "Adaptive robustness through incoherent signaling mechanisms in a regenerating brain". To get started, simply download or ... |
8c44578a7c7aeda69f2591cd79cfa3baaf0bf88b5d8a4d69e310bb123e8dd425 | Text | 3,695 | 36 | # STARDUST
[](https://zenodo.org/doi/10.5281/zenodo.11398198)
STARDUST (Spatio-Temporal Analysis of Regional Dynamics & Unbiased Sorting of Transients) is a pipeline that captures intracellular calcium (Ca<sup>2+</sup>) dynamics in confined, local micro-domains across ... |
085df14420979b3aa343325b874a9fcff81f990d5ea83659c9848b7a1026bdc3 | Text | 3,700 | 104 | # Automatic Segmentation of Spinal Nerve Rootlets
[](https://www.nature.com/articles/s41598-026-49164-0)
[](https://doi.org/10.11... |
43fc9816f3d960e73ad03b527187f60d824bd8c55e9334ec60ea945cddbf2853 | Text | 3,700 | 78 | # Neuromorphology alterations in Down Syndrome: a computational model of the motor cortex
This repository contains the data and software used in the scientific paper [Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations](https://journals.plos.org/ploscompbiol/article?id=10... |
587b7ee781050e64912cd27c30f61092f5ce150d1b7e6f1501bb0931f33b6b27 | Text | 3,703 | 72 | # Hybrid Static-Dynamic NN Models Library in MATLAB
MATLAB Codes for Training Different Candidate Hybrid All-Nonlinear Static-Dynamic Neural Network Models
Author: Angan Mukherjee (am0339@mix.wvu.edu)
Last Page Update: January 03, 2024
## Announcement
We are very welcome to your contribution. Please feel free to r... |
23af2f6215bed822742afe214cd81eff5e94d22a97d350c579fb6c6ec5c85902 | Text | 3,704 | 28 | # paingen-placebo-fmri-paper
Code and (behavioral) data for the paper on placebo effects based on the Paingen dataset. The preprint is available here: https://www.biorxiv.org/content/10.1101/2023.09.21.558825v2.
The MRI dataset is available on OpenNeuro, ds004746 (doi:10.18112/openneuro.ds004746.v1.0.0).
Since the sam... |
b9208a3232ffbcf835c2b3854bda2d1cb8d68f202638c4421d38e45485cde2ba | Text | 3,719 | 82 | scTab
=======
De novo cell type prediction model for single-cell RNA-seq data that can be trained across a large-scale collection of
curated datasets.
Model checkpoints and traning data
-----
* Training data (compatible with Merlin Dataloader infrastructure): https://pklab.med.harvard.edu/felix/data/merlin_cxg_2023_0... |
0802cab1f0acacdf3ecb42e9924bef9d2d159d6ba935370f3fccfa89edebcb59 | Text | 3,736 | 55 | # TransMut: Automatically optimize mutated peptide program from the Transformer-derived self-attention model to predict peptide and HLA binding
## webserver: https://issubmission.sjtu.edu.cn/TransPHLA-AOMP/index.html
### 1. All software dependencies and oprating system:
The dependencies is the pytorch environment on l... |
cfc0ab26ebce869c727c2f0fb9f9df39173ba5a2dfc6ef24aa6d1ca16126cbbc | Text | 3,774 | 77 | # gym-sted
OpenAI gym implementation of the [pySTED simulation tool](https://github.com/FLClab/pySTED).
## Installation
### Gym
We recommend using a dedicated `python` environment.
```bash
conda create -n gym-sted python=3.10
conda activate gym-sted
```
Then you can install `gym-sted`.
```bash
pip install -e gym-s... |
edfc43dd0250287d79e644111654fb179170e8bdeabe224b203fe7c455d15165 | Text | 3,785 | 54 | # ThorStackSplitter
This is an ImageJ macro which takes in the OME Tiffs output from ThorImageLS and does a variety of things to get them ready for image stabilization and processing.
NOTE: This splitter is specific for ThorImageLS output files. ThorImageLS writes Tiffs as XYZTC rather than the typical XYCZT which mes... |
d68c1d6ef720ebcb0ba0eddcd1b66f3df6664946f509dfbc790757fac1566925 | Text | 3,792 | 47 | PsPM-ViS dataset
=================
Repository Version: 2020.07.07
This dataset contains skin conductance responses (SCR), electrocardyogram (ECG), respiration, pupil size (PSR), and gaze coordinates measurements for 29 healthy unmedicated participants (17 females and 12 males aged 25.3 +/- 3.7) participating in ... |
670dd4abc58cf438875e1f7a2e4b78472881e2f9d333822e18eb45360294f9fc | Text | 3,800 | 93 | # Tensorflow Speech Recognition
Speech recognition using google's [tensorflow](https://github.com/tensorflow/tensorflow/) deep learning framework, [sequence-to-sequence](https://www.tensorflow.org/versions/master/tutorials/seq2seq/index.html) neural networks.
Replaces [caffe-speech-recognition](https://github.com/pann... |
6ba95f015774043ce0a77ee90b1b1cf46344cb93c9523f913ce33df40fa7cb20 | Text | 3,815 | 93 | ## Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information
Here is an official implementation for RMSF-net. (The current code is a temporary version which will be added more complete features in the future.)
This script is mainly f... |
e94ef85e0d33367df3414dcf9a83e2f5a51723d0e7af39fc41f2c302288426b0 | Text | 3,821 | 61 | # ESSES: Epidemic Spreading Seizure and Epilepsy Sugery framework.
This repository contains the MATLAB toolbox for the ESSES framework as defined in [1]. ESSES creates patient-specific seizure propagation models to investigate alternative resection strategies and estimate the outcome of a given resection for patients ... |
e86f1670d10af27319b1785dd1278cfca56ad4d660549e4ffdc04eeb2cf3a7c1 | Text | 3,865 | 96 | Note: Requires Python 3.8. For more information regarding setting up marugoto on your system and file management for your project, see [documentation](https://github.com/KatherLab/marugoto/blob/main/Documentation.md).
# まるごと—A Toolbox for Building Deep Learning Workflows ##
Our workflow uses a DL approach which perfor... |
50b5e2999a51fad1c31a59b4be7c8191f8130b90ae6a4631620ed7a68d1ce1dd | Text | 3,868 | 124 | # Eigen Manifold Cross Mapping (EMCM) Toolbox
<!-- <p align="center">
<img src="https://github.com/ParhamP/DENMD/blob/main/assets/DENMD-logos.jpeg?raw=true" width="305" height="305">
</p> -->
EMCM is a MATLAB toolbox for generating high-dimensional manifolds from time-series data using Eigen-Time-Delay Embedding and... |
d52374cc025d9e510a18e75cd111990f0681438eb88e6d1979894b1eea9e1ff2 | Text | 3,904 | 80 | ## Cell Magic Wand
ImageJ plugin for rapid human-assisted segmentation of cells in images.
### Description
Click on a cell. Get an ROI around the cell.
### Download and Install
Download: [Cell_Magic_Wand_Tool.jar](Cell_Magic_Wand_Tool/Cell_Magic_Wand_Tool.jar)
Version Required: [ImageJ... |
d8a3f8aa2cd131e3b474f6091ddfb6f39511d3e2f8dd340710581b3a4108ab90 | Text | 3,915 | 45 | # NMGrad
This is the source code described in the paper "NMGrad: Advancing Histopathological Bladder Cancer Grading with Weakly Supervised Deep Learning" by Saul Fuster, Umay Kiraz, Trygve Eftestøl, Emiel A.M. Janssen, and Kjersti Engan - under revision.
### 1 - Abstract
The most prevalent form of bladder cancer is ... |
dabdc30c4b973334bc7730e3ec7a163124073eebb3ee058ef282d106159538a8 | Text | 3,924 | 25 | # Visuomotor model of the left Superior Colliculus
>Model created by Kris Jensen (University of Cambridge) as Jupyter notebook in colab.
Three-layer network model of the left SC composed of a static spatial receptive field (ssRF) layer, a direction selective (DS) layer and a motor layer, of 500 neurons each. The conn... |
d3e66bfa667b1ae105a90fca45301d74516d425c0ae5dde77d575758c45fb32f | Text | 3,926 | 55 | # NSCLC_ResNet
Haowen Zhou, Mark Watson, Cory T. Bernadt, Steven (Siyu) Lin, Chieh-yu Lin, Jon. H. Ritter, Alexander Wein, Simon Mahler, Sid Rawal, Ramaswamy Govindan, Changhuei Yang*, and Richard J. Cote*. "AI-guided histopathology predicts brain metastasis in lung cancer patients." Journal of Pathology (2024).
## A... |
bc6143d4b70039a2882f949ca91881f2b7df97ff7e6b25f0563ee8e8a5ebc787 | Text | 3,939 | 48 | # Overview
This repository contains code and data pertaining to [High-level cognition is supported by information-rich but compressible brain activity patterns](https://www.biorxiv.org/content/10.1101/2023.03.17.533152v1) by Lucy L. W. Owen and Jeremy R. Manning.
The repository is organized as follows:
```
root
├── ... |
6f697d9bd2e5aa9198adacc33e3a673440f5c40a3ee8dec02f4390174dd235a2 | Text | 3,942 | 57 |
[](https://github.com/google-research/weatherbench2/actions/workflows/ci-build.yml)
[![Lint](https://github.com/google-research/weatherbench2/actions/workflows/lint.yml/badge.... |
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