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927022aa9c7d01ef5a17154b91e2d58aa0a0bf1cb340bf4a41953ce03a8a457c | Text | 4,181 | 69 | # SPECIALS - Spectral Extraction and Classification for ISM Analysis using Least Squares
[](https://opensource.org/licenses/MIT)
[]()
[
<img width="6379" height="3965" alt="Mosaic_thumbnail" src="https://github.com/user-attachments/assets/4d0b0e9b-8d97-4e7c-bfb0-aa20dfcfb109" />
## Overview
... |
af543b3fa294120f1a01f82194fea56e789f2e0bf5b54767acc6f188f6ed1247 | Text | 4,193 | 132 | # 🧠 Co-fluctuation Score Repository
Welcome! 👋
The **Co-fluctuation Score (CS)** is a novel dynamic measure for characterizing transient reorganization of the human brain functional connectome. This repository provides code to compute CS from BOLD time series and reproduce the main analyses.
📄 **Manuscript (bioRx... |
779774a0f35185b6d930bc17d1cca727ace2fea2d1cc2f7e64d75b35377ef6f7 | Text | 4,194 | 116 | # RNA-seq_ll100
The shell commands and scripts given serve for the RNA-seq analysis done for LL-100 cell lines, 100 leukemic and lymphoma cell lines + the normal cell line NC-NC (https://celldive.dsmz.de/rna/ll-100).
Samples were prepared as follows: miRNeasy mini plus Qiagen, polyA selection, GATC library prep, mRNA... |
93094f068b8ba3e14d9aafc481f5f4d2ccd8ee206a11800132f0567b2f45b26d | Text | 4,204 | 112 | # CRN (Coherent Resonant Netting) — reproducibility repository
## Software and datasets (Zenodo DOIs)
Software (canonical reproducibility hub):
- CRN software repository: https://doi.org/10.5281/zenodo.18338260
Datasets:
- Evolutionary game-theory companion dataset:
https://doi.org/10.5281/zenodo.18379850
- C. el... |
37de669b58bbe0359b4004cde2603f57453dfa32dc5dd5e65bc266bf643a17fc | Text | 4,206 | 153 | # Bipixel Rotation Method for Chirality Analysis
This repository provides a complete pipeline for quantifying structural chirality and asymmetry in filamentous or textured images (e.g., biological tissues, polymers). The method combines **Fiji/ImageJ** macros for image preprocessing and **Python** scripts for periodic... |
962e5f26af216d252c95f79405458221b9a764c7f7f7c4c017de4472a07b62b6 | Text | 4,209 | 77 | # dl-task-contrast-prediction
## Referenced Work
Soren J. Madsen*, Young-Eun Lee*, Lucina Q. Uddin, Jeannette A. Mumford, Deanna M. Barch, Damien A. Fair, Ian H. Gotlib, Russell A. Poldrack, Amy Kuceyeski, Manish Saggar. **Efficient Deep Learning Models for Predicting Individualized Task Activation from Resting-State ... |
9830feeeec25794042ad77d0428b8d98827e1b396ab0d46fb02712043b5f3e08 | Text | 4,220 | 115 | # DeDistortNet
🔥 Official implementation of "Dual-conditioned diffusion model with anatomical guidance for geometric distortion correction in prostate MRI" (European Radiology Experimental)
## Method
DeDistortNet corrects geometric distortions in prostate DWI by combining two conditio... |
37b6f7655d2065d401e18223916ba7ca8b61af04fb47a07c92097a8efde0cf16 | Text | 4,248 | 187 | # pci_snATAC
This repository contains scripts used in Han et al. (2026) for analyzing single-nucleus ATAC-seq data, identifying regulatory elements, and integrating with genetic and functional genomic datasets.
All scripts were developed and tested under the following environments: R v4.2.2 and Python v3.9.7.
All de... |
9e604c7f52dbef2816caead60fc156b957fb1c03ab18278870d2f9b57b65b13b | Text | 4,248 | 187 | # pci_snATAC
This repository contains scripts used in Han et al. (2025) for analyzing single-nucleus ATAC-seq data, identifying regulatory elements, and integrating with genetic and functional genomic datasets.
All scripts were developed and tested under the following environments: R v4.2.2 and Python v3.9.7.
All de... |
2f180b569253030d95b8d64cf4d192ad1f026637371832fc70bb2e82a9ecab80 | Text | 4,256 | 106 | # Shape-Expression Modeling
A bidirectional machine learning framework for modeling the interplay between single cell shape and protein expression, based on our paper - [Data-modeling the interplay between single cell shape, single cell protein expression, and tissue state](https://www.biorxiv.org/content/10.1101/202... |
c9d5f101f3feed2af45ff9657e769d28d00ed69103d69097e2939080eef42514 | Text | 4,258 | 125 | 
Alignment-free genome assembly polisher with an ML model trained on spaced seed hit/miss patterns.
- [Requirements](#requirements)
- [Installation](#installation)
- [Using `conda` (recommended)](#using-conda-recommended)
- [Manually](#manually)
- [For Developers](#for-develope... |
47c6c133b828e0d1291160b1862b39321cc8b4e6b255c09c5a4be484610f1ae7 | Text | 4,261 | 69 | # UnetBrainMS
This repository includes the code for running the model and the various scripts used for augmentation of data including restricting lesion size in the ground truth, scripts for the purposes of rotating the brain volumes and a utilities file containing various functions for running the model and a selectio... |
dad10084adeb89458538432336c445909801f1a9e900f056db9f4f4b006f7d7d | Text | 4,271 | 137 | # BT-CAP: Brain Tumor Compositional Augmentation Pipeline
 <!-- Replace with your project logo if available -->
Welcome to **BT-CAP**, a powerful Python-based tool designed to enhance brain tumor imaging datasets through advanced compositional augmentation techniques. Th... |
066164f46acf19f57583d4b4ee8355e9a11d14fd593f6c92f565425856a8f86a | Text | 4,274 | 99 | # salmon
[](https://github.com/COMBINE-lab/salmon/actions/workflows/ci.yml)
[](https://github.com/COMBINE-lab/salmon/releases/latest)
[ and [Faskowitz et al 2020](https://www.nature.com/articles/s41593-020-00719-y)), we proposed what we called ``edge time series'' as a way of obtaining framewise contributions to the ... |
ea574a3c70673ece9afd2c737411193b0d7b5a049f1405be63ae45e1e9f98ac0 | Text | 4,295 | 102 |
# HR-pQCT double-stack scan alignment using IPL
---
## Overview
This package performs batch processing in **IPL (Image Processing Language)** for **Scanco Medical** imaging datasets.
It is specifically designed to align double-stack scans *with no overlap* between the stacks, correcting rotational misalignments ar... |
a3bf199163cc87e9334653785be686de37d0a20e76337dbfc11f8c0e300cbc37 | Text | 4,301 | 87 | [](https://doi.org/10.5281/zenodo.1491733)
# The ENCODE Blacklist: Identification of Problematic Regions of the Genome
Functional genomics assays based on high-throughput sequencing greatly expand our ability to understand the genome. Here, we define the ... |
b1636e186570356f896b018eefcd60f1e3890bd644644de63fc2d4f7f7db6d4a | Text | 4,310 | 150 | # n-LMF: Neural Local Mixing Function Training with batches
Training code for **neural local-mixing-function (n-LMF)** based local-hybrid DFT models.
Implements a Keras/TensorFlow pipeline with a custom `DFTLayer` to evaluate XC terms on molecular grids and fit model parameters across standard benchmark test sets. **D... |
a649bd138163cb1ebf81a993aa0ef5876b599701f19cde38a6e7da2df6788dd8 | Text | 4,326 | 75 | # OMELETTE: Openly available sMall vEsseL sEgmenTaTion pipelinE
This is a easy-to-use and fast-to-tune vessel segmentation pipeline.
For vessel enhancement, the filter by Jerman et al. [1] was reimplemented in python.
To that end, scikit-image was leveraged.
To segment the vessels from the enhanced images, hysteres... |
908bbcaff0c9421d9f96758eb8de29ed41c0d4a15c1e28cf1d647870aad972d1 | Text | 4,334 | 190 | This repository contains the data and custom analysis code associated with the manuscript:
**“Animal acoustic communication maintains a universal optimum rhythm”**
It provides all materials necessary to reproduce the principal analyses, phylogenetic modeling, regression analyses, and figure generation pre... |
0393d50d6d7814123bb3ac12bdad5279d91681b0c9c1f2bf1d5a17f6ef2ca293 | Text | 4,335 | 123 | # 🧬 Machine Learning Pipeline for Omics Data
## Overview
This repository contains a **generalized machine learning (ML) and deep learning (DL) pipeline** for analyzing **tabular omics datasets**, including proteomics, transcriptomics, metabolomics, and other high-dimensional biomarker data. The pipeline is modular, r... |
1ac11c3fa0e2de09dedf46b662c308b6b45a0cc5e1b5f2799041e947f3f4cb07 | Text | 4,336 | 115 | # Video Preprocessing Pipeline
A Python package for efficient preprocessing of large video data (>300 GB), optimized for memory efficiency using dask array as well as time efficiency using JAX and CUDA.
## Features
This package processes high-resolution microscopy videos with:
- Support for ND2/TIF formats and multi-... |
d04f0af23b18575ae38820a9ea92ec65a9729e716fdaf24a87274aefdbcfdfbb | Text | 4,336 | 59 | # NucVerse3D – Data, Models, and Results
This repository provides volumetric microscopy datasets, processed data, trained models, and segmentation results used in this study on generalized 3D nuclear instance segmentation.
---
## Datasets (raw)
### Mouse Liver Tissue Dataset
The **Mouse Liver Tissue Dataset** cons... |
44eb997df80c5e489910c9dd8ff32c7885a5b30e67479eafb7c0e091173d1638 | Text | 4,338 | 136 | |PyPi| |CIStatus| |ReadTheDocs| |Codecov|
.. |PyPi| image:: https://badge.fury.io/py/joblib.svg
:target: https://badge.fury.io/py/joblib
:alt: Joblib version
.. |CIStatus| image:: https://github.com/joblib/joblib/actions/workflows/test.yml/badge.svg
:target: https://github.com/joblib/joblib/actions/workflows... |
dca5f4b88cc89ac35d6dddb18b054edb3f6a5c164e9650655ccd6026242fc678 | Text | 4,340 | 136 | # Binocular Perception Instance Authentication Learning for Few-Shot Visual Recognition
## How to use it
1. Download the plugin files `SettingsPlugin.py`, `WaveformPlugin.py`, `PSTHPlugin.py`, `CorrelationPlugin.py`, `SimilarityPlugin.py`on the GitHub repository.
2. Install `pandas` and `neo`.
```
conda acti... |
b5b6cfacf0ad9c9cfab9f61b71ff83632f3e6e2d82149f252383f76631722415 | Text | 4,349 | 94 | # The PI-CAI Challenge: Public Training and Development Dataset
## Reference
Please cite the following article, if you are using the PI-CAI: Public Training and Development Dataset:
A. Saha, J. J. Twilt, J. S. Bosma, B. van Ginneken, D. Yakar, M. Elschot, J. Veltman, J. J. Fütterer, M. de Rooij, H. Huisman, "A... |
2696ab5686427490764b9a57ea6d1f3d0389a3b12c3ed04cc2bec2c7e291b1cf | Text | 4,391 | 101 | # CycleGAN-3D-ULF
This repository provides a PyTorch-based framework for enhancing ultra-low-field (ULF) MRI using a 3D CycleGAN [1] framework and Residual Vision Transformer (ResViT) [2] generator models. The goal is to translate ULF-MRI volumes into higher-quality images that approximate high-field (HF) MRI while pr... |
6ca084c221f0f86a2500260f1f7994f9247ead53dfda530eac0b713468fd15db | Text | 4,394 | 163 | ## COSG in R
Accurate and fast cell marker gene identification with COSG
COSG is a cosine similarity-based method for more accurate and scalable marker gene identification.
* COSG is a general method for cell marker gene identification across different data modalities, e.g., scRNA-seq, scATAC-seq and spatially reso... |
abf2f6d2e90e0df702c3ce5e5f5610cd081e51b0bb618ad5e988049807b18105 | Text | 4,394 | 60 | # Noise-invariant representations of sound emerge along the canonical cortical hierarchy. Tomas Suarez Omedas and Ross S. Williamson, 2026
Documentation for the data and code used for this publication
## Neural Data
All data used in this publication is stored in the repository [insert link / doi]. Each subpopulation ... |
01ea020870ca2e0d9a3b7898374553d8d573e7b740d4fe99014a7e3fc9f4cd72 | Text | 4,404 | 128 | # PhenoLink
## Description
PhenoLink, former "Checkout" is a multipurpose open source high content image analysis software developped at [Ksilink](https://www.ksilink.com/) entirely written in C++ for computational speed purposes.
Dedicated to biological images produced with aut... |
a003fe448ca06aebb748467227d2dc8b8be263173c6c070400efb95dfb9cb618 | Text | 4,412 | 73 | <p align="center">
<img width="750" alt="dbt logo" src="assets/dbt-logo-full.png" />
</p>
<p align="center">
<a href="https://github.com/dbt-labs/dbt/actions/workflows/ci.yml?query=branch%3Amain"><img src="https://github.com/dbt-labs/dbt/actions/workflows/ci.yml/badge.svg?branch=main&event=push" alt="dbt CI sta... |
ef0f7b5c4b7fa2129f1456e2f414c9d5aaa82b0a1eda365e9f489b7a53180018 | Text | 4,414 | 115 | CAMERA CALIBRATION TOOLBOX FOR MATLAB (v3.0 10-17-00)
Installation
------------
Simply copy all the .m files into a directory 'calibr' and add it to your
MATLABPATH. Matlab version 4.0 or later is required.
Things to do
------------
If you have a 3-D calibration object, you can cope with a single image. In
order... |
6b2bdc4244d41d7b2ad5588cd0588be335e0189e4e836ef502199bc758eb8163 | Text | 4,421 | 58 | *Authors: Tomas Berjaga-Buisan, Juan Manuel Monti, Martina Cortada, Michele A. Colombo, Sebastian M. Geli, Gianluca Gaglioti, Simone Sarasso, Morten L. Kringelbach, Maurizio Corbetta, Maria V. Sanchez-Vives, Marcello Massimini, Yonatan Sanz Perl, Gustavo Deco*
### 🧠 Overview
This repository accompanies the manuscrip... |
75b8c403002acddb81e16538908aad20aacdcdf87d2aa45cd0f9c3da71ecd6d1 | Text | 4,439 | 219 | # AFsLF
Official implementation of **AFsLF (Autofocus for Scanning Light Field Microscopy)**, a real-time robust autofocus method for sustained intravital scanning light field imaging.
AFsLF estimates the defocus distance from the disparity between the central view and an edge angular view in scanning light field mic... |
9088fd6a91857e2f1da66fec1888a6fde755a92621c1af49c007e4f8e0760f89 | Text | 4,454 | 124 | <!-- # SSDLabeler -->
# SSDLabeler: Realistic semi-synthetic data generation for multi-label artifact classification in EEG
## Setup
### Environment setup: SSDLabeler
> - OS: **Windows 11**
> - MATLAB: **R2024a**
> - EEGLAB: **v2023.1**
SSDLabeler uses MATLAB to generate annotated semi-synthetic artifact contamint... |
d2ddde3077bd20a60bcbc042fe0cc895714c3a216cd25c180f377ed22e8a685f | Text | 4,458 | 79 | # Getting Started with bio-misc
__version__: `0.2.0a0`
The bio-misc package is essentially a collection of scripts to do various "biological" tasks, the sort of stuff that is useful post GWAS. It is not meant to be an API but I will try to write things to be generalisable and with a high-level API in mind. The script... |
a912c685388ed9c49748c171d2569a47c2ca301c8b5f015365fef3bf0cde6500 | Text | 4,469 | 107 | # LocoReach Dataset — Raw Electrophysiology and Behavior Recordings
## Overview
This dataset contains raw in vivo extracellular recordings from the cerebellum
(molecular layer interneurons, MLI, and Purkinje cells, PC) of head-fixed mice
walking on a motorized, runged treadmill (LocoReach). Recordings were performed ... |
b98a6ee986b51481d2fdf1ab735f989bc15232c41311d0ab2e79a0df0daf66bc | Text | 4,485 | 35 | # ClinicalNetDynamics
IMPORTANT NOTE: upon external code review, this repo contains select scripts that are an older version, and more importantly, gaps in usage notes that were intended to be covered by the manuscript's Methods section. However, upon review, we believe the source scripts themselves would benefit from... |
cdc01c0174bcf50094ea07327925e4551205bc2ce2b9b41a625841ad4c3f90f5 | Text | 4,486 | 68 | | :warning: WARNING |
|:----------------------------|
| [SCENIC](https://github.com/aertslab/SCENIC) is deprecated, use [pySCENIC](https://github.com/aertslab/pySCENIC) instead. |
# SCENIC
**SCENIC (Single-Cell rEgulatory Network Inference and Clustering)** is a computational method to infer Gene Regulatory... |
8e2b212d884f962b655369817e2f47cfa710e78767b7a2298b3abd378364f939 | Text | 4,516 | 55 | ### VertexModel.jl
Open a Julia REPL at the project root directory.
Activate environment with `using Pkg; Pkg.activate(".")`, or `] activate .`.
(If running for the first time) Run `Using Pkg; Pkg.instantiate()` or `] instantiate`.
Load package by running `using VertexModel`
Once `VertexModel.jl` has been precom... |
96ecf5eafe119c0d9f9d765fb3f7dfc2bb2c8010764bf2f829596870f79c552b | Text | 4,520 | 101 | # ERA: An AI System to Help Scientists Write Expert-Level Empirical Software
[](https://arxiv.org/abs/2509.06503)
[](https://google-research.github.io/era/... |
8d95f42dfb03cd571a4a10dc35d94704f1ddcd143738c5fd5ea755b38cce971a | Text | 4,525 | 66 | # DMG-Longitudinal
Code Repository for automatic MRI-based classification of tumor progression in Diffuse Midline Glioma (DMG). Two pre-trained models (Longitudinal and Independent) were used independently to compare their respective performance.
## Requirements
- Python environment with nnUNet dependencies*
- qsiprep ... |
41605a8070e90e60b077b697ed0146192010e92d81bef6c8ec5d1afbcf6eced0 | Text | 4,529 | 105 | ### fMRI-timescales
> Estimating fMRI Timescale Maps
<img src="./figures/hcp-tstats.png" width="400"/>
<a href="https://doi.org/10.1162/IMAG.a.1248">
<img src="./figures/img-neuro.png" width="150" alt="Neuroscience Image"/>
</a>
[
Repository: https://github.com/animalmodel/Philipp_eLife_2025
Data DOI: https://doi.org/10.5281/zenodo.18058525
📝 Overview
This repository contain... |
ccd5049e4c75ad4faed5819357bc8d9e43784aadcc5f2bce9ce92b7045bfd865 | Text | 4,535 | 101 | # DeepFaceMouse
Directory to two software tools used in [DeepFaceMouse enables scalable prediction of large-scale brain activity from facial dynamics in mice](https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(26)00180-3).
Published in Dr. Murat Yildirim's [Lab](https://www.lerner.ccf.org/neurosciences/yild... |
a945fa74099d006e151766cc0c60efa053a66d84596001111c57bcdc303236ef | Text | 4,540 | 89 | alleninf
========
Compare an unthresholded statistical map of a brain with gene expression patterns from [Allen Human Brain Atlas](http://human.brain-map.org/). See the [OHBM 2014 poster](http://f1000research.com/posters/1097120) for more details.
**This pacakge is depracated** in favour of the Gene Decoding function... |
fd0a914ee51cafdf3a10dee9cf64a8648615dc6c014e3758db329ed3731aefbf | Text | 4,556 | 82 | README
From Lipid Dynamics to Precision Predictions: A New Approach Methodology for Precision Modeling of Phosphoinositide Signaling (https://doi.org/10.1101/2025.07.03.663046)
Overview
This repository contains all MATLAB source code required to reproduce the computational figures in the manuscript. Each folder corre... |
e025a2e91d2a7d1c930eb64032f1f0d009e3e82a5110345ff508ae7fca49ab88 | Text | 4,567 | 80 | **IDTrack**
===========
|PyPI| |PyPIDownloads| |Python Version| |License| |Read the Docs| |Build| |Tests| |Codecov|
.. |PyPI| image:: https://img.shields.io/pypi/v/idtrack.svg
:target: https://pypi.org/project/idtrack/
:alt: PyPI
.. |Python Version| image:: https://img.shields.io/pypi/pyversions/idtrack
:tar... |
8be6e7e4e6259726fef27a9900e43a13aad225e4f8c02b6f02209a7b950dadc7 | Text | 4,573 | 116 | # Bi-component Modeling of CSF Transport Using Time-SLIP MRI
[](https://doi.org/10.5281/zenodo.17982328)
This repository contains MATLAB code for analyzing cerebrospinal fluid (CSF) transport dynamics using non-contrast Time–Spatial Labeling Inversion Pu... |
0491ad0fc58add059ad68cd982bbe544116b4c26d39e0739cfb2a65a32f80da7 | Text | 4,583 | 110 | # AI-TOD
[[Paper]](https://drive.google.com/file/d/1IiTp7gilwDCGr8QR_H9Covz8aVK7LXiI/view?usp=sharing) AI-TOD is a dataset for tiny object detection in aerial images.
[[Dataset]](https://github.com/jwwangchn/AI-TOD) Please download the [xView trainig set](http://xviewdataset.org/#dataset) and [AI-TOD_wo_xview](https... |
54ab35c2ca03716507d6990e96fa4ae8daa037e7054e873a575e3e4a502b3be9 | Text | 4,583 | 125 | # TF-MInDi: Transcription Factor Motifs and Instances Discovery
[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]
[badge-tests]: https://img.shields.io/github/actions/workflow/status/aertslab/TF-MInDi/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/tf-mindi
**TF-MInD... |
27a842bb591362ed0432fc1eb11e76ae16e64106255fb4428b4677cd85022aa4 | Text | 4,589 | 110 | # Reproducibility Archive
## An Integrated Matrix-Free Framework for Epidemic Threshold Analysis
**Author:** Etienne Kouokam | **ORCID:** 0000-0002-4064-0200
**Contact:** etienne.kouokam@facsciences-uy1.cm
**Affiliations:** University of Yaoundé I / IRD-UMMISCO, Sorbonne Université
**Journal target:** Mathematic... |
60b991ca63d2d5fc2078fd78d4d0f64fdb2654c076d263c7a8f600ad2e31f9ac | Text | 4,605 | 62 | # Modeling Attention and Binding in the Brain through Bidirectional Recurrent Gating
This is the code code repository for the paper [Modeling Attention and Binding in the Brain through Bidirectional Recurrent Gating](https://doi.org/10.1101/2024.09.09.612033)
](https://zenodo.org/badge/latestdoi/118142261)
[](https://github.com/tommyod/KDEpy/actions/workflows/test_master.yml)
[![Documentation Status](https://readthedocs.org/pro... |
67d5e76b37e38c0baa8d4882a4720653016f234535f1fdb621d4da763219ac4a | Text | 4,646 | 68 | # Chromosome-scale genome assembly of the European common cuttlefish *Sepia officinalis*
Code and analysis scripts accompanying the assembly, annotation, and downstream analyses of the *Sepia officinalis* genome.
## Citation
Rencken S, Tushev G, Hain D, Ciirdaeva E, Simakov O, Laurent G.
*Chromosome-scale genome ass... |
249fbc9d30cf62ac8d2d40c1c8aacd48284cef7fa63cd8557ea874e478eece3f | Text | 4,650 | 100 | # Activity Cliff Awareness
<a href="url"><img src="./doc/image/logo.png" align="left" height="130" width="140" ></a>
[](https://github.com/bidd-group/MPCD)
[](https://www.researchsquare.com/arti... |
64d47be01acf2274b7bc1a4f2eaa545f6009f2c0714e60973dbfb87b527af4bc | Text | 4,659 | 75 | [](https://github.com/scverse/scanpy/stargazers)
[](https://pypi.org/project/scanpy)
[](https://pepy.tech/project... |
8cbf2663f316589672224a19bd1d5dc8e4f9beee619eb5ad871a9daed02e9f46 | Text | 4,664 | 147 | # VIB + Attention for Inverse Design of High‑Hardness Metallic Multi‑Component Glasses
This repository contains the code and data used for the article **Attention-Enhanced Variational Learning for Physically Informed Design of Exceptionally hard Multicomponent Metallic Glasses** for designing exceptionally hard multi-... |
bc475208162e1843f74e62708edfaacad6d26dca8aa2e49a0316a18543ea3bcd | Text | 4,666 | 132 | 
EdgeVolution is a software-hardware end-to-end pipeline that allows to optimize preprocessing and neural network architectures for microcontrollers in an end-to-end fashion. It features different building blocks that can be customized individually.
# Getting... |
0932828228d22c59b89b5623616d05d33a68096657edcab67fad09f0e1d07148 | Text | 4,670 | 72 | # PMEmo: A Dataset For Music Emotion Computing
PMEmo is a popular music dataset with emotional annotations:
> Music Emotion Recognition (MER) has recently received considerable attention. To support the MER research which requires large music content libraries, we present the PMEmo dataset containing emotion annot... |
c9b6ea26bbc6bab4656fb541310313e28e320b8d4759f0e1802172a8b99c1544 | Text | 4,672 | 51 | # The ZETA-test repository
Repository containing ZETA-test functions and dependencies.
**Most up to date version is located at https://github.com/Herseninstituut/zetatest**
For an example of how to use the code, check runExampleZETA.m in the /example/ subfolder. Your output should look like the images in the same di... |
06e05b24834d566a210630e3cd6766164c57e48a2c441189bec1bcb5562f6e66 | Text | 4,676 | 109 | # SAMS - Semi-Automatic MEA Spike Sorting
A MATLAB-based pipeline for semi-automatic spike sorting and network burst analysis of multi-electrode array (MEA) recordings.
> **Note:** SAMS is currently developed and tested for **Windows only**. macOS/Linux support may be added in future versions.
## Features
- **Autom... |
e79e799193934871afbfda068f88101c01a3ce816b71452e345c681b21eab115 | Text | 4,686 | 53 | Deep Learning-Enabled Versatile Shape Perception for Soft Robots via Single-Ended Multimode Fiber
This is the official open-source repository for the data, code, and results corresponding to the three core modules in the Results section of the above paper. It fully supports the reproduction of all key experiments fo... |
e2e55888a02a9cd87ccffe1ea8e0acec2cc070e09d4946906da3a986e6e3759b | Text | 4,692 | 143 | # Evolutionary analysis of m6A RNA modification in mammals
This repository contains the main scripts used for the analyses presented in the manuscript:
**Evolutionary Landscape of m6A RNA Modification in Mammals**
The scripts include analyses for m6A site alignment, tissue- and species-level m6A modification compari... |
89151116f7469a8f9f8d5dda33c06acd0ecfa990768ba32855ae34d844b2b903 | Text | 4,695 | 98 | # DANT: Density-based Across-day Neuron Tracking
[](https://github.com/jiumao2/DANT)
[](https://dant.readthedocs.io/en/latest/)
**DANT** is a MATLAB toolbox designed for th... |
7a655429b4bc0c251294caf474085e632394d66ab018d8624b8d5f8679e0b375 | Text | 4,704 | 77 | # The effect of shape and illumination on material perception: model and applications
Code for Siggraph 2021 paper: The effect of shape and illumination on material perception: model and applications.
<div align="center">
# The effect of shape and illumination on material perception: model and applications
[](https://pypi.python.org/pypi/great_expectations)
[](https://pypi.org/project/great-expectations/#history)
[](ht... |
eacb1a03582298d5f0b664c058dbcfc6e09bbd7bdf5bb2a2e3edb2bac102bf43 | Text | 4,709 | 61 | # Interactions across hemispheres in prefrontal cortex reflect global cognitive processing
Data analysis and figure generation for the following reference:
- McDonnell, M.E.*, Umakantha, A.*, Williamson, R.C.*, Smith, M.A.†, & Yu, B. M.† Interactions across hemispheres in prefrontal cortex r... |
8658a4c62fe96065a5f7d8f470bac1dd014eb69dca527988f1d36c53498a4725 | Text | 4,716 | 108 | # TRPC4-TRPC5-are-critical-for-neuronal-modulation-of-tFUS-in-mouse-retrosplenial-cortex
Transcranial focused ultrasound (tFUS) non-invasively regulates neuronal activity, yet its underlying molecular mechanisms remain largely unknown. This study identifies TRPC4 and TRPC5 as critical mediators of tFUS-induced neuronal... |
babd77e6329832c14bcd2e8ec00e8a96b4ea378c119d3cd857483b2d11848bdf | Text | 4,728 | 103 | # Vision-Based Tactile Sensing Enhanced by Microstructures and Lightweight Convolutional Neural Network
---
**Authors and Affiliations** <br/>
Mayue Shi, Yongqi Zhang, Xiaotong Guo and Eric M. Yeatman<br/>
Department of Electrical and Electronic Engineering, Imperial College London, London, UK<br/>
College of Science... |
87b67ea8076bfb74b3275a8be650544248f46a3ee52e25dda7310e5898e08929 | Text | 4,739 | 102 | # DANT: Density-based Across-day Neuron Tracking
[](https://github.com/jiumao2/DANT)
[](https://dant.readthedocs.io/en/latest/)
<p align="center">
<img src="./Overview.pn... |
0b870cef46281ed356550d8cb41b9bcfd14b40b85fbd5e90d8507e0930cea139 | Text | 4,747 | 63 | # qMRI MSPM Age Fx
Overall the code in this repo was developed by Soodeh Moallemian and Christophe Phillips, to re-analyze "quantitative MRI" data from Martina F. Callaghan.
The code contains a series of scripts to generate the main results (not yet the figures though), described in our pre-print ([S. Moallemian et al... |
520a9ed72e54bd7fdd4c3f59671e753aeff153a12cfd99b68775313781b1bcca | Text | 4,749 | 34 | # Analysis-and-modeling-of-voltage-gated-sodium-channels-clusters
The Python code used in the manuscript: Tarasov et al. Clustering Dynamically Modulate the Biophysics of Voltage-Gated Sodium Channels: How Nanoscale Phenomena Determine Health and Disease. bioRxiv 2025.05.31.657169; doi: https://doi.org/10.1101/2025.05... |
e750d968bed944b69864949a8d739027e97b58e59e03571065b9dc81bf36ea5c | Text | 4,751 | 53 | # Tanybase - Combined and Curated Tanycyte Database
# Introduction
Tanycytes are ependymal-like glial cells that play a crucial role in regulating the neuroendocrine system, metabolism, and glucose homeostasis. Tanycytes lie in the wall of the third ventricle and coordinate various functions. Traditionally, tanycytes ... |
aa51047313bd08f8095b531758a65b87c0f1b2e8f2f853ffe9d819490dd4010b | Text | 4,752 | 107 | # Inferring Exon and Intron Annotations from Genome Feature Files (.gff)
## Overview
This pipeline extracts exon and intron metadata from .gff files using only coordinate information. It classifies exons into the following splicing categories:
- **Constitutively spliced exons** (always included in mRNA)
- **Skipped e... |
da6ef3e1df9b624a1517419c86d7e41ff73cd49082ed501d6d506863169eed45 | Text | 4,768 | 136 | # DaT Prediction with Contrastive Learning
This repository contains the implementation of our DaT prediction pipeline.
The code contains:
1. The preprocessing of the multispectral data
2. Training of the pipeline
3. Evaluation
The multispectral MRI data are available from the corresponding authors upon reason... |
32a1461c1a4c368205c19669d78e7bda7024f71373e9827c5e27157a89d3415f | Text | 4,779 | 109 | # AI-driven vibration-based event classification in railway switches and crossings
Code and extracted-feature dataset accompanying the paper:
> M. Adoul Amin, T. Najeh, A. Ghoul. *AI-driven vibration-based event classification
> in railway switches and crossings.* Scientific Reports (under review).
This repository c... |
e192fd06dcc994549f6b84a91b933fa68ee8f719410db986bc8d611473bd4b52 | Text | 4,779 | 36 | # Analysis-and-modeling-of-voltage-gated-sodium-channels-clusters
The Python code used in the manuscript: Tarasov et al. Clustering Dynamically Modulate the Biophysics of Voltage-Gated Sodium Channels: How Nanoscale Phenomena Determine Health and Disease. bioRxiv 2025.05.31.657169; doi: https://doi.org/10.1101/2025.05... |
e3f645b0fd2f745174228978e0a6a3d1fee7f945d503203784be36bc5b3b6e32 | Text | 4,779 | 112 | <div style="color:#0d6efd;">
<h1>Hybrid Multi-Objective Neural Architecture Search for Lightweight Patch-Based Mistletoe Classification in UAV Imagery.</h1>
</div>
<p>
This repository contains the data and workspace for testing a lightweight Convolutional Neural Network (CNN) model designed for mistletoe classific... |
63f8f2b35220036677fbdfad1cc1102820573d2fc8c9f5dc3a88df9476042fc6 | Text | 4,782 | 88 | <p align="center">
<img align="center" src="https://user-images.githubusercontent.com/693511/117350563-b58b9900-ae7a-11eb-83ce-9f5f9213145e.png" / width="25%">
<h1 align="center" fontsize="2em">d o t m o t i f</h1>
</p>
<p align="center">Find graph motifs using intuitive notation</p>
<p align="center">
<a href="ht... |
ed8c5503051ee9d0de2e87044b413028f5a5c9eda77b1c8daa6705f563457bbe | Text | 4,787 | 105 | # pseU_NN
The code for computational implementation of "Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species". A LSTM-transformer-GNN architecture that integrates RNA secondary structural features with sequence information to predict poten... |
65612b35b449f54fe1b0bcf6120cef94ddcd7ee191d998d4000cf5121554eef8 | Text | 4,790 | 100 | # HAPQ: A Hardware-Aware Pruning and Quantization Pipeline for Event-Based SNN Detection
[](https://opensource.org/licenses/MIT)
[](#)
This repository contains the official implementa... |
ad3fff7c41b65ffaf5a77d6ede0f13a9d56953992519b7d580d1b61a7adc5789 | Text | 4,797 | 143 | # harmonypy
[![PyPI][pb]][pypi] [![Downloads][db]][pypi] [![Tests][gb]][yml] [![DOI][zb]][zen]
[pb]: https://img.shields.io/pypi/v/harmonypy.svg
[pypi]: https://pypi.org/project/harmonypy/
[db]: https://img.shields.io/pypi/dm/harmonypy?label=downloads
[gb]: https://github.com/slowkow/harmonypy/actions/workflows/pytho... |
5029f6aea90f508b75aa5a2a5adb8e953a953fb606c1868541b361617b303b4e | Text | 4,805 | 161 | # 🐟 CryptoVision
Welcome to **CryptoVision**! This project focuses on building a hierarchical deep learning model to classify **cryptobenthic fishes** 🐠, a group of small reef fishes. Using transfer learning with various pre-trained models, the aim is to identify the **family, genus, and species** of these fishes wi... |
c2e6e1aae5570ba7470150133738289188197dc04882d323bd92b44399234457 | Text | 4,811 | 158 | # Thyroid Hormone Signaling in Ciona
Analysis code and data for thyroid hormone receptor dynamics during *Ciona* development.
## Repository Structure
```
thyroid_hormone_ciona/
├── code/
│ └── Files.qmd # Main analysis script
├── data/
│ ├── kallisto.merged.gene_counts_length_scaled.rds
│ └── Files.xl... |
d332373914d673e4966fab188afec48b3af277bc33734270cc52a3caac0e4530 | Text | 4,811 | 100 | MAXIM
=============================
MAXIM is a model-based analysis and pipeline of dCas9 Capture-3C-Seq data of multiplexed version. It uses multiplescale Bayesian models for the significance calling of chromatin interactions. It oprovides a versatile and flexible pipeline to analyze the dCas9 Capture-3C-Seq data V2.... |
6b9fc3d09583786c9e190613c19309b3e62631dd2198200e4ee6898d70f994cd | Text | 4,823 | 100 | # trashnet
Code (only for the convolutional neural network) and dataset for mine and [Mindy Yang](http://github.com/yangmindy4)'s final project for [Stanford's CS 229: Machine Learning class](http://cs229.stanford.edu). Our paper can be found [here](https://cs229.stanford.edu/proj2016/report/ThungYang-ClassificationOfT... |
b86d687eeda6689218f24c06745899f0ad918cf8b5a14cdec4c7d6680d0519c6 | Text | 4,824 | 221 | # Spiking Traffic Sign Recognition
This repository contains convolutional and directly trained spiking convolutional neural networks for traffic sign recognition on the German Traffic Sign Recognition Benchmark (GTSRB). The project includes training, evaluation, and inference energy estimation for CNN, SCNN, and SCNN ... |
e3fcd4bf2942bcb02a7c6d52ecc211cc934c79c929303db43b9b627030c958c4 | Text | 4,834 | 155 | # Federated Learning Framework for Medical Image Analysis with Perspective-Aware Contrastive and Mixture of Experts (FedPAC-ME)
This repository contains the official implementation of FedPAC-ME, a federated learning framework that integrates Multi-Perspective Contrastive Learning (MPCL) with a Mixture-of-Experts (ME) p... |
401425b85736083ebeed1161191ba6eb016f76191331aa9e539a9565f095bd7c | Text | 4,837 | 145 | # Evolutionary analysis of m6A RNA modification in mammals
[](https://doi.org/10.5281/zenodo.20085328)
This repository contains the main scripts used for the analyses presented in the manuscript:
**Evolutionary Landscape of m6A RNA Modification in Mammals**
The scripts ... |
79b789dad80e9fb671f9a0699858396d6978b1d1e076e0b109702684d6cd1d12 | Text | 4,839 | 157 | # calcifying-tendinopathy
**Artificial intelligence for detection of calcifying tendinopathy of the
rotator cuff (CTRC) on conventional shoulder radiographs.**
This repository contains the experimental pipeline (Jupyter notebooks)
used to develop, evaluate, and interpret AI models for **binary
classification of sh... |
bf09713986ad774cd15dc4fefa16d3e0c53fd0da9a6e6c8168e97a0bfc6aebfa | Text | 4,856 | 173 | # ConstrainedSmoothing
ConstrainedSmoothing (csmooth) performs anatomically informed smoothing of fMRIPrep preprocessed BOLD images using cortical surface + volume constraints.
## Quickstart
You only need Docker installed. The image `ellisdg/csmooth` will be pulled automatically if not present.
1. Create (or identi... |
79dc800f3074aaa7deb9e1b38b924312fbd48cb0976772afe3318733c3b041a5 | Text | 4,868 | 73 | # CNMF_E
Constrained Nonnegative Matrix Factorization for microEndoscopic data. 'E' also suggests 'extension'. It is built on top of [CNMF](https://github.com/epnev/ca_source_extraction) with supports to 1 photon data.
## Download
OPTION 1: download the package using this [LINK](https://github.com/zhoupc/CNMF_E/archi... |
b53e5283065d0a0ce60e704706daf04a1e7d45330b4df80f6fe795deeac8ea04 | Text | 4,875 | 104 | # Machine Learning in MatLab/Octave
> _For Python/Jupyter version of this repository please check [homemade-machine-learning](https://github.com/trekhleb/homemade-machine-learning) project._
This repository contains MatLab/Octave examples of popular machine learning algorithms with code examples and mathematics behi... |
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