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9bbb6c7c835d612e979f24b3aebc8bdf44b61b48583954805d3c3650c6ed7d11 | Text | 2,304 | 47 | # CNV chromothripsis
This is the source code to replicate GECNVNet proposed in the paper: Chromothripsis Detection and Multiple Myeloma Prognosis Inference Based on Deep Graph Learning.
The dataset used in the paper is also accompanied.
The prerequisites are Python 3.9 with arm architecture support, PyTorch 1.9.0, an... |
e630415f4b6749bd10df6fd6998b26c98f923d5fc2bfec7f83c5bab5a4f1886f | Text | 2,322 | 14 | # r2s_iso_estimation
Source code and data used for the paper "Deciphering the fibre-orientation independent component of R2* (R2,iso*) in the human brain with a single multi-echo gradient-recalled-echo measurement under varying microstructural conditions" from Fritz et al 202X."
The two main codes are located in "Code/... |
183057939643931771bbc83b629f497288adbffa8d6e67e53cf9900a87012b87 | Text | 2,336 | 67 | This repository contains all the code to reproduce the analysis and figures
of the following paper and letter, which analyses and models the ORN-LN circuit in the
antennal lobe of the Drosophila larva:
## Normative and mechanistic model of an adaptive circuit for efficient encoding and feature extraction
### Nikolai ... |
ec112cc8d62cb88df6635fb5e5aea48b32083878be7a72dcaabdbac0fd7a3819 | Text | 2,352 | 62 | # DeepEvent Version 0.4
We propose a new application (_DeepEvent_) of long short term memory recurrent neural network to the automatic detection of gait events.
The 3D position and velocity of the markers on the heel, toe and lateral malleolus were used by the network to determine Foot Strike (FS) and Foot Off (FO).... |
316f55ca9d738f22eb214ee2bba12470f4f6435cb120d9af364bef770ed0f126 | Text | 2,384 | 48 | ## Overview
This repository contain the code needed to reproduce the results described in
the paper on MEG sensor array optimization by Zhdanov, Nurminen, Iivanainen
and Taulu expected to be published somewhen around 2023.
The code is written in Python and uses Anaconda for installation.
## Instructions for use
The... |
af7a5878807dff8ae3f91efa6af3a2042eac0ebdac3fe896ab97a93f2d0caead | Text | 2,395 | 41 | # interplayPFC
The experimental data for the findinds reported in the main figures of [Barbosa & Stein et al. (2020)](https://www.biorxiv.org/content/10.1101/763938v1) can be downloaded from [Data](https://github.com/comptelab/interplayPFC/tree/master/Data) (monkeys) from [an OSF repository](https://osf.io/qa34s/) (h... |
fefeb5d56a56ea1d2edb3e69a2f1f409d724b345cc4e93d0e4d775ad44f105c1 | Text | 2,424 | 68 | ===============================
pcrp
===============================
pcrp (plant circadian rhythm protein predictor) uses random walk with restart and subgraph automorphism to learn representations for vertices in a protein interaction network and return nodes having similar representations to the seed nodes.
Usage
-... |
99622444b27d81854a5f2ffc8d2473ef03150bd79d576382fa8f83b1ee1201d7 | Text | 2,442 | 42 | # Functionnectome
The `Functionnectome` is a python package which apply the eponym method and combines the functional signal from distant voxels of the classical
fMRI 4D volume using their probabilistic structural relationship given by anatomical priors of the involved brain circuits.
# Documentation
The complete manu... |
1d1be0b9805bdd704defb5c398a2f5a2499b7d12f8114c3a6920c76e15ec037b | Text | 2,492 | 67 | # scProjection
Projecting RNA measurements onto single cell atlases to achieve single cell resolution. Refer to our paper:
## Tutorials
First follow the install instructions below, at the bottom of the page, before following the tutorials.
[Tutorial 1: Deconvolution of CellBench mixtures](https://github.com/quon-ti... |
ecc21e985290f314b5ae1ca087c565b47ac8e2673777d2896bafe0b346d66b7d | Text | 2,509 | 48 | # Servalcat
[](https://github.com/keitaroyam/servalcat/actions/workflows/ci.yml)
[](https://pypi.org/project/servalcat/)
**S**tructur**e** **r**efinement and **val**idation for **c**rystal... |
69163868b0a98a4b11990128bf3829604a8d37b68d3e0a7568d866b8d93eb4be | Text | 2,516 | 36 | MSSEG-2 individual pipelines results
This zenodo repository contains every metric results for all patients of the testing set and all pipelines evaluated during the MSSEG-2 challenge. Each excel file contains the results for a given pipeline evaluated (see https://portal.fli-iam.irisa.fr/msseg-2/challenge-day/ for a l... |
dfae687192b3d37ac5fbad90f8f1d55f757d551cd00da1974876f04e2915fdc3 | Text | 2,558 | 34 | # 
<!--
[](https://travis-ci.org/nf-core/rnaseq)
-->
[](https://www.nextflow.io/)
<!--
[](https://zenodo.org/badge/latestdoi/363403124)
# ImageSumming
Workflow addon for [DeepSTORM2D](https://github.com/HenriquesLab/ZeroCostDL4Mic) to train with experimental data. </br>
This includes summation of random patches of low density emitter movies and respective lo... |
b431b72db7b609a458f15c15ba2eb0a005c8d88f712aa0ec8b8a5aa756d00207 | Text | 2,582 | 64 | # AlphaCrystal
AlphaCrytal: Contact map based deep learning algorithm for crystal structure prediction
Developed at:
University of South Carolina, 2021
Hu, Jianjun, Yong Zhao, Qin Li, Yuqi Song, Rongzhi Dong, Wenhui Yang, and Edirisuriya MD Siriwardane. "Deep Learning-Based Prediction of Contact Maps and Crystal Str... |
cb66943da3abc0172307a697150e9e5ae8681f2cf4ee8787f40fe9924d152597 | Text | 2,582 | 67 | # scProjection
Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection. Refer to our paper:https://www.nature.com/articles/s41467-023-40744-6
## Tutorials
First follow the install instructions below, at the bottom of the page, before following the tut... |
ee3abde62bc854694f06876bec84a345f81fb4f61f519c440bc806b7e326d858 | Text | 2,595 | 15 | # spinDrop
### De Jonghe, Kaminski _et al._ spinDrop: a modular droplet microfluidic platform to maximise single-cell sequencing information content, Nature Communications (2023).
Droplet microfluidic methods have massively increased the throughput of single-cell RNA sequencing campaigns. The benefit of scale-up is, h... |
03c45e96a32ab400b7b441eb19293aaeee0d4fd5ffb6002e84f1a25c1f274a4b | Text | 2,629 | 39 | # F-value time-frequency (FTF) analysis
<div align="center">
<a href="README.md"><strong>English</strong></a> |
<a href="README.de.md">Deutsch</a> |
<a href="README.es.md">Español</a> |
<a href="README.fr.md">français</a> |
<a href="README.ja.md">日本語... |
fe1a9480edf369881290fd0ca48e120707d4e85c46f1df87eac9e7e5a0e8eec2 | Text | 2,665 | 60 | # KISN-PyLab (v3.0.0)
### Data processing pipeline for e-phys and 3D tracking experiments
---------------------------------------------------------------------------------
This repository should facilitate the data processing pipeline for e-phys, IMU and 3D tracking experiments.
... |
3ab68069cce72408314ebae73059e9f430c452be408025fdea3add362afb957a | Text | 2,712 | 46 | # Scientific_Data_2023
<div align="center">
<a href="README.md"><strong>English</strong></a> |
<a href="README.de.md">Deutsch</a> |
<a href="README.es.md">Español</a> |
<a href="README.fr.md">français</a> |
<a href="README.ja.md">日本語</a> |
<a href="README.k... |
a6e178a26fd91f3ddd541cd9133e212ab3c1e1675a7094be9fe2a788daa7572c | Text | 2,722 | 93 | # SZ_PINT
scripts used for analysis of PINT in SZ samples
## now using docker for a reproducible env
It docker is installed. Start the rstudio env. Set your current directory to base of this repo
```sh
docker-compose up rstudio
```
My change here.
## The SSD PINT paper repo
This is a repo of code (and some data l... |
0e5120a1b4dfba1d78329407904271f65bfe9728dd9e73969ed3a6de34c82678 | Text | 2,793 | 42 | # Organic redox potentials from quantum chemsitry/ML with GPs
A mixed quantum chemistry/machine learning approach for the fast and accurate prediction of biochemical redox potentials and its large-scale application to 315,000 redox reactions
Preprint link: <https://doi.org/10.1101/2453... |
8d576a04bc33a3c3d2bddc97adfae228c82acb7889e7ce7ba73b1d6b496947f5 | Text | 2,803 | 48 | # Targeting AAV vectors to the CNS via de novo engineered capsid-receptor interactions
Now published in PLOS Biology! [https://doi.org/10.1371/journal.pbio.3002112](https://doi.org/10.1371/journal.pbio.3002112)
Code and documentation supporting "Targeting AAV vectors to the CNS via de novo engineered capsid-receptor ... |
f022b673239b193647933553d1dcca346ae1b44ae97303eb9c93b0b17a8ae8b7 | Text | 2,826 | 62 | Neuronal Dynamics: Python Exercises
===================================
This repository contains python exercises accompanying the book
`Neuronal Dynamics <http://neuronaldynamics.epfl.ch/>`_ by Wulfram Gerstner, Werner M. Kistler, Richard Naud and Liam Paninski. References to relevant chapters will be added in the `T... |
7fc94469c4aa1afa0782c5bce0e468dbe0e86e462e2003d54ae509c794a3830a | Text | 2,834 | 66 | [](https://github.com/G-Node/nix/actions)
[](https://ci.appveyor.com/project/G-Node/nix/branch/master)
[, as well as creating neurally-informed models of the behavioural data (dataModelling.m).
Code is depending on:
1) [EEGLAB](https://eeglab.org/others/How_to_download_EEGLAB.html) (including... |
0d106071beacdbcba41bc00b14cf63ba503616bb19bfa5c174f6d649ee60d84b | Text | 2,888 | 94 | # Flickr Feature Extraction
A robust toolkit designed for extracting, processing, and scoring features from Flickr photos using its API. This project integrates advanced image processing models to evaluate aesthetic qualities through AI, providing a customizable solution for researchers and developers.
## Getting Sta... |
3a3050c9cd1897acc87cbe5217423d4381ced93eff2b10659d1776e3288d9451 | Text | 2,904 | 44 | # Classification of Alzheimer's Disease stages from Magnetic Resonance Images using Deep Learning
[](https://zenodo.org/badge/latestdoi/587370693)
## Authors
Alejandro Mora-Rubio<sup>1</sup>, Mario Alejandro Bravo-Ortiz<sup>1</sup>, Sebastián Quiñones-Arredondo<sup>1</su... |
13763f1e31e0b31439c6efb620760c442e40a0947bfa123d8f052f094767d0e1 | Text | 2,930 | 78 | # Focused-view CTA for selective visualization of stroke related arteries
This repository contains the experimental code and analysis scripts used for the study "Focused view CT angiography for selective visualization of stroke rela... |
2f58029c2e870d41cb352844a5bbec927ac9ef0f6f48a9411162284368c1c9e0 | Text | 2,935 | 54 | [](https://pypi.org/project/otscomics/)
[](https://ot-scomics.readthedocs.io/en/latest/?badge=latest)
[](https:... |
3d90217361da04cd1a9d942588339db98760968cb54d6b8f05850b9c3166e6f7 | Text | 2,960 | 45 | # ArtBench
### [Preprint](https://arxiv.org/abs/2206.11404) | [Kaggle](https://www.kaggle.com/datasets/alexanderliao/artbench10) | [Papers With Code](https://paperswithcode.com/dataset/artbench-10)
**The ArtBench Dataset: Benchmarking Generative Models with Artworks**<br/>
[Peiyu... |
5a318b7416d131317b0cd51f29db5827081c3ff4e0a25ee14cb879d436790dd1 | Text | 2,969 | 97 | # CellBench
[](https://travis-ci.org/Shians/CellBench)
[](https://codecov.io/github/Shians/CellBench?branch=master)
<img src="https://github.com/Shian... |
1713679f3c14ff4c8f005252c30e8bef37707deadae41665ed4045bad5360b0d | Text | 2,991 | 89 | # Generation of training pairs for network
To achieve the simulation-supervision training and increase the generalization of the neural network, we proposed a forward propagation model to simulate physically the imaging process of the miniaturized microscope.
The corresponding implementation is written in MATLAB.
# ... |
65939b029b8e547cd4af67977cb08201ed7afd6bb2b658f46575da1a00f3e24c | Text | 3,000 | 43 | # S3-CIMA
Supervised Spatial Single-Cell Image Analysis for identification of disease associated cell type composition in the tissue microenvironment
S3-CIMA implements a weakly supervised CNN model to identify cell subsets whose frequency distinguishes the considered phenotype labels (i.e., disease associated conditio... |
5e9b9ef91b6ddea5c84972cb86b5640a87534066c7b39b974f2d071be1b21fad | Text | 3,033 | 47 | # EELS ID
Electron energy loss spectroscopy identification (EELS ID) is a deep learning tool for automated element identification in core-loss EELS spectra. A series of neural networks are trained on simulated data to identify the following elements based on their respective edges. This repo shares some minimal example... |
c22c932f583ab0d8db05a5edfdff2c33f27d07b04356cbbf31956915aa2eccaa | Text | 3,098 | 86 | # iclamp-glm
iclamp-glm is a Python module for the analysis of electrophysiological patch clamp data by using encoding and decoding neural models. It is built on top of SciPy.
## Example
### Loading and preprocessing patch clamp data
```python
import matplotlib.pyplot as plt
import numpy as np
from icglm.iclamp import... |
4a682acf3ba941a7543f618e22ef6b52e9d9ad76eb751c4239b11dfbf73b9456 | Text | 3,113 | 57 | # Tensorflow Implementation of Neural network models for influenza forecasting with associated uncertainty using Web search activity trends
<!-- ================================================================================================================================ -->
This repository provides minimal code to ... |
f53525baa0dc1f7bc2ea2a623d571ef95b3464c6a60fa97775b4e81aee04d53e | Text | 3,120 | 22 | <picture>
<source media="(prefers-color-scheme: dark)" srcset="src/frontend/cellprofiler/data/images/splash-white-text-alpha.png">
<img alt="CellProfiler" src="src/frontend/cellprofiler/data/images/splash-black-text-alpha.png">
</picture>
[](https... |
b2d02f2c1be67c168b3061ed35d0c96db665cb0c986a1f62d3fcfaf73d92ce05 | Text | 3,167 | 57 | # Allen Institute Patch-seq documents and tools
Patch-seq is powerful technique that allows for multimodal characterization of individual neurons – electrophysiological, morphological and transcriptomic. At the Allen Institute we have optimized this technique to efficiently collect high-quality data. On this GitHub rep... |
54d94158255ac30eeca4956aef50521a8bfeef7a5b471b438d06d5fb271461f7 | Text | 3,168 | 55 | [](./static/images/banner.png)
[](https://twitter.com/afids_project)
[. We employ the superstatistics perspective to augment mechanistic cogni... |
6f1cdfb9dd9335050313a6a4988ab3c77da007341c87b63a20adcf7a2dae496c | Text | 3,256 | 80 | MolVS: Molecule Validation and Standardization
==============================================
.. image:: https://img.shields.io/pypi/v/MolVS.svg?style=flat-square
:alt: PyPI package
:target: https://pypi.python.org/pypi/MolVS
.. image:: https://img.shields.io/conda/vn/conda-forge/molvs.svg?style=flat-square
... |
858ef8d030806912c76589524d3c82fe0f975d9d6a22d431145ea1e191901ba6 | Text | 3,280 | 47 | # Emphysema Subtyping on Chest CT using Deep Neural Networks
## News
- The source code (v1.0) is now available.
### Table Of Contents
- [Introduction](#introduction)
- [Usage](#usage)
- [Main Results](#main-results)
## Introduction
 package, and mostly just
provides a database and API for storing, querying, and analyzing multi... |
f0114015c5d81892dedff997bc904045583c2d72e2778cef5384ae48dfa2a78a | Text | 3,412 | 56 | # Neural ODE for Noisy and Irregular Time Series Data
This repository contains the Python implementation using the PyTorch framework to learn nonlinear dynamical systems using neural networks from irregular and noisy data. For this, we focus on learning an approximate implicit representation of data such that a neural... |
e09c61b514ce2e878ebc7b8e0060675a8b821f95055be4fadda1a5f60356aace | Text | 3,469 | 70 | # CeLEry
## Leveraging spatial transcriptomics data to recover cell locationsin single-cell RNA-seq with CeLEry
### Qihuang Zhang, Shunzhou Jiang, Amelia Schroeder, Jian Hu, Kejie Li, Baohong Zhang, David Dai, Edward B. Lee, Rui Xiao, Mingyao Li*
Single-cell RNA sequencing (scRNA-seq) has transformed our under... |
63a7d7e7da105424989874ef4c7303a0b066ccac676cc9c72ed9294dcfb0accd | Text | 3,510 | 90 | # Banapple
[](https://github.com/innoisys/Banapple)
[](README.md)
[](https://opensource.org/license... |
e1e6e36fed11fdf3a6dced5bd31744f464217aa8bb59d567f41a7fe520248dd4 | Text | 3,523 | 122 | # ClinicalASL Tool - Release v1
**Repository:** [https://github.com/JSIERO/ClinicalASL](https://github.com/JSIERO/ClinicalASL)
**Author:** Jeroen Siero, UMC Utrecht
**Contact:** j.c.w.siero@umcutrecht.nl
**Release Date:** 2025-06-24
**Version:** v1.0.3
## Description
Official ClinicalASL processing pipelin... |
536387c55db3a4f59ec582f80c3d254d1e86d4ae81a4eee0885ff6a40a45dcc3 | Text | 3,545 | 56 | [](https://zenodo.org/badge/latestdoi/570550727)
# Sparse-Recurrent DFC
This codebase contains the implementation of sparse-recurrent DFC, as well as support for continual learning on split-MNIST in both the domain-IL and class-IL learning paradigms. Moreover, this reposi... |
3c102df9174d2262884750714e7922a9d01d91fc385d081fa47ab7b7261899d0 | Text | 3,611 | 77 | # VariabilityEarlyVisualCortex
This repository contains all source code necessary to replicate our recent work entitled "Variability of visual field maps in human early extrastriate cortex challenges the canonical model of organization of V2 and V3" available on [bioRxiv](https://www.biorxiv.org/content/10.1101/2022.1... |
ff496f3db274933f37647d2ae91cbef023b9e047497096e66b0be9f4ba2ae2ab | Text | 3,670 | 55 | # Article repository
"Deep learning-based automatic action extraction from structured chemical synthesis procedures".
Available online: doi: 10.7717/peerj-cs.1511
Required: python 3.8; tensorflow 2.4.1; RDkit 2021.03; The code is in Jupyter Notebook/Jupyter lab format for more convenient prototyping, Anaconda enviro... |
004eaa77a4596a6fc1b26f58dbc0e0f902b6fb7d0e44fb634ec5c70b0df4834c | Text | 3,728 | 53 | # Code for Rowland, van der Plas, Loidolt et al.
Code for analysis of all-optical neural data obtained in Packer lab, Oxford. Figures were generated in whole by code, using notebooks in `popping-off/notebooks/Paper Figures/`. This is the code of the following paper:
Rowland*, J.M., van der Plas*, T.L., Loidolt*, M. e... |
2bf774d892834c2538f82964732df855d80bbd830c6f14645e74be832b091090 | Text | 3,759 | 86 | ## Fast Saliency
This repository contains the code for our two fast saliency detection papers: "**[SAMNet: Stereoscopically Attentive Multi-scale Network for Lightweight Salient Object Detection](https://ieeexplore.ieee.org/document/9381668)**" (IEEE TIP) and "**[Lightweight Salient Object Detection via Hierarchical V... |
774ccc93643f061ddf52ef4b729472791c581629be7d4fe7ef47b0abe57d91e3 | Text | 3,788 | 75 | README
The data files are all in csv format, organized in columns for each variable and rows for each instance.
The column names denote the variables, explained below.
---BINOCULAR RIVALRY DATA---
The experiment consisted of reporting the perceived orientation of a Gabor patch. Participants observed two
di... |
b1b49d753a201b12e0564be3f2bca409665edb1348cffd5da6c81ed9610a496e | Text | 3,875 | 90 | # mCREATE
Example code for generating analyses and plots for the multiplexed CREATE paper
by Kumar et al. (2019). The code is divided into three parts: alignment,
variant analysis, and clustering. The scripts given in the Juypter notebooks
are "demo" versions with example data or input files in the relative
"example_d... |
d041823a9438e450483ecdb338f0b2311b1d6b4c1678297a7a4932c09a8ef734 | Text | 3,973 | 66 | ## [High Quality Monocular Depth Estimation via Transfer Learning (arXiv 2018)](https://arxiv.org/abs/1812.11941)
[Ibraheem Alhashim](https://ialhashim.github.io/) and Peter Wonka
**[Update] Our latest method with better performance can be found here [AdaBins](https://github.com/shariqfarooq123/AdaBins).**
Offical Ke... |
ecd21ee59724a66d1ddefaee14cab36325b323d74c277e886a0aedc6c9b92d03 | Text | 4,033 | 39 | [](https://doi.org/10.5281/zenodo.5283595)
[](https:/... |
ea3adaf8ebf794c5fecb7efaf89ac5dfd5e3fecbf8bfca2f43b2f335bc257e40 | Text | 4,077 | 44 | # BMC_AdaptdcosFigures
This is the GitHub repository for the following manuscript in preparation:
Does V1 response suppression initiate binocular rivalry?
Brock M. Carlson, Blake A. Mitchell1, Kacie Dougherty, Jacob A. Westerberg, Michele A. Cox, & Alexander Maier
- Corresponding author: alex.maier@vanderbilt.edu
... |
aad80ae413aecbba404168bfbc0aaf098d66c5a50a64465919bd9f1bf799db31 | Text | 4,142 | 46 | # PINN4RDE
This is the code repository for "Rotating Disk Electrodes Beyond Levich Approximation: Physics-Informed Neural Networks Reveal and Quantify Edge Effects" submitted to *Analytical Chemistry* and "Removing 65 Years of Approximation in Rotating Ring Disk Electrode Theory with Physics-Informed Neural Networks" ... |
dc1ea63de8b585f89e40194a797227d0f2aa41bab92a5ab1893addf3671e0896 | Text | 4,382 | 56 | [](https://pypi.org/project/s2cloudless)
[](https://anaconda.org/conda-forge/s2cloudless)
[](https://github.com/rveltz/SynapseElife/actions/workflows/ci.yml) [ published in Nature Scientific Reports 2023.
Examples taken from the paper.
![instance segmented c. elegans](readm... |
9eb53471bdf3bd2a5f715d46707e5658184b29f9966cd10812b526f53112622f | Text | 4,651 | 130 | # Cellformer
An implementation of Cellformer from our publication: Berson et al. *"Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature"*
## Installation from source
The lastest source version of Cellformer can be accessed by running the following command:
```
git clone https://github.com/elo... |
75490bafa423e33822330e226fc822cb2251864e995e0029894504a89adc4d46 | Text | 4,770 | 134 | [![Contributors][contributors-shield]][contributors-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issues-shield]][issues-url]
[![MIT License][license-shield]][license-url]
<!-- PROJECT LOGO -->
<br />
<p align="center">
<a href="https://github.com/FunctionalGeneticsLab/... |
af59c31948393ddfb4e9dce5168b3937cd1adc476ff851e7add2dde47a5de9cb | Text | 4,785 | 152 | # perlin-numpy
I wrote two articles on my blog about this project, the [first one](https://pvigier.github.io/2018/06/13/perlin-noise-numpy.html) is about the generation of 2D noise while the [second one](https://pvigier.github.io/2018/11/02/3d-perlin-noise-numpy.html) is about the generation of 3D noise, feel free to... |
71c4f0598b893d7cef76b296305a88e8d22cbe04ea43316716e34c8d08912510 | Text | 4,800 | 73 | [](https://zenodo.org/badge/latestdoi/390024608)
# Code related to the RIFF
The RIFF is an interactive arena for freely moving rats.
This repository contains code related to the publication
*Jankowski M. M., Polterovich A., Kazakov A., Niediek J., Nelken I.: An automa... |
173491d496eaef7f6ff0f3817dcd09ed680a5a11ce9e07fb3f81823f17db8f1e | Text | 4,866 | 136 | [![Contributors][contributors-shield]][contributors-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issues-shield]][issues-url]
[![MIT License][license-shield]][license-url]
[](https://zenodo.org/badge/latestdoi/623305557)
<!--... |
125e56df0d1dcd709185a593edd0aa2e2af0e885b328d3d9a2229f9c953394f6 | Text | 4,881 | 134 | # Getting started with pyOS5
## Requirements
python- 3.6
numpy
pandas
PyQt5
pyqtgraph
pyserial
Download the code zip or git clone from the link https://github.com/KaetzelLab/Operant-Box-Code. After Downloading Code, move required task files from task sub-folder (contains specific task files) to main task folder.... |
0e65d3ba5570b0fa240e463dab13f6e822a21ce8c1f7ca4b2f14f0ca1340ca65 | Text | 4,907 | 101 |
<font size="10"> <img src="FinchScope/img/im1.png" width="50"/>FreedomScope Project</font>
=======
============
## Overview
FreedomScope is an umbrella project for several customizable and scaleable single-photon fluorescent imaging microscope systems that take advantage of developing open-source landscape to p... |
e0a9e4da82f89f83d145839a75a88afbec2b7a0407c60fad0f1ccef42f7f2d55 | Text | 4,956 | 75 | # Pressure mat data
pressure_mat_data.zip
## Description of the data:
This data set consists of 1776 files containing pressure map data (5s long, sampling rate 100 Hz) obtained from 45 infants. File names contain infant ID number, e.g., idxp115 corresponds to ID 115, age of the infant in days at the recording,... |
10e51bcb14d97b5340690ed4883ffbc193b33f8d79898306461b635b0b193d09 | Text | 5,036 | 99 | # imskaper
This project consists of two separate tools, one for radiomics feature
extractions, and the second tool is for running experiments with different
feature selection algorithms with various classifiers.
1. [ Getting Started ](#getting-started)
1.1. [ Prerequisites ](#prerequisites)
1.2. [ Instal... |
8718faf2fd442d0a105634a87b01f6421578cf713ee8e105bf1738a2188d24a3 | Text | 5,053 | 105 | # HistoBistro
Pipeline for weakly-supervised learning on histology images. The pipeline contains various models for multiple instance learning with different aggregation models. Based on Pytorch Lightning. All aggregation modules can be loaded as model files in the classifier lightning module. Loss, models, optimizers... |
073e23b3fd77713d31e0efcd112c82dcb56d0b54e64f5451aa36da67519a3848 | Text | 5,060 | 132 | [![Contributors][contributors-shield]][contributors-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issues-shield]][issues-url]
[![MIT License][license-shield]][license-url]
<!-- PROJECT LOGO -->
<br />
<p align="center">
<a href="https://github.com/FunctionalGeneticsLab/... |
f1d122c6da9e4fbb6fe628feb7b62e6f7b70edfa7760ceceb22175aa1da3ae7f | Text | 5,109 | 72 | # A large-scale fMRI dataset for human visual processing of naturalistic scenes
Natural Object Dataset (NOD), a large-scale fMRI dataset containing responses to 57,120 naturalistic images from 30 participants. NOD strives for a balance between sampling variation between individuals and sampling variation between stimul... |
833b980c87d660e81cb8684bc5241c29bcd85ebed835aba09ee81808f0360121 | Text | 5,119 | 131 | # uwot
<!-- badges: start -->
[](https://github.com/jlmelville/uwot/actions)
[](https://app.codecov.io/github/jlmelville/uwot?branch=master)
[](https://pypi.org/project/rvt-py/)
[](https://anaconda.org/channels/rvtpy/packages/rvt_py/overview)
[](https://zenodo.org/badge/latestdoi/517749799)
<!-- ... |
7df7494b3d99b0f732f8fa56a8af280eeda9a2598044f4dcbcd58b2b1e57408a | Text | 5,182 | 101 | # Graph-based Fully Convolutional Network (GFCN)
## Main script "training.py"
Run from project directory
```
python traininig.py # runs default MNIST
```
## Datsets
A model is generated in the path ./ with the name {netwo... |
be75630f9fdbc72d85daca3b9e3a163243ab12d1593b4509b7bf2e0907937eaf | Text | 5,274 | 168 | # kneed
Knee-point detection in Python
[](https://pypi.org/project/kneed/)
[](https://pepy.tech/project/kneed)
[](https://pepy.tech/project/kneed)
 and 18000+ instances. Feel free to download and obtain the dataset, and please cite our paper if you use the dataset in your work.**
Source code for ACL ... |
3b85714b9b1667ff63e488bd3f918347690a449c4e414820956a7eb8e874501e | Text | 5,289 | 177 | # Datamonger <img src="https://raw.githubusercontent.com/jolars/datamonger/refs/heads/main/assets/logo.png" align="right" width="139" alt="A datamonger carrying a box of data" />
[](https://github.com/jolars/datamonger/actions/workflows/ci.y... |
64677018e762eec8265cef482696176aaab4b4fefb17c688fd3d193c66b1dd8d | Text | 5,426 | 29 | # Context dependent target detection within a continuous task
> Geuzebroek AC, Craddock H, O’Connell RG, & Kelly SP (2022). Balancing true and false detection of intermittent sensory targets by adjusting the inputs to the evidence accumulation process. doi: https://biorxiv.org/cgi/content/short/2022.09.01.505650v1
... |
67dce040aec3847e8be4407227f3240da2990693bb3430c47650437f91e352ac | Text | 5,467 | 112 | # HistoBistro
Pipeline for weakly-supervised learning on histology images. The pipeline contains various models for multiple instance learning with different aggregation models. Based on Pytorch Lightning. All aggregation modules can be loaded as model files in the classifier lightning module. Loss, models, optimizers... |
e3f6ebd359dab04eae8e3cfb513c96dd8c7d63b10451dbc6b3c22af391a83da0 | Text | 5,469 | 71 | # SingleR is now on Bioconductor
**Update: September 2019**
A new and improved version of SingleR is on Bioconductor - https://bioconductor.org/packages/release/bioc/html/SingleR.html. The version of SingleR in this repository will not be maintained further.
# Legacy version of SingleR
# SingleR - Single-cell Reco... |
631ac4049bfedce5756cedacb585a2c1a667b300002e6bc8847df180ff742184 | Text | 5,612 | 136 | [](https://github.com/AlexVCaron/mrHARDI/actions/workflows/build-release.yml)
[](https://github.com/AlexVCaron/mrHARDI/actions... |
53e440ab85fbcd2fa3c40c98cddd65be6c3725b744cdd2c3101794667e333412 | Text | 5,643 | 83 | MIRO
=====
MIRO (Multiscale Image Restoration through Optimally-sparse representation) is a software for microlocal noise correction designed for fluorescence microscopy. Thanks to the optimal sparsity of the shearlet domain and a physics-based noise estimation, MIRO improves the quality of microscopy images acquired ... |
97d38260d8e96739b693451ae594d9e2a7b793b39974ccdbc5651cadfdaf371f | Text | 5,684 | 66 | # AFIDs
An open framework for evaluating correspondence in brain images and teaching neuroanatomy using anatomical fiducial placement
[](./docs/img/afids_cover_for_github.png)
**Documentation:** https://afids.github.io/afids-protocol/
**Join our channel:** <a href="ht... |
bda647a1a52629a24cefec6aa4f02f49dfe03f877b85127884f296b2f1fb34d1 | Text | 5,695 | 53 | AIMS V1.0 is an artificial intelligence assisted diagnosis modeling software platform. It is jointly developed by the Medical Image Processing Group in the Suzhou Institute of Biomedical Engineering and Technology and Suzhou Guoke Kangcheng Medical Technology Co., Ltd.. The main advantages of AIMS V1.0 are as follows: ... |
465f7163ecf85df39374fd867e660088ec97f13920f41d88b066f8a6c5bed9c1 | Text | 5,767 | 95 | # IntellEvent
## Introduction
*IntellEvent* is a robust deep learning-based framework for gait event detection across various pathologies for 3D motion capture data. By leveraging deep learning models, *IntellEvent* accurately detects gait events (initial contact (IC) and foot off (FO)) in patients with different clin... |
b0fe52d86bc76a59e8644d09c64dc65354b4463fa5bea4ffa0ff9abd96673cde | Text | 5,783 | 107 | +-------------------------------------------------------------------------+
| Geometric transformation of cognitive maps for generalization |
| across hippocampal-prefrontal circuits |
+-------------------------------------------------------------------------+
README.txt
Copyr... |
b7cafad679af623882e9935cc69192a720d3cf081ddd556faa64d1d79aeb10c1 | Text | 5,807 | 35 | # Tensor-Decomposition-for-Analysis-of-fNIRS-Signals
Abstract: The analysis of functional near-infrared spectroscopy (fNIRS) signals has not kept pace with the increased use of fNIRS in the behavioral and brain sciences. The popular grand averaging method collapses the oxygenated hemoglobin data within a predefined tim... |
df96d25b526c69aa2e33606cfc0386b21ffc02e4032592a26ccc5f72575be7db | Text | 5,866 | 110 | # nematic-learning
<p align="center">
<img src="logo.png" width=50%>
</p>
---
This repository contains all the scripts used to generate and analyze the data in the paper "[Machine learning the microscopic form of nematic order in twisted double-bilayer graphene. Nat. Commun., 14(5012), 1–9. doi: 10.1038/s41467-023-40... |
34f5242e9e81148ab4f4165ff598f1bd9490ec9ceebe3e8855117a255bdb7496 | Text | 5,914 | 78 | =========
Normalisr
=========
.. image:: https://img.shields.io/pypi/v/normalisr?color=informational
:target: https://pypi.python.org/pypi/normalisr
.. image:: https://zenodo.org/badge/242889849.svg
:target: https://zenodo.org/badge/latestdoi/242889849
Normalisr is a parameter-free normalization and statistica... |
5adde926a4176699d811820ff84ba80fe892e023bbeba9bd4f7a31845ecb9ee7 | Text | 5,986 | 191 | # Flight trajectory prediction enabled by time-frequency wavelet transform
# Introduction
This repository provides source codes of the proposed flight trajectory prediction framework, called WTFTP,
and example samples for the paper "Flight trajectory prediction enabled by time-frequency wavelet transform".
This is ... |
571bdb305db46a7f76e52a296735f9101afe14efd1306d167f0af9b52a285c0c | Text | 6,030 | 142 | # LIONESS
---
Copyright ©2023. Institute of Science and Technology Austria (IST Austria).
This file is part of the code developed for the paper "Dense 4D nanoscale reconstruction of living brain tissue". This code is free software: you can redistribute it and/or modify it under the terms of the MIT License.
This pr... |
c5867d7470731de0272eeee8025b8a02acdc691e724c0784b87b4bfe828e1b4a | Text | 6,055 | 74 | # PsychDetect
## Introduction
PsychDetect is a software framework for conducting **acoustic psychophysical experiments**.
It is less a single ready-to-use program to immediately run experiments, but rather it provides components to build and set up a program to your own needs. (But see also the motivation section fo... |
2e038c6aab96bd242dc672783bb5f0b701aa759a5db1d53836370164b3b7028e | Text | 6,077 | 109 | # SapBERT: Self-alignment pretraining for BERT
**\[news | 22 Aug 2021\]** SapBERT is integrated into NVIDIA's deep learning toolkit NeMo as its [entity linking module](https://docs.nvidia.com/deeplearning/nemo/user-guide/docs/en/main/nlp/entity_linking.html) (thank you NVIDIA!). You can play with it in this [google co... |
e987d8a649b240174cdbb07adaf6df4e6bf17f115a9b0ee0526e78fa2bbee103 | Text | 6,117 | 125 | # Brain tumor plasma metabolomics (Godlewski et al., 2023)
This is a lossless CSV representation of Supplementary Table S2 from
[Godlewski et al. (2023)](https://doi.org/10.1038/s41598-023-38243-1).
It contains measurements of 138 plasma metabolites in 235 samples from
patients with gliomas, patients with meningioma, ... |
f1c61785908c3ffa8b6a6a02261136132c3a1d58a5d1864368657a30a63547ab | Text | 6,184 | 128 | <img src="logo.png" width:100px >
## SigmaCCS
This is the code base for the paper *Ion Mobility Collision Cross Section Prediction Using **S**tructure **I**ncluded **G**raph **M**erged with **A**dduct.* We developed a model named SigmaCCS which can be used to predict CCS of compounds,and a [dataset](https://zeno... |
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