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794043cb07e3b67d9d0e4a8dae5f8a5204b6292c8c1eab4f5f303278275eb4c4 | Text | 1,222 | 38 | # cfdr.pleio
The `cfdr.pleio` package implements conditional and conjunctional false discovery rates to leverage and study pleiotropic gene variants between pairs of phenotypic traits, as originally described by [Andreassen et al. (2013)](https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23375658/).
## Installation
You... |
f785029f3eb03ec30e310e27ce5dd5e3aa87dfe5e0fce6bd27f36d4312a7d35b | Text | 1,236 | 35 | # Export units to NWB
## NWB_Packaging_Units
### Description
This capsule is designed to append units information to an existing NWB file.
### Inputs
The `data/` folder must include an input NWB file and the output of the
[aind-ephys-result-collector](https://github.com/AllenNeuralDynamics/aind-ephys-results-col... |
d8e23665435b4cdec2dc08054e9859d335b557f2b19fea23587a206e9d3dbdd0 | Text | 1,243 | 20 | The code for this "Low Activity Syntax" project is broken down into the following subdirectories:
- "functions": some custom functions used throughout the scripts;
- "preprocessing": scripts for a preprocessing a sample subject (these were largely the same across subjects, except for hard-coded trial and electrode e... |
3dbf2e81c1721b2cd2c60514c43f3641587754b3b7ecee563b5ab00f60630392 | Text | 1,244 | 19 | # Bioacoustic Neural Network Training
**This program trains a convolutional neural network (CNN) for acoustic recordings.** It was developed specifically for amphibians within **Banff National Park**. The program is designed to conduct a grid search across all user-defined hyperparameter values, including acoustic sig... |
8832d29823f7b0829b3a0306dda9b89a374f267ac8504d684b113a119397fbe5 | Text | 1,249 | 10 | # Brainstem-neurons-coordinate-the-bladder-and-urethral-sphincter-for-urination
Data analysis of photometry, bladder pressure, and EUS-EMG recordings
This toolbox is an open-source MATLAB program for analyzing fiber photometry, bladder pressure, and EUS-EMG data. The toolbox is demonstrated in the paper "Brainstem neu... |
3e6a547fb689b02d0e791548fb45726d4cd4666bf2f661c694c9c2d01fbcb747 | Text | 1,372 | 48 | # Curation for AIND ephys pipeline
## aind-ephys-curation
### Description
This capsule is designed to curate spike sorted data for the AIND pipeline.
It uses a quality metrics based *recipe* to flag units as passing or failing default quality control (QC).
The recipe is based on the following quality metrics:
- i... |
0eeda77bedf3a3c49d51cce2a6010cfb3e42c969d85596c9742593749854fc97 | Text | 1,380 | 29 | # Evaluate spike sorting performance on hybrid study
## aind-ephys-hybrid-evaluation
Evaluate the performance of spike sorting options on hybrid data.
## Description
This capsule aggregates results from multiple spike sorting jobs and produces results dataframes and figures for further analysis.
## Inputs
The `dat... |
fdee79aff3dcf2fc5e7d89a5ca69c84819329ac85de5e060c6ddaa73009ebf9f | Text | 1,395 | 45 | # csf donuts
nina fultz - n.e.fultz@lumc.nl - dec 2025 - run in MATLAB2020b -
purpose: code for csf donuts manuscript
1) preprocessing
2) figures
# preprocessing of data
1. preprocessing of data can be done by running csfdonut_lydiane_preprocessing_scripts.m
# figures
Figures can be generated ... |
cf9f95e839f664cc253798020408ceaef282eec9ad9bfe027315fc1bf0828a0f | Text | 1,493 | 52 | # ndtest
Multi-dimensional statistical tests with python
- 2D Kolmogorov–Smirnov test (KS test)
- 1D and 2D energy distance statistics test
## Citation
The code has been cited in ~40 papers
according to [Google Scholar](https://scholar.google.com/scholar?q=%22syrte%2Fndtest%22) :star_struck:
If you used this *code*... |
6d13ac4e70974618e3253c3974671d7d0c57cb25d353747721be84e86a922587 | Text | 1,505 | 25 | # Amphibian Bioacoustics User Interface
This repository contains the majority of the files needed to run an **interactive user interface for the manual and automated classification of amphibian vocalizations**. The neural network model files are not included due to GitHub size restrictions. If you need access to these... |
e9e9bb8f4b4fbe426045db5566d1b465e85e73a5eabda5cdd57496884a46c10a | Text | 1,525 | 40 | # SOFI-MISRGRU Release Repository
Release repository accompanying our publication.
Tested on: Linux + NVIDIA GPU + CUDA 12.1
CPU may work but is not validated
## Install - (Adjust versions/CUDA to match what you used.)
```bash
python -m venv .venv_resurf
source .venv_resurf/bin/activate
pip install -U pip
pip instal... |
ab377fe70fe26ee62172a7d0454837cc9b4a5eacd174a48db450c07f172a3397 | Text | 1,535 | 62 | R studio docker container for scRNA-seq analyses build on bioconductor_docker:RELEASE_3_18 and R v4.3.2.
The Docker image is build in three layers:
1. Installation of R packages on top of the bioconductor image: docker build -f Dockerfile_R . -t jsschrepping/r_docker:jss_R432_bioc318
2. Installation of pip packages o... |
6eca9aaf79e8d4255cf5485dbe6418b879cc3c8011f4960fb1d0514d1db5727b | Text | 1,578 | 43 | # Gruskin-eLife2026
Analysis code for:
> Gruskin DC, Vieira DJ, Lee JK, Patel GH (2026).
> **Heritability of movie-evoked brain activity and connectivity.**
> *eLife* 14. https://doi.org/10.7554/eLife.106081
This repository contains the MATLAB, R, and Python code used to quantify the
heritability of movie-evoked bra... |
e76af96cedf3bee9acabcd107b7a113dcee47c649280194aa92206cc197b9970 | Text | 1,588 | 35 |
Step 1 Computation of visual emotion code
-------
### 1. Train the VAE model
* Use [imagen_main_cv.py](https://github.com/hanluyt/EmotionConcept_reg/blob/main/code_VAE/imagen_main_cv.py) to perform hyperparameter selection for the VAE model.
* Hyperparameters are determined using 5-fold cross-validation.
### 2. Co... |
1ab2a3fc87d9763be179af9d85aa570b6c6f40567173b4b44ab71210413bf08a | Text | 1,695 | 37 | # Brunoise
[](https://zenodo.org/badge/latestdoi/238418598)
<a href="url"><img
src="https://github.com/portugueslab/twop_python/blob/master/icons/GUI.PNG"
align="left"
height="190"
width="270"></a>
Brunoise is a software package for control of two-photon laser scanning... |
2dcab19953a73cf679a6f35fd5a8cab90a729372619dda2d7a0ae62dc8ef4db3 | Text | 1,861 | 37 | # Quality Control for AIND ephys pipeline
## aind-ephys-processing-qc
### Description
This capsule is designed to compute Metrics following the `QualityControl` schema
form `aind-data-schema`.
The following metrics are computed:
- **Raw data**: snippets of AP and LFP traces at multiple points over the session
- **... |
7c1bd88d4a31de9f95172b89fd80db6750da5ec96df00ff6b1c2dd6e7741b675 | Text | 1,972 | 70 | # NeuroSuite for Long-term Functional and Structural Studies of Air-Liquid Interface Cerebral Organoids
### Supplementary Files
#### Overview
This Zenodo repository contains the files associated with the manuscript: NeuroSuite for Long-term Functional and Structural Studies of Air-Liquid Interf... |
e0eb9eb868d6a16390b7c4a0d24b2da49de7d0161b225ec68d693cc64474dbe7 | Text | 2,056 | 42 | # Collect results for AIND ephys pipeline
## aind-ephys-results-collector
### Description
This simple capsule is designed to collect the results for the AIND ecephys pipeline.
### Inputs
The `data/` folder can include several outputs from upstream capsules, including:
- outputs of the [aind-ephys-preprocessing]... |
7c4a236a8d4f50e8d9be1821f68fb9c4205d5f096206316c74d80acb2f0cd35e | Text | 2,260 | 101 | 
📄 [Click here to view full PDF](gitpage.pdf)
# Relationship Learning: Code Repository
This repository contains all Jupyter notebooks used to generate the figures and results reported in the manuscript.
---
## 1. System Requirements
- **Operating System**: Linux, macOS, or W... |
7451096c5a8959b9399705b03022619f4dfd12e6b919743a653becb96a875381 | Text | 2,327 | 44 | # aind-data-schema-models
[](LICENSE)
[](https://github.com/semantic-rele... |
aca1a255eaffc3e0d6f6216873867151d8abf500ddf998b10350f4ec31a2568f | Text | 2,358 | 57 | SUITPy: Analysis and visualization of cerebellar imaging data.
==============================================================
The package provides some basic functionality of the original SUIT toolbox for Matlab (https://github.com/jdiedrichsen/suit).
Currently, only mapping of volume data to the flatmap and display o... |
30ccebafd55a012ec02923649316524c39c410572520c1e0647f5cda12d75045 | Text | 2,371 | 45 | # Export ecephys to NWB
## NWB Packaging Ecephys
### Description
This capsule is designed to append device, electrodes, LFP and raw (optional) electrical series information to an existing NWB file.
### Inputs
The `data/` folder must include:
- the raw data in any supported format (e.g. AIND ephys format, OpenEph... |
10b9ebb0548add1d5ec445ee67745df73bcc545df754454cf2aa07c59b53fb31 | Text | 2,439 | 33 | # Fine-Scale Individualized Gyral Folding-Based Cortical Similarity Networks Reveal Distinct Organizational Patterns in Alzheimer’s Disease and Lewy Body Dementia
<img src="/fig/fig1.png" style="max-width: 100%; height: auto;"/>
## Introduction
In this work we propose a fine-scale, folding-informed cortical similarit... |
1f97526cb58c5a79cadf2c20bd2a6a423b90f71c93ec0564bf27b5c9299af6ae | Text | 2,499 | 40 | # Scissor: Single-Cell Identification of Subpopulations with bulk Sample phenOtype coRrelation #
### Introduction ###
`Scissor` is a novel approach that utilizes the phenotypes, such as disease stage, tumor metastasis, treatment response, and survival outcomes, collected from bulk assays to identify the most highly ph... |
a99badf26efa0a36e848307dea87da12ef1c637c6dac5a1a05254b1d6c1e370d | Text | 2,516 | 62 | # swallowing-meg-connectivity
MATLAB / FieldTrip pipeline for source-level MEG connectivity analysis of swallowing-related cortical interactions.
## Overview
This repository contains the core analysis scripts used for source-level MEG connectivity analysis between predefined cortical regions of interest during event... |
4fb0af30b73d9e09c9b2c1f1983403585fc4032afa2a29d77ea2fca5fbee9a21 | Text | 2,526 | 52 | # Generate hybrid recordings for spike sorting evaluation
## aind-ephys-hybrid-generation
Generate hybrid datasets from existing recordings, by injecting known ground truth into the data.
## Description
This capsule generates hybrid ground-truth datasets by combining existing recordings with hybrid ground-truth spik... |
236aa4c5c5757bb93dd4bf697c813004a1f8661f89beb588883ffcf762ce5ad2 | Text | 2,534 | 63 | # Deep learning-based physical exercise assessment of older adults using single-camera videos
## Overview
This repository contains the code used in the paper:
Stefanova, V., Maeyens, E., Brughmans, J., Vargemidis, D., Lebleu, J., Stulens, L., ... & Vanrumste, B. (2025). [Deep... |
896736a61232a2102a72a074d8b2a7de37fc1fb015c6f6eeba54e3ff8c370511 | Text | 2,665 | 67 | # METTL3 m6A and Bulk RNA-seq Analysis Pipeline
This repository contains a reorganized collection of R and shell scripts for reproducible analysis of public and in-house sequencing data.
## Overview
This project was prepared by reorganizing previously used R and shell scripts into a clearer and more reusable workflo... |
b8d8fd05a1ef35b0c4ccceda7398abfe15ea2e318114b0cfba204b9696f8e31f | Text | 2,743 | 62 | # About DL+DiReCT
DL+DiReCT combines a deep learning-based neuroanatomy segmentation and cortex parcellation with a diffeomorphic registration technique to measure cortical thickness from T1w MRI.
If you are using DL+DiReCT in your research, please cite ([bibtex](citations.bib)) the cor... |
80200b1a39befe7b10ce404d6b1a8161f5b4b3f6a2c64dd18f12c5ce6a97ca60 | Text | 2,859 | 58 | ================================================================================
SOHAI-Chess (Simulation of Human-AI Interaction in Complex Health Services)
Version 1.0.3
================================================================================
OVERVIEW
----------------------------------------------------------... |
8268314b914828825dd92c322f4d2dee931869ecce2f0ac8d7e8df278149219a | Text | 2,899 | 99 | # README
## Table of Contents
- [01_Analysis.py](#01_analysispy)
- 0\. Setup and Helper Functions
- 1\. Data Loading and Within-Dataset Predictions
- 2\. Permutation Importance Analysis
- 3\. Across-Dataset Predictions
- 4\. Statistical Model Comparisons
- 5\. Subgroup Analysis
- 6\. Post-Hoc Matched Sam... |
7bd530e80ade9c77bd0e827a00c64a7e7ea2bcd559780ff605cab4f1879ceb8a | Text | 3,149 | 84 | SigPy
=====
SigPy is a package for signal processing, with emphasis on iterative methods. It is built to operate directly on NumPy arrays on CPU and CuPy arrays on GPU. SigPy also provides several domain-specific submodules: ``sigpy.plot`` for multi-dimensional array plotting, ``sigpy.mri`` for MRI reconstruction, and... |
01b521c8dafbaf8dfb8e1581fd56313b1fcf6068200871d973533115e5ba2e84 | Text | 3,355 | 46 | # scEPI-Immune
### Abstract
Melanoma plasticity drives immune evasion and therapy resistance through dynamic cell-state transitions beyond genetic alterations. Although epigenetic remodeling is central to this process, its impact under therapeutic pressure remains unclear. We profiled longitudinal biopsies from melano... |
3958668af325dfae61530a24af93fb3519ab6f2f9f015cfb68958dec2d056ce5 | Text | 3,403 | 102 | # CaImAn-based-Ca2-Processing
Custom scripts used to run and adapt the open-source CaImAn package for calcium imaging data processing in the associated eLife manuscript.
## Repository Contents
- `CaImAn/CaImAn_Pipeline.py`: batch pipeline for motion correction, CNMF source extraction, seeded CNMF refinement, compone... |
2b15c1fb5fa49f0215382bb27a046150f6b07d6dbc337abb74cc21f0959dbcc8 | Text | 3,466 | 89 | # swallowing-meg-connectivity
MATLAB / FieldTrip pipeline for source-level MEG connectivity analysis of swallowing
# Source-level MEG Connectivity Analysis Pipeline
This repository contains MATLAB scripts implementing a complete source-level MEG connectivity analysis pipeline based on FieldTrip. The pipeline is desig... |
f80aea8995419f6c8cf4cd9e5eeef673e9c334814463b499bd58d6dc7e33005f | Text | 3,690 | 79 | # Visualization for AIND ephys pipeline
## aind-ephys-visualization
### Description
This capsule is designed to visualize ephys and spike sorted data for the AIND pipeline.
Visualizations is done using the [`sortingview`](https://spikeinterface.readthedocs.io/en/latest/modules/widgets.html#id6) backend of the `spik... |
dc7fedd8b3b31ef1fb4157e43a9c38c9805dc9e7d92b2641f683b0c1b9352d1b | Text | 3,842 | 91 | # navis-mousebrains
Transforms and meta data to map between different mouse template brains and coordinate systems. This package is intended to be used with [navis](https://github.com/schlegelp/navis) and is analogous to [`navis-flybrains`](https://github.com/schlegelp/navis-flybrains).
Currently `mousebrains` ships w... |
f3b972aedcf9274931fc0515b292b9195ebd40aa9d659d4c897241b10a56bbff | Text | 3,885 | 121 | # Sound Classification Analysis Pipeline
This repository contains the full MATLAB pipeline used to analyze participants’ textual labels and ratings of environmental sounds.
The workflow consists of:
1. **Text-based similarity analysis** (Step 1 of the algorithm)
2. **Clustering of sounds based on the similarity m... |
84746c9aad183b8b3270337c5337c571b3e4cb902bdb426f8fabeed7ea8f662c | Text | 3,904 | 132 | # V1 Interneuron snRNA-seq KO analysis
## Overview
This repository contains the code used to generate the single-nucleus RNA sequencing (snRNA-seq) atlas of mouse spinal V1 interneurons in global global En1 KO P0 pups and littermate controls.
Trevisan AJ, Han K, Chapman P, Kulkarni AS, Hinton JM, Ramirez C, Klein ... |
48b9f0ebdd2def9bd5587060503795817fd0bd451c4464517be5807d40223abc | Text | 4,199 | 59 | # Dispatch jobs for AIND ephys pipeline
## aind-ephys-job-dispatch
### Description
This simple capsule is designed to dispatch jobs for the AIND pipeline.
It assumes the data is stored in the `data/` directory, and creates as many JSON files
as the number of jobs that can be run in parallel. Each job consists of ... |
f04cadc6f12d348a911dff00d7e83c7ce7d5b58961a0ce3ea563c11f7ba22b2e | Text | 4,261 | 93 | # AIND Ephys Pipeline
## aind-ephys-pipeline
Electrophysiology analysis pipeline with [SpikeInterface](https://github.com/SpikeInterface/spikeinterface).
# News
[Jul 3rd 2026]: New release 1.3.0 is out! Check out release notes [here](https://aind-ephys-pipeline.readthedocs.io/en/latest/releases/1.3.0.html)
# Over... |
8bc64c499f8fe0b06a96745304e37818e3cdd20f27d8032b2c37201a3beb1aae | Text | 4,889 | 117 | # Preprocessing for AIND ephys pipeline
## aind-ephys-preprocessing
### Description
This capsule is designed to preprocess data for the AIND pipeline.
This capsule preprocessed the ephys stream with the following steps:
- Phase shift correction (see [phase_shift](https://spikeinterface.readthedocs.io/en/latest/mod... |
57cdc8685691590543bfe4e5ebc764176fd2422e35eccccdc6023772ea0b8ece | Text | 5,606 | 78 | # scEPI-Immune
### Abstract
Melanoma plasticity drives immune evasion and therapy resistance through dynamic cell-state transitions beyond genetic alterations. Although epigenetic remodeling is central to this process, its impact under therapeutic pressure remains unclear. We profiled longitudinal biopsies from melano... |
7818efd232d3cb7137388fb8cec7262c8667fa6d7dccc4da87e2960ac95ee043 | Text | 6,023 | 148 | # ENEEGMA
**ENEEGMA - Exploring Neural EEG Model Architectures - is a Julia package for constructing, simulating, and optimizing networks of neural population models.**
[](https://opensource.org/licenses/MIT)
[. Then, it
computes *sparse* waveforms and then in computes several additio... |
0e56045503f6758b2f3b6872fd9a9e36665ce480e58a75b623a9c418e5b0cbad | Text | 6,956 | 159 | # Identifiable learning of dissipative dynamics
This repository contains an implementation of UIDD, a deep learning framework for learning not only stable and interpretable, but also **Identifiable** dissipative dynamics from data.
## Requirements
- Python 3.8+
- JAX and related libraries
- Equinox for neural networ... |
a5d45d6d4b11ca296179f89f251b8e38367e1a409deec0aa5cd24d119b95b562 | Text | 7,286 | 229 |
# Subgrid Optimization
`SubgridOptimization` is a Python package for spatially constrained channel selection in high-density ECoG decoding. It is based on the methodology described in the manuscript [Optimal Size and Placement of Electrocorticography Grids for Classification of Hand Movements](#). The package searche... |
d62ea3c2f72e5220f5efc5e6aa50942bc1aa6e725e83949c468ded0b6f50ede2 | Text | 7,715 | 129 | SEUnglab neuRON pipeline
========================
A system for managing (distributed) reconstruction of neurons from electron microscopic image stacks.
Highlights
----------
1. ### 3D Reconstruction from EM images (Neuroglancer screenshot)
2. ### Slack and JupyterLab frontends
This repository contains the training and deployment code for a convolutional neural network (CNN) that detects the presence or absence of sample pins on a... |
fdc58fbaac38883ce7ae0a1a97f5003bcb0a2c59adba35584e2f64b91dc71f66 | Text | 8,549 | 169 | # spatchcocking
**Supplementary data and code for Chahare, Imamura, and Nerurkar (2026)**
This repository contains the Python scripts, example data, and pre-computed meshes cited as supplementary materials in:
> Chahare N., Imamura C., and Nerurkar N.L. (2026). *Morphometric analysis reveals that the chick cranial n... |
b47466e8e978a041ec192897b4b3af7f3b3572cd481bd80cda1b68c220dace70 | Text | 8,601 | 96 | # Welcome to the Artificial Metabolic Networks repository
This repository is entirely written in **python**. We make use of **jupyter** notebooks,
calling custom functions libraries storing the main objects and functions used in the project. We detail here two ways of using the repo, either on **Colab** or **locally**... |
fe3bef497020d0dcb70fd79f78ca3f57ff70a580ce20bf2250fc86c6f9f00941 | Text | 8,939 | 230 | # EINN: Enzyme-Informed Neural Network
](https://github.com/lh3/bwa/actions)
[](https://sourceforge.net/projects/bio-bwa/files/?source=navbar)
[
# Modkit
A bioinformatics tool for working with modified bases from Oxford Nanopore.
Specifically for quickly converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.
Detailed document... |
178488e88a176ba1b2c1c656c978935a2019b46579425370d87c02a178ac3f42 | Text | 12,118 | 456 |
## Introduction
As a novel analysis tool developed for quality control and preprocessing of FASTQ and SAM/BAM data, SOAPnuke includes 5 modules for different usage scenarios, namely **filter**, **filterHts**, **filterStLFR**, **filtersRNA** and **filterMeta**.
**filter**: Preprocess FASTQ files, include trimming (... |
c4f715eb38dfb5c08e0153cb1e7f59aed7846ca10e6b89e2616f0e3b698872d7 | Text | 12,766 | 212 | # Dorado
Dorado is a high-performance, easy-to-use, open source analysis engine for Oxford Nanopore reads.
Detailed information about Dorado and its features is available in the [Dorado Documentation](https://software-docs.nanoporetech.com/dorado/latest/).
## Features
* One executable with sensible defaults, automa... |
cc35559b6d2d4bc22e6ee5d09ebac2b6a2f1c7634894556aeaa4757046eafbbd | Text | 13,077 | 248 | # PlantVillage-AugNoLeaves
This repository contains the code and data representing outcomes of the paper "A TinyMLOps-Based Edge AI Approach for Early Detection of Emerging Plant Diseases," accepted at [IEEE MetroInd4.0&IoT 2025](https://www.metroind40iot.org/).
<p align="center">
<img width="260" src="readme/me... |
bc0867629059ff766223535a51c6728ff623fafbac747f292252bcfe0b69736b | Text | 13,646 | 264 | # AIND Ephys Hybrid Benchmark
## aind-ephys-hybrid-benchmark
Hybrid benchmark pipeline with [SpikeInterface](https://github.com/SpikeInterface/spikeinterface).
The pipeline is based on [Nextflow](https://www.nextflow.io/) and it includes the following common steps:
- [job-dispatch](https://github.com/AllenNeuralDyna... |
298efd149fd3f98f8531585a5c96244c0d1db9c656bef7409f37e4724f88ef7a | Text | 14,893 | 176 | # PINNs for DAEs — Symmetry-Driven PDE Dynamics
Reproducibility repository for the paper:
> Kavousanakis, M. E., Fabiani, G., Georgiou, A., Siettos, C., Kevrekidis, P. G., and Kevrekidis, I. G.
> *"Going with the Flow to Solve for Symmetry-Driven PDE Dynamics with Physics-Informed Neural Networks."*
> Nature Communic... |
352472211e351b90cff2df73388ea570a047c41783764f2e7d19d607f8c94d4e | Text | 15,010 | 180 | [](https://doi.org/10.5281/zenodo.21133348)
MN-PINNs for DAEs and Symmetry-Driven PDE Dynamics
=====
Reproducibility repository for the paper:
> Kavousanakis, M. E., Fabiani, G., Georgiou, A., Siettos, C., Kevrekidis, P. G., and Kevrekidis, I. G.
> *"G... |
9429f004495ea4ac1afe54b240928548322f45572ce85061613fa100c9b5f3a6 | Text | 17,702 | 342 | # README file for: **Clustered inputs engage dendritic nonlinearities and calcium signaling to support efficient place-field formation in CA1 pyramidal neurons**
*Simone Tasciotti, Daniel Maxim Iascone, Spyridon Chavlis, Luke A. Hammond, Yardena Katz, Attila Losonczy, Franck Polleux, Panayiota Poirazi*
Preprint doi: [h... |
1ba1be7eabcce90ef75f7f85f88b31ccae4cae8bca96290e409bfd2bc61048e5 | Text | 20,546 | 334 | [](https://pypi.org/project/stardist)
[](https://anaconda.org/conda-forge/stardist)
[](https://github.com/star... |
d714fe11976a467552299e532f44d74c929fea7d0a90776a5b677623e6b3cb05 | Text | 25,747 | 565 | # Somnotate
*Automated polysomnography for experimental animal research: annotate vigilance states from arbitrary time series data.*
Somnotate combines linear discriminant analysis (LDA) with a hidden
Markov model (HMM). Linear discriminant analysis performs automatic
feature selection by projecting the high-dimensio... |
131e7f57bad34edd34448543fb8ab45ed655f2d3cf123106ba5c7de27740e366 | Text | 48,711 | 743 | [](https://badge.fury.io/py/cloud-volume) [](https://drive.google.com/open?id=1RKtaAGV2f7F13opnkQfbp6YBqmoD3fZi) [](https://... |
1d10a2cc578d75caef7635903b54f5ed0cce714f3c491bec2c9a0ed0d944c0d0 | C | 130 | 3 | void cross(double *a, double *b, double *n) {
n[0]=a[1]*b[2]-a[2]*b[1]; n[1]=a[2]*b[0]-a[0]*b[2]; n[2]=a[0]*b[1]-a[1]*b[0];
}
|
4723b5ce8d5445e44158023cd9fd049721a66378a1931ccbcde7e87d7deedfbb | C | 176 | 7 | #include "../include/lsl_c.h"
#include <stdio.h>
int main() {
printf("LSL version: %d\n%s\n%f\n", lsl_library_version(), lsl_library_info(), lsl_local_clock());
return 0;
}
|
3435c977a384c7a7c5eff005be088f2fbc2316be98c52d8455a6015e0751aa33 | C | 635 | 24 |
bool CheckInsideFace(double *VN0, double *VN1, double *VN2, double rx, double ry, double *mi, double *ma, bool ignore_corners) {
bool inter;
double Lambda[3];
double mv, vv;
if((rx<mi[0])||(rx>ma[0])||(ry<mi[1])||(ry>ma[1]))
{
inter=false;
return inter;
}
BarycentricCoordin... |
94446cf8cde67c30e64d0a335b0c941fd3fbad2e77f30180d12e61f9c2a5a6b8 | C | 678 | 25 | /* gzclose.c -- zlib gzclose() function
* Copyright (C) 2004, 2010 Mark Adler
* For conditions of distribution and use, see copyright notice in zlib.h
*/
#include "gzguts.h"
/* gzclose() is in a separate file so that it is linked in only if it is used.
That way the other gzclose functions can be used instead to... |
53bbc11567781645bec89e29c740a68ed65d2032ae0a8d131791d448cadae270 | C | 703 | 24 | #include "mex.h"
#include "math.h"
#include "func_BarycentricCoordinatesTriangle.c"
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] )
{
/* Size of output */
int odims[2]={1, 3};
double *Lambda;
double *VN0, *VN1, *VN2,*RX, *RY;
VN0=(double *)mxGetDat... |
b21d462d6ba60109651538736a6770a707a8a04f33f80394087672242a40512e | C | 754 | 44 | #include "local.h"
int lf_error;
lfit lf;
design des;
void calllf(x,y,n)
double *x, *y;
int n;
{ lfdata *lfd;
fitpt *fp;
int i;
lfit_init(&lf);
lfd = &(lf.lfd);
lfd->x[0] = x;
lfd->y = y;
lfd->n = n;
lfd->d = 1;
startlf(&des,&lf,procv,1);
// startmodule(&lf,&des,"std",0);
fp = &lf.fp;
... |
457f777640100d24b9b60fc1071ade3388ee96f5720489efc3554b798528e9fb | C | 809 | 25 | /*
* Recursive definition of determinate using expansion by minors.
*/
double Determinant(double **a, int n) {
int i, j, j1, j2;
double det = 0;
double **m;
if (n < 1) {
} else if (n == 1) { det = a[0][0];
} else if (n == 2) { det = a[0][0] * a[1][1] - a[1][0] * a[0][1];
} else { det = 0;
... |
7aac32786f8ab5f4545703f3dee04ee335d8d24175359ddb0640b1d8afc8667f | C | 816 | 26 | #include "mex.h"
#include "math.h"
#include "func_cross.c"
#include "func_BarycentricCoordinatesTetrahedron.c"
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] ) {
/* Size of output */
int odims[2]={1, 4};
double *Lambda;
double *p1, *p2, *p3, *p4, *RX, *RY, *RZ;
... |
859d1dd849070fadd810c3f34f91ea8574fb39d47405e80a0ef1f572fe38b504 | C | 895 | 58 | #include <Python.h>
static PyObject *hello(PyObject *self) {
return PyUnicode_FromString("Hello");
}
static PyMethodDef module_methods[] = {
{
"hello",
(PyCFunction) hello,
METH_NOARGS,
PyDoc_STR("Say hello.")
},
{NULL}
};
#if PY_MAJOR_VERSION >= 3
static struct PyMo... |
3cae1160fce9bb88d0626fbd07a8c8bb4c8a686a4043d9d6668842f35dffd20c | C | 921 | 27 | #include "mex.h"
#include "math.h"
#include "func_Determinant.c"
#include "func_SphereFrom4Points.c"
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] ) {
int odims[2]={1, 1};
double *PA, *PB, *PC, *PD;
double *Cx, *Cy, *Cz, *L;
PA=(double *)mxGetData(prhs[0]);
PB=(d... |
4611140405269548220f1fc06a5c53becca74a94465b7e0c041879dc3177eb19 | C | 974 | 33 | #include "mex.h"
#include "math.h"
#include "func_BarycentricCoordinatesTriangle.c"
#include "func_CheckInsideFace.c"
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] ) {
/* Size of output */
int odims[2]={1, 1};
double *VN0, *VN1, *VN2, *RX, *RY;
double *MI, *MA;
... |
281b6adf2686d239e1ce54e01c31482cda958b64691f31a516aff7dd1cb340e2 | C | 1,130 | 27 | void BarycentricCoordinatesTriangle(double *VN0,double *VN1,double *VN2,double rx, double ry, double *Lambda)
{
double f12, f20,f01;
double g12x, g20x, g01x;
double g12y, g20y, g01y;
double c12, c20, c01;
/* Normalization factors */
f12 = ( VN1[1] - VN2[1] ) * VN0[0] + (VN2[0] - VN1[0] ) *... |
20ccda1274b2e35efdd19d7b32126ef4178f186080b0d5c8e22ab7504d8aec33 | C | 1,168 | 36 | #include "mex.h"
#include "math.h"
#define mind(a, b) (((a) < (b)) ? (a) : (b))
#define maxd(a, b) (((a) > (b)) ? (a) : (b))
#define absd(a) (((a) < 0) ? -(a) : (a))
#include "func_BarycentricCoordinatesTriangle.c"
#include "func_CheckInsideFace.c"
#include "func_LineTriangleIntersection.c"
... |
d3ab1b296c7de82b9b14787397085a1013916b968821e6e76d4ea8b3ead385c0 | C | 1,261 | 46 | /*
* CORE_histxt.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_histxt.c
*
* samar@cs.stanford.edu, 07/31/05
*/
#include "mex.h"
#include "matrix.h"
#include "CORE_libra... |
e265706a7d1840b0ec9cd2404601525c423df35012a54f3dbea95233728e3e3a | C | 1,281 | 48 | /*
* CORE_testfile.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* mex CORE_testfile.c
*
* samar@cs.stanford.edu, 07/12/05
*/
#include "mex.h"
#include "matrix.h"
#include <math.h>
/... |
691f15cb7145153224758f16a01d8c8b294a0e66c29d768a6df741083df37935 | C | 1,290 | 43 | #include <stdio.h>
#include <stdbool.h>
#include <stdlib.h>
#include "kvec.h"
#include "medaka_common.h"
#include "medaka_trimbam.h"
#include "medaka_pytrimbam.h"
seq_set PY_retrieve_trimmed_reads(
const char *region, const bam_fset* bam_set, size_t num_dtypes, char *dtypes[],
const char tag_name[2], const i... |
632f85680981bae2242e4b78c551e2cd1c0c03f8c36078276cdfdea6525fa1c6 | C | 1,294 | 45 | /*
* CORE_pxcorr.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_pxcorr.c
*
* samar@cs.stanford.edu, 07/31/05
*/
#include "mex.h"
#include "matrix.h"
#include "CORE_libra... |
0e234918598204543e0768ba5c0d2b8fff573466f96d8e798e9204e75b2e20f5 | C | 1,331 | 44 | #include "mex.h"
#include "math.h"
#define mind(a, b) (((a) < (b)) ? (a) : (b))
#define maxd(a, b) (((a) > (b)) ? (a) : (b))
#define absd(a) (((a) < 0) ? -(a) : (a))
#include "func_LineLineIntersect.c"
void mexFunction( int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[] ) {
/* ... |
718448a2e8100d1db4eae60924c7a82d0884350c337f954f33d97dabf33cf583 | C | 1,337 | 46 | /*
* CORE_histxy.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_histxy.c
*
* samar@cs.stanford.edu, 07/31/05
*/
#include "mex.h"
#include "matrix.h"
#include "CORE_libra... |
c16cba8916b23a67f524e48a6f6dea34b2cf8652d65a8d3f16bd8b2c2a85c7a5 | C | 1,350 | 54 | #include <zlib.h>
#include <stdio.h>
#include "kseq.h"
#include "medaka_common.h"
#include "fastrle.h"
KSEQ_INIT(gzFile, gzread)
void rle(char *in, int inlen, size_t block_size, char *out, char *outruns) {
if (block_size > 94) {
fprintf(stderr, "Invalid block length %i (> 94)", block_size); exit(1);
... |
0563524bbd8e212d7a0274a9eb7fc1662135ae291ed8e7a2040714235dc709f7 | C | 1,352 | 35 | #include <lsl_c.h>
#include <stdio.h>
/**
* Example program that demonstrates how to resolve a specific stream on the lab network and how
* to connect to it in order to receive string-formatted markers.
*/
int main(int argc, char* argv[]) {
lsl_streaminfo info; /* the streaminfo returned by the resolve call */
lsl... |
039db681b20e5382681f00d82517a91c7bde33a78b13062b1bf4a22fc875428e | C | 1,371 | 37 | #include <lsl_c.h>
#include <stdio.h>
/**
* Example program that demonstrates how to resolve a specific stream on the lab network and how
* to connect to it in order to receive string-formatted markers.
*/
int main(int argc, char *argv[]) {
lsl_streaminfo info; /* the streaminfo returned by the resolve call */
... |
4269b4b428a8af9cb6c75c02ddad14d4ee7270cbcf9cdacf2a6e35375724ca56 | C | 1,398 | 50 | /*
* CORE_resetintegrator.c
* ----------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_resetintegrator.c
*
* samar@cs.stanford.edu, 02/20/06
*/
#include "matrix.h"
#include "mex.h"
... |
b9a039b5a01b6c1efa342e25b45d143697b5272e10faec3e377be6a1c04b7322 | C | 1,477 | 47 | /*
* fast_interface_energy.c - Matlab mex file
*
* This is a MEX-file for MATLAB.
*/
#include "mex.h"
#include "matrix.h"
/* ********************************************************** */
/* ********************* MEX GATEWAY *********************** */
/* ********************************************************** ... |
ab882285a3a75c9b6bf084c1b738632002376ddb0dbeb2d9f22dd678c99f46c5 | C | 1,541 | 52 | /*
* CORE_minmax.c
* --------------------
* The syntax for this function is described in the M file of
* the same name.
*
* This is a MEX-file for MATLAB. It was compiled using:
*
* COREmex CORE_minmax.c
*
* samar@cs.stanford.edu, 07/31/05
*/
#include "mex.h"
#include "matrix.h"
#include "CORE_libra... |
731b62fccb13e75f846f9fec2775702b1728a8e5678cc9fea2f385e195dc81b9 | C | 1,542 | 56 | #include "mex.h"
#include "math.h"
#include "func_cross.c"
#define absd(a) (((a) < 0) ? -(a) : (a))
double CheckVolumeFaceMesh(double *V, int *sizeV, double *F, int *sizeF)
{
int i;
double volume=0;
double k[3],a[3],b[3],c[3];
int Fi1, Fi2, Fi3;
double v;
for (i=0; i<sizeF[0]; i++)
... |
81cd43a5555e134f0b9b8013d1d1ade7ce03956467d8e4b049d3399f1cfee585 | C | 1,593 | 61 | #include "mex.h"
#include "math.h"
#define mind(a, b) (((a) < (b)) ? (a) : (b))
#define maxd(a, b) (((a) > (b)) ? (a) : (b))
#include "func_BarycentricCoordinatesTriangle.c"
#include "func_CheckInsideFace.c"
#include "func_LineTriangleIntersection.c"
void mexFunction( int nlhs, mxArray *plhs[], int n... |
adfabf399f23af589d3b2e3fc98175c34377815562779c4d62eb764dc39c6dee | C | 1,644 | 48 | void BarycentricCoordinatesTetrahedron(double *p1, double *p2, double *p3, double *p4, double rx, double ry, double rz, double *Lambda) {
int i;
double rt[3];
double r1[3], r2[3], r3[3];
double r4[3], r5[3], r6[3];
double g1[3], g2[3], g3[3], g4[3];
double c1, c2, c3, c4;
double r_b[3];
... |
9047830fd7bac5b85ab3021ec3d6d883468ab676d4f10146323595195a03439d | C | 1,655 | 48 | bool CheckPointOutInside(double *P3, double *V, int *sizeV, double *E, int sizeE)
{
double P4a[2], P4b[2], P4c[2];
int k;
ka=0; kb=0; kc=0;
double *lista, *listb, *listc;
int kam=10;
int kbm=10;
int kcm=10;
lista=(double*)malloc(kam*sizeof(double));
listb=(double*)malloc(k... |
41fd4a47993a42791d1516a501955aa93ab52cb2412539bd268140c6236c5c37 | C | 1,691 | 52 | #include <lsl_c.h>
#include <stdio.h>
#include <stdlib.h>
#ifdef _WIN32
#define WIN32_LEAN_AND_MEAN
#include <Windows.h>
void sleep_(int ms) { Sleep(ms); }
#else
#include <unistd.h>
void sleep_(int ms) { usleep(ms * 1000); }
#endif
/**
* This example program offers a 1-channel stream which contains strings.
* The st... |
faf7b6002065a83031540b5725ad56f37ac3282ca02a3caee6bd719fa39716ea | C | 1,721 | 51 | #include <lsl_c.h>
#include <stdio.h>
#include <stdlib.h>
#ifdef _WIN32
#define WIN32_LEAN_AND_MEAN
#include <Windows.h>
void sleep_(int ms) { Sleep(ms); }
#else
#include <unistd.h>
void sleep_(int ms) { usleep(ms*1000); }
#endif
/**
* This example program offers a 1-channel stream which contains strings.
* The strea... |
6f21214feeedb7a81169eaf5c562013f48318b5d129e06698cda828b70a2b15c | C | 1,740 | 44 | #include <lsl_c.h>
#include <stdio.h>
/**
* Example program that demonstrates how to resolve a specific stream on the lab network and how to connect to it in order to receive data.
*/
int main(int argc, char* argv[]) {
unsigned k,t; /* channel index */
lsl_streaminfo info; /* the streaminfo returned by the resol... |
e8d259fbbd096b158d0611336290247a8cc661ef1a5be8671450d2ec62a3ee69 | C | 1,759 | 68 | /***********************************************************************
* mexnnz.c: get number of non-zero elements of a matrix M
*
* nnz = mexnnzt(M);
*
* SDPT3: version 3.0
* Copyright (c) 1997 by
* K.C. Toh, M.J. Todd, R.H. Tutuncu
* Last Modified: 2 Feb 01
*******************************************************... |
bc91e311d6234517c4b9cb6a9d6ff1267ff5b439bdb27b54957affc3371c7c90 | C | 1,776 | 61 | #include "mex.h"
#include "math.h"
#include "func_cross.c"
#define absd(a) (((a) < 0) ? -(a) : (a))
double CheckVolumeTetraMesh(double *V, int *sizeV, double *F, int *sizeF)
{
int i;
double volume=0;
double k[3],a[3],b[3],c[3],d[3];
int Fi1, Fi2, Fi3,Fi4;
double v;
for (i=0; i<sizeF... |
3d58d98f947b186f98cbedae4b4cb6c10c7492f2c36419fb6205823d6764851b | C | 1,786 | 60 | /** @file planar_edges_mex.c
* @copyright Stanford University, 2008
* @author David F. Gleich
* Get extra sets of edges for a planar graph
*/
/** History
* 2008-10-05: Initial version
*/
#include "mex.h"
#if MX_API_VER < 0x07030000
typedef int mwIndex;
typedef int mwSize;
#endif /* MX_API_VER */
#include "mat... |
5b6e4e25aae615a3427275b18fa5eea715e36d8cfd497573f79df1a2a56e969f | C | 1,788 | 73 | /**
* @license
* Copyright 2022 William Silversmith
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicabl... |
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