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|---|---|---|---|---|
1e4e4837b720b1c1cb856f8bda52d1b680856c42b1299a0cc4f1e6edf940c1c8 | Text | 9,485 | 131 | [](https://github.com/RangamaniLabUCSD/smart/actions/workflows/test_fenics_smart.yml)
[](https://pypi.org/project/fenics-smart/)
[ and dynamic parameters (slope, time to peak, and dynamic slope ratio) from 18F-FDOPA PET images o... |
7b2904701cd2fc9c204deb30455eebe6f308f09c94d648738657588c2b088eb4 | Text | 9,674 | 202 |
The BLASTOSPIM Instance Segmentation and Tracking Pipeline can be run by installing the software packages or by using Jupyter notebooks.
# Running BLASTOSPIM with Jupyter notebooks
Follow the instructions here to use the [Jupyter notebooks](https://github.com/haysconun/blastospim-processing-pipeline-Jupyter).
# Fu... |
02495f38182910b6759e573bc4514cadcde07afd7594ba80c82782dbaabb5e9f | Text | 9,697 | 58 | # pyBoxshade
Desktop application for colouring/shading sequence alignments
### Purpose
pyBoxshade is a program for creating good-looking printouts from alignments of multiple protein or DNA sequences. The program does no alignment by itself, it takes as input a file already processed by a multiple alignment program or... |
2a07d18c84ef65dcf49778ae526196c944a6961587657646b3fbce6f92a98ec5 | Text | 9,711 | 125 | ======================
Flex ddG Tutorial
======================
The most up-to-date version of this tutorial `is available on GitHub <https://github.com/Kortemme-Lab/flex_ddG_tutorial>`_.
Introduction
------------
In this activity, you will utilize the Flex ddG [KB2018]_ protocol within Rosetta to computationally mo... |
99da0fe8bcde2e460d41f51ea2c7cf12afa4fd505cb762b2c737bf38c6cf2f4e | Text | 9,721 | 269 | # Karawun
[](https://github.com/richardbeare/karawun/actions)
## Introduction
[_Karawun_](https://DevelopmentalImagingM... |
a7be0be4061c5d70dc6fe117d225789be0a924c06fec5481a47e2a0e36a980d8 | Text | 9,726 | 167 | ngsParalog
==========
ngsParalog is a program for detecting genomic regions that are problematic for short reading mapping using population-level, next generation sequencing (NGS) data.
ngsParalog implements a likelihood method for estimating the probability that reads covering a particular site are mismapped based o... |
520a6d7cdb398eace485a6ce7249ed185d0c4bf9a5e0dcc3ad435f0effea5cdd | Text | 9,783 | 204 |
The BLASTOSPIM Instance Segmentation and Tracking Pipeline can be run by installing the software packages or by using Jupyter notebooks.
[](https://doi.org/10.5281/zenodo.13286318)
# Running BLASTOSPIM with Jupyter notebooks
Follow the instructions he... |
1160a82f0d744fa773c73a6b9ef3c65497276349511993b69a96d15fe4288a33 | Text | 9,907 | 91 | 
# Markos 2024: Cell type and regulatory analysis in amphioxus illuminates evolutionary origin of the vertebrate head
## Introduction
This repository contains scripts and input data used for analysis of single cell RNA-Seq data presented in Markos 2024[^1]. Data consist... |
0278568c6d5c1ebab7384620f9e1830a216f7c7a1ff804a13d8ac9c91b44d927 | Text | 9,965 | 189 | # Hybrid approach to knowledge extraction from scientific publications using structured ontology models, graph neural networks, and large language models
This repository contains the code and models for a hybrid approach to knowledge extraction from scientific publications, combining structured ontology models, pairwi... |
41666d76d491494674a7f57913fbd3ccb2c0ce8d72c9ee09607364f4738823bc | Text | 10,063 | 206 | # FlyWire sign determinacy, version 1.0
This record contains one table. For each of 126,419 neurons in the FlyWire adult
Drosophila connectome, it reports whether the underlying image data determines the
neuron's neurotransmitter, and therefore the sign of its outgoing connections.
Coverage: 126,419 neurons and 120,5... |
b054a10c4e69795c27d66de233d7bff96434db13074e2ba0578ad073f430d4ac | Text | 10,131 | 170 | ## overhang_surrogates: a Python package for sampling, training and visualising surrogate models for building energy simulations
The package, which can be installed by `pip install overhang_surrogates`, contains selected methods that:
- offer Python implementation of the iterative sampling method mc-intersite-proj-th ... |
dff339c9b88457d26099b4ed213305ff1e16978702224650d6b95e17de1a8bcb | Text | 10,163 | 261 | # neurorad_pipeline
## Installation
See https://github.com/pennmem/event_creation for instructions on how
to install this repository as part of the submission utility.
If you want to use by itself or integrate it into a different utility,
simply clone the repository.
To install dependencies:
Install miniconda for ... |
bb13de24d25f52726307ac83f943164af00323d7f57114ca505c88548d458b0d | Text | 10,183 | 113 | # Code for Picard et al., A distributed brain response predicting the facial expression of acute nociceptive pain
[![DOI:[10.7554/eLife.87962.2]](http://img.shields.io/badge/DOI-10.7554/eLife.87962.2-blue.svg)](https://doi.org/10.7554/eLife.87962.2)
---
**NOTE**
The scripts were developed to analyze already preproc... |
c5346484e9fd7944f64249e1922ae9f758e65f5cf763f23d858fdff7a683a302 | Text | 10,204 | 368 | <img align="left" width="100" height="100" src="images/RNAflow_logo.png" alt="RNAflow">
# RNAflow: A snakemake-based pipeline for standard transcriptomic analysis
[](https://snakemake.readthedocs.io/en/stable/) [
### Written in the Written Description Language (WDL) version 1.0 more info [here](https://github.com/openwdl/wdl)
## Before running the pipeline
We have the whole environment containerized, the definition file is available in the `environme... |
9f0d9d0f49e5db4a543a9f82b71f93df8c07a9d3fa7be02897f49caeab898823 | Text | 10,431 | 157 | <!-- vscode-markdown-toc -->
- 1. [Setting up environment](#Settingupenvironment)
- 1.1. [Few-clik-ready setup](#Few-clik-readysetup)
- 1.2. [Manual setup](#Manualsetup)
- 1.2.1. [Install dependencies](#Installdependencies)
- 1.2.2. [Set up environment variables](#Setupenvironmentvari... |
bd83e1c9d969b335dfdb9c6ba8b81206820789163ba2254b6aa5bec6757ff7f9 | Text | 10,777 | 312 | <h1 align="center">Parallel development of object recognition in newborn chicks and deep neural networks</h1>
<p align="center"> Lalit Pandey, Donsuk Lee, Samantha M. W. Wood, Justin N. Wood </p>
<p align="center">†S.M.W.W. and J.N.W. contributed equally to this work.</p>
<h2 align="center">Journal: PLoS Computati... |
8064e391d1e8eade924d4af5a95b6d8c18caf79c9e2de39c3ec859af1d6cc84d | Text | 10,797 | 145 | # 脑电特征提取工具箱 | All-In-One EEG Feature Extraction Toolbox
I’m trying to make an all-in-one EEG feature extraction toobox, including statistical features, Hjorth parameters, entropy, nonlinear features, power spectral density (PSD), differential entropy (DE), empirical mode decomposition (EMD), common spatial patterns (C... |
974c49b0548690be018ef1bc390c043cc68845a5e665613e814185ec4f3af2cd | Text | 10,823 | 198 | # Fuzzy
[](https://zenodo.org/badge/latestdoi/218554957)
[](https://github.com/verificarlo/fuzzy/actions/workflows/build-fuzzy.yml)
[
μBrain a 3D digital atlas of the developing brain at micrometre scale based on a [public resource](https://www.brainspan.org/) of 81 serial histolo... |
c7c544e4306797326e627a9d2f9c83138ab0054fb2a04f29b100997b34578d14 | Text | 11,040 | 135 | # ActflowToolbox
## The Brain Activity Flow ("Actflow") Toolbox
A toolbox to facilitate discovery of how cognition & behavior are generated via brain network interactions
## Version 0.3.2
## Visit [https://colelab.github.io/ActflowToolbox/](https://colelab.github.io/ActflowToolbox/) for more information
### Version ... |
aad4b5d19692227db2cd4d4d634663e95efabaaffac1cdae68b6159822a70d38 | Text | 11,334 | 118 | # Molecular Nodes 🧬🍝💻
<img src="https://raw.githubusercontent.com/BradyAJohnston/MolecularNodes/main/docs/images/logo.png" align="right" style="height:250px;"/>
[](https://github.com/BradyAJohnston/MolecularNo... |
367b1cc43dbf409cbc89e70c4efedbc160134fef31d8af43ec9009b8d0163db0 | Text | 11,424 | 226 | <h1 align="center">Face Mask Detection</h1>
<div align= "center"><img src="https://github.com/Vrushti24/Face-Mask-Detection/blob/logo/Logo/facemaskdetection.ai%20%40%2051.06%25%20(CMYK_GPU%20Preview)%20%2018-02-2021%2018_33_18%20(2).png" width="200" height="200"/>
<h4>Face Mask Detection System built with OpenCV, Ke... |
0ce94a29d979341c81aa5ab6a4cd483903b3b310404c916caf801620f2829548 | Text | 11,608 | 161 | # Multi-Scale Spiking Network Model of Human Cerebral Cortex
This code implements the multi-scale, spiking network model of human cortex developed at the Institute of Advanced Simulation (IAS-6), Research Center Jülich. The model has been documented in the following publication:
- [1] Pronold, J., Meegen, A. van, Shi... |
7f8548d4a79030734149afef60a1c7336be53c9c9718cd18dad8c9eef78c57c0 | Text | 11,630 | 202 | # **Section1:Overview**
This document provides details on how to use the functions for generating various types of simulated spatial transcriptomics data, including descriptions of the specific code and parameter meanings for each data type, as well as instructions on generating simulated SRT data from custom scRNA-s... |
058d7be3b7c8c1af38eb5f0eb13a55f001a4693e2234641cdc441d1f9ccdfa65 | Text | 11,904 | 113 | [](https://pypi.org/project/fba/)
[](https://bioconda.github.io/recipes/fba/README.html)
[ | [Supplementary](http://www.cvlibs.net/publications/Chitta2022PAMI_supplementary.pdf) | [Talk](https://www.youtube.com/watch?v=-GMhYcxOiEU) | [Poster](http://www.cvlibs... |
c32b987895969020b2eb200a0b57b185914e043cb91cf6502aea241be26e8ec4 | Text | 12,047 | 160 | ## MR-JTI [](https://github.com/gamazonlab/MR-JTI/blob/master/LICENSE)
[](https://doi.org/10.5281/zenodo.4164740)
For questions:
Dan Zhou <zdangm@gmail.com>
Eric R. Gamazon <e... |
34f269cf93699b9c425d283b35c480af2033a742dc9d1ceef78396c8a60e1d66 | Text | 12,253 | 244 | # Computational Optimization of DNA Activity (CODA)
[Preprint on bioRxiv](https://www.biorxiv.org/content/10.1101/2023.08.08.552077v1). For legacy reasons, this repo is currently listed as boda2. The model, model weights, and code defining the model architecture are covered under the MIT license, and the rest is covere... |
6dccd617f22fa6d924db6da9e8cf8374bee0f83cb777b7c1ba4fad2bba830485 | Text | 12,266 | 174 | <div align="center">
# Simulated Bias in Artificial Medical Images
</div>
<p align="center">
<img src="figures/paper1779_fig1.png?raw=true" width="600">
</p>
Implementation for the SimBA 🦁 framework presented and utilized in our papers:
* [A flexible framework for simulating and evaluating biases in deep learn... |
8ff5a7b5169d9624fd2a3ad43fe14ded9850abba4a61699dbcba17fca1897e89 | Text | 12,364 | 148 | # [BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae590/7808857)
### [PAPER (Oxford Bioinformatics)](https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btae590/78088... |
58e635047e076f4cfb10c43d6437e3ce0c7ac46e96277259057831c38ee11229 | Text | 12,425 | 160 | # FastGlioma: foundation models for fast, label-free detection of glioma infiltration
[**Paper**](https://www.nature.com/articles/s41586-024-08169-3) /
[**Interactive Demo**](https://fastglioma.mlins.org) /
[**Models**](https://huggingface.co/mlinslab/fastglioma) /
[**MLiNS Lab**](https://mlins.org)
Code repository ... |
9f9d9f185334f49f86b3b52a603f8f81085301626526bcdee8a18843a6464815 | Text | 12,457 | 287 | 
[](https://github.com/jacquemi-bbp/arch/actions)
[](https://github.com... |
5265d2577c4ff7462728809f55da3daf4c49a710893e933aa79f1541f855d28b | Text | 12,522 | 406 | <div align="center">
<img src="img/jasmine-logo.png" alt="jasmine logo" width="135px" align="center"/>
<h1>Jasmine</h1>
<p>Call select base modifications in PacBio HiFi reads</p>
</div>
## Table of contents
- [Overview](#overview)
- [Input data](#input-data)
- [Running Jasmine](#running-jasmine)
- [Suppor... |
5467c356223a0279b29f54bd8dd2daa9692f5c06f655ccbe7f4132d2e07c787e | Text | 12,576 | 298 | **Project Overview**
](https://doi.org/10.1371/journa... |
36f0e9ccc8656480d9e5942dd59fa1efbe7069dfcd6c68fd4574483682bb2454 | Text | 12,751 | 183 | # Task-Modulated Functional Connectivity (TMFC) <br/> Methods Comparison
Repository for code and simulations from <br/>
**"Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics"** <br/>
by Masharipov, R., Knyazeva, I., Korotkov, A., Cherednichenko, D. & Kireev, M.
U... |
8b2fa675a6e334aa9fecd5fe1d4ebbb92434b9fb7e35282470706f4178dc5e71 | Text | 12,893 | 95 | # PyTorch CIFAR Models
## Introduction
The goal of this project is to provide some neural network examples and a simple training codebase for begginners.
## Get Started with Google Colab <a href="https://colab.research.google.com/github/chenyaofo/pytorch-cifar-models/blob/master/colab/start_on_colab.ipynb" target="_... |
aaf88de1ad0fa58c80fcb733ad1aa525b589f50a5fad37ad3e0bda071c560cc2 | Text | 13,035 | 241 | # CryoVesNet
CryoVesNet is a deep learning-based method for automatic segmentation of synaptic vesicles in cryo-electron tomography (cryoET) data. It is based on a U-Net architecture trained on manually segmented tomograms and postprocessing steps. Notably, our method's ability to generalize across different datasets,... |
0d2b16648dbcf6a1ab9e4c0f3cef03ae294b7838bb3cdc12344bbd395636ac06 | Text | 13,163 | 112 | Small brains: Body shape constrains tissue allocation to the central nervous system in ant-mimicking spiders.
DATA & CODE FILE OVERVIEW
This data repository consists of 1) Supplementary material S1 (PDF), 2) Dataset S1 (excel spreadsheet), 3) Supplementary file 1 - R project files, 4) Analyze 7.5 files, 5) Segmenta... |
9068f6b4ebe6f8e40cd8756f0c9af6e9bd75f1805b9182204eb4565fbf136717 | Text | 13,318 | 325 |   [](https://qlty.sh/gh/hed-standard/projects/hed-python) [
[](https://travis-ci.org/life4/textdistance) [](https://pypi.python.org/pypi/textdistance) [ for Resting-State Functional Connectivity Analyses
This is a MATLAB software package to accompany the article:
Williams JC, Tubiolo PN, Luceno JR, Van Snellenberg JX. Advancing motion denoising of multiband resting-state functional connectivity fMRI data. Neuroimage... |
2e0905a74a106a5138212c7ec2e624f9444c79da535d8928bda6b9734ef5b9ac | Text | 13,558 | 228 | # MEGneto 3.0
This MEG analysis pipeline is built on MATLAB using the FieldTrip toolbox to analyze MEG data. Developed @ SickKids Research Institute, Toronto, Canada. See docs folder for additional documentation.
- [Credits](#credits)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation... |
0144615638f5338e71be79d52503edf4c710233c12054c0ad4839ac3e674c1d5 | Text | 13,743 | 242 | # NeuroDataManagementSystem
The NeuroDataManagementSystem is an integrated solution designed to streamline and enhance the management of neuroimaging and clinical data.
## Overview
The folder **NeuroDMS** represents the final NeuroDataManagementSystem and contains the SQLite database and the BIDS organized imaging d... |
c24a8a13226f7f2714354b7a3a47fc1b08fb818f0cd1f801201334398c3748ed | Text | 13,973 | 132 | [](https://doi.org/10.21105/joss.00671)
[](https://zenodo.org/badge/latestdoi/128659224)
# BioSigKit
BioSigKit is a set of useful signal processing tools in Matlab that are either developed by me personally... |
2a47a3d8b7b76107a4f5a0190a150eee6a9b624534aafc6b51db44b1600727b4 | Text | 13,978 | 320 | # LFPykit
The online documentation of `LFPykit` can be found here:
https://lfpykit.readthedocs.io/en/latest
`LFPykit` is a freestanding implementations of electrostatic
forward models incorporated in LFPy
(https://github.com/LFPy/LFPy, https://LFPy.readthedocs.io).
The aim of the `LFPykit` module is to provide electr... |
95d751d10772eec4c4a5569fd8cb181cbe22785e8c3684da7ab842d376650fbd | Text | 14,068 | 385 | This README.txt file was generated on 28-Feb-2024 19:10:05 by Emilio Salinas
GENERAL INFORMATION
1. Title of Dataset:
Dataset: Coupling of saccade plans to endogenous attention during urgent choices
2. Author Information:
Author 1
Name: Allison T Goldstein
Institution: Wake Forest School of Medicine... |
936c84532863e754fca24c7f3985170c33eeb0a7e992cf38956a5673322b27ae | Text | 15,151 | 203 | # *ngs-bits* - Short-read and long-read sequencing tools for diagnostics
## Downloading ngs-bits
Binaries and Docker containers of *ngs-bits* are available via Bioconda:
[](http://bioconda.github.io/recip... |
d91ef5835fa7ebb7f8494949d90adfc2738c55975fa5a9851d7753470b41d4bb | Text | 15,256 | 210 | InSTAnT
=========
[](https://zenodo.org/doi/10.5281/zenodo.10994621)
[](https://github.com/bhavaygg/InSTAnT/blob/main/LICENSE.txt)
[]... |
a2e4acee0febca42b79314b43f08f5907941acd4a6f4ab4cb5a8ee0d4461538f | Text | 15,481 | 243 | # DeepSignal2
[](https://www.python.org/)
[](https://github.com/PengNi/deepsignal2/blob/master/LICENSE)
[](https://pypi... |
70e9ad3b1da7817319215137a85355dea0b8aee538b7c68e54b950d9abe2f718 | Text | 15,504 | 250 | # XAI_in_genomics
This repository contains the code of the experiments performed in the following paper\
[A Comparative Analysis of Gene Expression Profiling
by Statistical and Machine Learning Approaches]()
by Myriam Bontonou, Anaïs Haget, Maria Boulougouri, Benjamin Audit, Pierre Borgnat, Jean-Michel Arbona.
## Ab... |
6029f2f9d42148e8f7f0826cd9d3d35c0cf16602dabb66090e148941a0679e01 | Text | 15,615 | 187 | # [](https://github.com/unfoldtoolbox/Unfold.jl)
[](https://unfoldtoolbox.github.io/UnfoldDocs/Unfold.jl/stable/)
[](https://github.com/hsseung/OpticLobe.jl/actions/workfl... |
fada2b55a05f15116b8302d3acd6f0d5469524027ff30a91013f55754a7e9c68 | Text | 15,957 | 308 | # :rocket: SuPar
[](https://github.com/yzhangcs/parser/actions)
[](http... |
7f328880601ec913d8cb42d5924a87417e377e4d6d5e2ce9fa487e5dd5747320 | Text | 16,001 | 322 | 
## The best pre-computed word embeddings you can use
ConceptNet Numberbatch is a set of semantic vectors (also known as word embeddings)
that can be used directly as a representation of word meanings or as a starting point
for further machine learning.
ConceptNe... |
f4d410501f5285b73a9d13e3860febd05406966df0d78db71d98e435080c1fa8 | Text | 16,145 | 428 | [](https://doi.org/10.5281/zenodo.11097260)
# bifrost
Template building and multi-modal registration
# System Requirements
## Hardware Requirements
Image registration is a memory-intensive computation. For example, it takes on the order of 128G of
me... |
9d236c31ad84a3a6211c133ef4b434a0e992db68413e470b5127d4c815fa22fb | Text | 16,171 | 213 | # The KymoToolBox plugin
# Chapter 1: How to install the plugin?
First, close ImageJ in case the software is already running. Copy and paste the KymoToolBox.jar file you(ve downloaded from the [release section](https://github.com/fabricecordelieres/IJ_KymoToolBox/releases) into the ImageJ/Plugins folder. Restart Ima... |
340aa39f356ec82b4ab65e85b0f63f529546c1adf05c6407893be95388d00832 | Text | 16,185 | 250 | [](https://www.hedtags.org/hed-schemas) Standard:[](https://doi.org/10.5281/zenodo.7876037) SCORE:[](https://doi.org/10.52... |
4ab2e69c31458d745c4162523a46a62e10d9cc3ea7fdfacc1a4b6f45a47516f3 | Text | 16,285 | 154 | # tedana: TE Dependent ANAlysis
[](https://pypi.python.org/pypi/tedana/)
[](https://pypi.python.org/pypi/tedana/)
[](https://zenodo.org/bad... |
ad87893b2982034c3a4673f2d95e2071769f726994ffd5ef4838d75e4b1d67a1 | Text | 16,381 | 311 | LFPy
====
Summary
-------
LFPy is a Python module for calculation of extracellular potentials from multicompartment neuron models.
It relies on the NEURON simulator (<http://www.neuron.yale.edu/neuron>) and uses the
Python interface (<http://www.frontiersin.org/neuroinformatics/10.3389/neuro.11.001.2009/abstract>) ... |
bd49bc2937b6d731cef97e352b90a593098b4994c7063b869557519ecd38211c | Text | 16,447 | 311 | # VertexWiseR <img src="man/figures/logo.png" alt="logo" align="right" style="float:right; height:200px;"/>
## A package for simplified vertex-wise analyses of whole-brain and subcortical surface in R
<!---start of badges-->
[](https://CRAN.R-project.org/... |
685088e1b117612f285a5bc5e923eaddeb00fe598f9ae7f3af9eed6e522bf874 | Text | 16,503 | 383 | # TrAnnoScope
**TrAnnoScope** is a comprehensive workflow designed to process long and short reads to generate full-length transcripts and perform comprehensive functional annotation.
TrAnnoScope is built on the **Snakemake**, offering a robust suite of features for generating full-length transcriptomes from multiple... |
d0a13607913ea94e65a91ac864b969683a41a45b0aec16e0ae64271649d0364d | Text | 16,548 | 272 | <p align="center">
<img src="assets/realesrgan_logo.png" height=120>
</p>
## <div align="center"><b><a href="README.md">English</a> | <a href="README_CN.md">简体中文</a></b></div>
<div align="center">
👀[**Demos**](#-demos-videos) **|** 🚩[**Updates**](#-updates) **|** ⚡[**Usage**](#-quick-inference) **|** 🏰[**Model ... |
279623c77697090fe5fa896fb5980f2ddab43fe48f1cfb0a2e69c354714460f3 | Text | 16,568 | 190 | # Boney
This is the Boney toolbox, an extension to [SPM12](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/) and its [CAT12](http://www.neuro.uni-jena.de/cat) toolbox, supporting the extraction of measurements related to the bone and head structure. It is developed by *Polona Kalc* and *Robert Dahnke* and is a free but... |
fefb34d3c564ed5e99a3ad40def7464acdc1c06cddaf14b791a85aea37bb0aa2 | Text | 16,879 | 397 | <!-- PROJECT LOGO -->
<p align="center">
<h1 align="center"><img src="media/logo.png" width="60">NICE-SLAM: Neural Implicit Scalable Encoding for SLAM</h1>
<p align="center">
<a href="https://zzh2000.github.io"><strong>Zihan Zhu*</strong></a>
·
<a href="https://pengsongyou.github.io"><strong>Songyou P... |
220c940a8dac6ebd8f7f4fa880b2585ce06f224505a7ecc6621d5c5dba3ede96 | Text | 16,953 | 439 | [](https://doi.org/10.5281/zenodo.11097260)
# bifrost
Template building and multi-modal registration
# System Requirements
## Hardware Requirements
Image registration is a memory-intensive computation. For example, it takes on the order of 128G of
me... |
bfc420df1cc4b33556721abc67c9b8d56fc6e9bd0b38087ad6f6ad793257499d | Text | 17,027 | 157 | ---
# urOMT (unbalanced regularized optimal mass transport)
---
# Introduction
## Mathematical Formulation
This project works on an unbalanced version of regularized optimal mass transport (urOMT) problem by adding a new relative source variable and its indicator function into the formulation. Specaifically, we d... |
7171cedad8ecc3e04bef5b3d6929233ca52c23f72e06cbd8134cd6cb73898adb | Text | 17,054 | 201 | [](https://github.com/mastodon-sc/mastodon/actions/workflows/build-main.yml)
[![Image.sc Forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fmastodon.json&que... |
5cb1df6cde8996e8799c4d544d1a11e9d1ab83e2eb21db52d233ccbfbd5e2a3e | Text | 17,262 | 615 | # MorphoGlia
<img width="1161" height="260" alt="LOGO_MG3" src="https://github.com/user-attachments/assets/5f2376df-bfb2-413e-b89f-d29b77152570" />
**MorphoGlia** is a cell-morphology analysis pipeline for image preprocessing,
instance segmentation/postprocessing, morphometrics, morphology-state
estimation, tissue... |
d8305fd647cbb3a4034c30899fc6a155b2efda203c2522c859ff5fe91a351092 | Text | 17,275 | 231 | InSTAnT
=========
[](https://zenodo.org/doi/10.5281/zenodo.10994348)
[](https://github.com/bhavaygg/InSTAnT/blob/main/LICENSE.txt)
[]... |
de06e5ace4611d48d24bc076acd3c7124a52166452c55de513b4e173594c7d08 | Text | 17,282 | 413 | # 🔬 DSMIL-KOH: AI-Powered Fungal Keratitis Detection on Whole Slide Imaging
[](https://www.ophthalmologyscience.org/article/S2666-9145(24)00189-1/)
[](https://www.python.org/download... |
fafa364ebdea6ae31e22b7cbc2e1c0d65565a05170e6f83d797ae68b3abfde2c | Text | 17,472 | 296 | # MCGLPPI
### Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction ###
__The original bioRxiv version link: [https://www.biorxiv.org/content/10.1101/2024.03.14.585015v1.abstract]__
__The accepted version link: [https://www.natur... |
16f807902bb0c8cfc35bad3876eefd4fa6f22e428714655bbb48d6a79e91e54c | Text | 17,496 | 171 | [](https://zenodo.org/badge/latestdoi/101246939)
# The SAMPL6 Blind Prediction Challenge for Computational Chemistry
This repository gives challenge details and inputs for the SAMPL6 challenge. First part of SAMPL6 phase was composed of host-guest, pKa, SAMPLing challenge... |
f3365b37dc478455c1ab8de7c502c1e956dcd2ba65b88b181e914d013a1fc43c | Text | 17,616 | 331 | # DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image
Pytorch implementation for the multiple instance learning model described in the paper [Dual-stream Multiple Instance Learning Network for Whole Slide Image Classification with Self-supervised Contrastive Learning](https:/... |
fabda659922fa4964380ea188e5ecd60309a3b9d1f6b86d56e022d27250cb8b2 | Text | 17,690 | 316 | # HORNET
HORNET: Holistic RNA Structure Determination by Unsupervised Learning and Deep Neural Networks. HORNET is a software package for determining 3D topological structures of RNA conformers using atomic force microscopy topographic images and deep learning.
## I. Requirements
The software has been designed to b... |
f85763e3af76634c337f9544ad690015d23345f011bb5eaf9c12d10ccef0e470 | Text | 17,897 | 368 | # nda-tools
`nda-tools` is a Python-based command-line client designed for submitting data into and downloading data from the National Institute of Mental Health Data Archive (NDA). It enables users to programmatically **validate, package, submit, and download data** while ensuring compliance with NDA’s required form... |
bb3cf20574bd920623e8b7fe2b74403c53b6b95d3314b82a9f2428e48cd066f1 | Text | 17,935 | 314 |
# A Scalable System for Real-Time Behavior Analysis (SARTAB)
Original Title: Real-time Behavior Analysis (RBA)
Publication: https://www.frontiersin.org/journals/behavioral-neuroscience/articles/10.3389/fnbeh.2024.1509369/full
## Motivation
Understanding the biological mechanisms that lead to complex behavior is a c... |
ac008115f96bc6642ac49bbea1be128d3681fc663e4caf288af6f8b1506889f5 | Text | 17,947 | 275 | <a href="https://rega.kuleuven.be/cev/viralmetagenomics" target="_blank"><img src="img/JM_icon.png" height="12.5%" width="12.5%" align="right"/></a>
# ViPER - Virome Paired-End Reads pipeline
[](https://github.com/Matthijnsse... |
ab8227bd59e4e50f64df013070cac37ede5fdf99f1449ac687e1c62a3697e486 | Text | 18,023 | 486 | med2image 2.6.6
==================
Quick Overview
--------------
- Convert ``DICOM`` or ``NIfTI`` inputs to ``jpg`` or ``png`` outputs.
Overview
--------
``med2image`` is a simple Python3 utility that converts medical image formatted files (such as ``DICOM`` and ``NifTI``) to more web friendly ones, such as ``png`... |
2600efd691a0d758cc93c308e40e8e02cf5b8cee50b446abc28d75129a9bd71a | Text | 18,204 | 385 | # GT4SD (Generative Toolkit for Scientific Discovery)
[](https://badge.fury.io/py/gt4sd)
[](https://github.com/gt4sd/gt4sd-core/actions)
[](https://zenodo.org/badge/latestdoi/184310568)
Challenge details, inputs, and (eventually) results for the SAMPL7 series (phase) of challenges. Each individual SAMPL7 challenge may be broken up into mu... |
b05bec677a12e7bb1c255a3a40860859e88e1c068be6516d9a621dae867f5e57 | Text | 18,744 | 393 | TorchEEG
========
|PyPI Version| |Docs Status| |Downloads| |Join the Chat|
`Documentation <https://torcheeg.readthedocs.io/>`__ \| `TorchEEG
Examples <https://github.com/torcheeg/torcheeg/tree/main/examples>`__ \|
`Paper <https://www.sciencedirect.com/science/article/pii/S0957417424004159>`__
TorchEEG is a library b... |
52320ffe0e887bd99692d6512a31d37ca97e47ee0985b402ab72b3081fa6a30d | Text | 19,107 | 325 | # Kiwi : 지능형 한국어 형태소 분석기(Korean Intelligent Word Identifier)
x86_64:
[](https://github.com/bab2min/Kiwi/actions)
[
[](https://codecov.io/gh/MouseLand/rastermap)
[](https://... |
ba1573417a8421f8021009cd3f32005d7147a8c3e9c429ab036bcc2114e27eb5 | Text | 20,228 | 355 | <p align="center">
<img alt="Header image of neurolib - A Python simulation framework for
easy whole-brain neural mass modeling." src="https://github.com/neurolib-dev/neurolib/raw/master/resources/readme_header.png" >
</p>
<p align="center">
<a href="https://github.com/neurolib-dev/neurolib/actions">
<img alt=... |
cea9e78455eca460fe26dc7e3c154f426de99fc16331d26db8720ff3b13de633 | Text | 20,291 | 477 | # MetBrewer <img align="right" src="https://github.com/BlakeRMills/MetBrewer/blob/main/PaletteImages/Hex/MetBrewerHex.jpg" width=400>
Palettes inspired by works at the Metropolitan Museum of Art in New York. Pieces selected come from various time periods, regions, and mediums.
![CRAN Version](https://www.r-pkg.org/ba... |
ffcf19a3fe21f9b8410ff8ac231c4e38dfaf2ff81a25cccb68e3590817c07be6 | Text | 20,544 | 473 | <p align="left">
<img width=20% src="https://dai.lids.mit.edu/wp-content/uploads/2018/06/Logo_DAI_highres.png" alt="sdv-dev" />
<i>An open source project from Data to AI Lab at MIT.</i>
</p>
[](https://pypi.org/search/?c... |
991da02e04b77f5f6a3eed3c630f7c908793a82b84f743a9e32d0b7aad9e98df | Text | 20,814 | 386 | # LiquidAion Neural Observatory
[](https://github.com/Patternity/LiquidAion-Neural-Observatory/actions/workflows/ci.yml)
[](LICENSE)
[![Data: CC BY-NC 4.0]... |
c2cd3264ab50811a98e45414eefb897efd97f7159e1fe97b08f35e1dfaa6ff90 | Text | 20,986 | 349 | [pypi-image]: https://badge.fury.io/py/torcheeg.svg
[pypi-url]: https://pypi.python.org/pypi/torcheeg
[docs-image]: https://readthedocs.org/projects/torcheeg/badge/?version=latest
[docs-url]: https://torcheeg.readthedocs.io/en/latest/?badge=latest
[pepy-image]: https://static.pepy.tech/badge/torcheeg
[pepy-url]: https:... |
36e66ec3f329cb3859c9d1c71f029794c8ab24a571872f0a51d8c41a4d316010 | Text | 22,273 | 244 | # HyperKAN: Kolmogorov-Arnold Networks make Hyperspectral Image Classifiers Smarter
The objective of this research is to replace classical neural network layers with Kolmogorov-Arnold layers for the
classification of hyperspectral data.
A novel approach to enhancing the efficacy of hyperspectral classifiers is propos... |
7c0169ddfa7488ad5868eee01ff9175a1b464d3f67fbd95c398904b3f1f343fb | Text | 24,431 | 554 | # py-clesperanto
[](https://github.com/tbepler/topaz/actions/workflows/ci.yml)
[](https://topaz-em.readthedocs.io/en/latest/?badge=latest)
[![Anaconda-Server Badge... |
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