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|---|---|---|---|---|
318822ed4f176f202ec90c184a4829ee153d955fbae62d86270f0331bb65a070 | Text | 1,393 | 17 | # NatMEG-PD data preparation
Scripts for preperation of data for The Swedish National Facility for Magnetoencephalography Parkinson's Disease Dataset (NatMEG-PD). The dataset was collected at the NatMEG facility (www.natmeg.se) at Karolinska Institutet, Stockholm, Sweden. The dataset is available through EBRAINS (www.... |
5648c1f8a5ade4e0617d0e656705526fa397c0bcb927eb9962160bbcb6067459 | Text | 1,401 | 39 | ## 2D Registration BrainAtlas ImageJ/Fiji
This is part of an on going project of Prof Rohini Kuner lab (Heidelberg University, Germany)
#### Short description
This tool has been developed to register 2D fluorescence image located in an input source directory containing subdirectories of images with brain atlas imag... |
4ef574532547a40ae4c6f70d575167003af93728afe2c1009789bc7ebe102a8c | Text | 1,404 | 72 | # SEEGFusion
Fuse a CT image with an MRI image from a Stereotactic ElectroEncephalography (SEEG).
This method is explained in the following article
[10.3390/diagnostics13223420](https://doi.org/10.3390/diagnostics13223420)
## Prerequisites
To use SEEGFusion, the followin... |
38a0a93c50472855014394d43eb864ea5c861e8623a91b1db4d32951c21425b4 | Text | 1,417 | 48 | # hicpileup
hicpileup uses [https://github.com/open2c/cooler] to plot the observed/expected HIC signal piled up around a BED file of features
## Dependencies
All dependencies to run the script can be downloaded using conda:
```
conda create -n pileupenv -c bioconda cooltools numpy cython bioframe
conda activate p... |
c9b89f2937990f6df739e6447b6598c7b2bd0790b7aae2bc6d75040f3e08cbf5 | Text | 1,429 | 25 | The most important programs are:
vsvectoEF.m: calculates the coefficients {E_n, F_n} in the cytoplasmic flow solution for a prescribed cortical flow v_s(zeta);
vfun_full.m: uses these {E_n, F_n} to compute to flow field (v_tau, v_zeta) and streamfunction psi at a given position (tau,zeta);
Auxiliary programs... |
ff43f0d09c2fc9329ee48a4041036d55f3cfe850c9cc09ce429d9666f85fd363 | Text | 1,429 | 54 | # Craniosource-GAN-PCA-SSM
## Overview
This is a repository to use a GAN, PCA, and statistical shape models to create
[craniosynostosis distance maps](https://github.com/KIT-IBT/cd-map), for
example for the classification of craniosynostosis on purely synthetic data.
## Requirem... |
8059503be0ac1f5a0b6c7558c30a5965d5c9ad2cad83c5161bd1709b51834705 | Text | 1,430 | 33 |
## Temporal Encoding for fNIRS-based BCI communication
The initial commit was made on **22.07.2023**
This repository contains scripts for analysis and figures of the paper **It takes two (seconds): Decreasing Encoding Time for Two-Choice FNIRS BCI Communication**.
Real-time analysis of encoded answers was pe... |
13d3ad86ed3370057ac282a11bfe3515899aa632c7ec6ed6732f52121afc9b5a | Text | 1,434 | 40 | # GSDensity_manuscript_code
Simulation scRNA-seq data with SERGIO:
sergio_steady_gen.R: generate SERGIO input file (steady state mode)
run_sergio_code.py: run SERGIO (steady state mode)
sergio_dyn_gen.R: generate SERGIO input file (dynamic state mode)
run_sergio_dyn.1.py: run SERGIO(dynamic mode only)
normalize_si... |
ba88ff02c8acb9d19430cf9f23761e67ac63be2e2d3b4690bf771adc48868bcf | Text | 1,435 | 17 | # pynapple-paper-2023
Notebooks of the analysis shown in the 2023 pynapple paper
## Examples of foundational analysis across various electrophysiological datasets using Pynapple.
<table><tr><td>
<img src="Figure4.png" />
</td></tr></table>
A) Analysis of an ensemble of head-direction cells. From left to right: ... |
f533a8fa78db2deb0c6e32046870cf44f4de51579c5c3ca82e1006bf1d45378a | Text | 1,451 | 56 | ========
stringdb
========
.. image:: https://img.shields.io/pypi/v/stringdb.svg
:target: https://pypi.python.org/pypi/stringdb
.. image:: https://api.travis-ci.com/gpp-rnd/stringdb.svg
:target: https://travis-ci.com/gpp-rnd/stringdb
.. image:: https://readthedocs.org/projects/stringdb/badge/?versio... |
a60cd652fcbbfff3e6c8913faff41e9150f9ecbf05f5836072c6caee98b43973 | Text | 1,460 | 37 | Part of the accompanying code repository to the "Hierarchical temporal prediction captures motion processing along the visual pathway" paper. This repo contains the code to perform the neural V1 fits.
## Installation
```bash
conda env create -f envs/environment.yml
conda env create -f envs/prednet.yml
```
## Clone co... |
5027205074fd0cc5708353ec87d86f6118932a942f334dabc28a53954eaf0fb1 | Text | 1,475 | 14 | # Temporal dynamics of normalization reweighting (code)
These materials are a computationally reproducible version of the paper:
Baker, D.H., Marinova, D., Aveyard, R., Hargreaves, L.J., Renton, A., Castellani, R., Hall, P., Harmens, M., Holroyd, G., Nicholson, B., Williams, E.L., Hobson, H.M. & Wade, A.R. (2023). T... |
f4215f3b4551a464aed519993247bfb19a23698748400d417c273bbd75dbac58 | Text | 1,477 | 19 | # Masuda et al, 2023
Masuda, F.K., Sun, Y., Aery Jones, E.A., Giocomo, L.M. (2023, February). [Ketamine evoked disruption of entorhinal and hippocampal spatial maps](https://www.biorxiv.org/content/10.1101/2023.02.05.527227v1). bioRxiv doi:10.1101/2023.02.05.527227.
### System Requirements
* This code has been tested ... |
952641a902eed1e23e55ef4e046bdc2e89081adde34d06293178fd96b874a24d | Text | 1,484 | 36 | # R package “pwr”
## Basic functions for power analysis
[](https://github.com/heliosdrm/pwr/actions/workflows/check-standard.yaml)
[](http:... |
26a1f4e835dc135655ac0b7cdd61baed5e5230c90d8caa8bc6254b8ff49f075a | Text | 1,491 | 33 | # Zero-Shot Multi Speaker GradTTS
This repository provides audio samples of Zero-Shot Grad-TTS.
### Audio Samples
The audio samples for Zero-Shot Grad-TTS can be found in [link](https://www.amclab.kr/demo/zero_shot_gradtts/).
### Comparison Dataset
For the comparison of synthesis performance for the Seen s... |
6856c1d233021d3674c8e94984920b9e0e9878dca5cc4c295cd1af187c879cf2 | Text | 1,491 | 17 | # MotionAnalyser
<img src ="https://github.com/BoullandLab/MotionAnalyser/assets/115705215/6e8ca692-5ad1-4fc5-8cc1-a34cdef4332c" width="70" style="float: left; margin-right: 15px">
**MotionAnalyser** is a GUI designed to facilitate the handling, preprocessing, and analysis of motion tracking data together with electro... |
3157a87b73a9362e2428e17532857689002201ab6b092246058f3fe6d80ba4c6 | Text | 1,493 | 32 | # PFC - Basal-ganglia network model
This repository contains code used to generate the neural network model figure from the [manuscript](https://www.biorxiv.org/content/10.1101/2021.06.25.449995v3):
> Blanco-Pozo, M., Akam, T., & Walton, M. (2023). **Dopamine-independent state inferen... |
2495efe939dd9eba09b3f5a72c606276365b5b8e96f05d19fafe74f1cffc9cb2 | Text | 1,494 | 30 | # The Role of Experience in Prioritizing Hippocampal Replay by Huelin Gorriz et al 2023
Code repository for "The Role of Experience in Prioritizing Hippocampal Replay". If you use this code in your research, please cite this paper.
### Prerequisites and installation
- MATLAB 2017a or newer (working on MATLAB 2021a an... |
9b4a22e36f4b53a8a0552f431c343c61713b759c23b221ad9bf54d839fd78222 | Text | 1,524 | 36 | # Trialhistory_lapses_EA
## Overview
This repository contains the code necessary for generating figures related to the manuscript titled "Trial-history biases in evidence accumulation can give rise to apparent lapses."
The associated data for this manuscript can be found at dx.doi.org/10.6084/m9.figshare.24113793
#... |
40ed8abf1d5ab4190bb7c8fb7e6fac177b85a57a931a573b39e1b571d10f519d | Text | 1,531 | 46 | # Number Sence using Multimodal VAE
This repository contains the code for "Emergence of Number Sense through the Integration of Multimodal Information." Please, see [paper](https://osf.io/preprints/psyarxiv/4bfam) for details.
The experiment code in this repository is based on "Variational Mixture-of-Experts Autoenco... |
0e8a9b775e057678209a242c626305b2a6b2e2ce96417ad8ee728c30f7d1d904 | Text | 1,538 | 29 | # Flexible modeling of neuroimaging data in R, point by point
<img src="docs/logo.jpg" alt="Neuropointillist logo" height="250"/>
# Overview
Note!!! [Documentation is hosted on github pages.](http://ibic.github.io/neuropointillist)
This project contains an in-development R package (called
`neuropointillist`) which ... |
115561836e12e107d6d2181cfb406f75f22f5835c5503c3f0c3e2d5dc64155ad | Text | 1,543 | 30 | <img src="./chroma.png" width="550px"></img>
<i>figure 1 in <a href="https://www.biorxiv.org/content/10.1101/2022.12.01.518682v1">paper</a></i>
<img src="./rfdiffusion.gif" width="450px"></img>
*generating a protein that binds to spike protein of coronavirus - Baker lab's concurrent RFDiffusion work*
## Chroma - Py... |
7976eec30f723382b0f85499bd51642a74a2cb46fd5bd66a1e33fe23bf0e2d29 | Text | 1,547 | 28 | This repository contains the source code of the following paper:
Imani, E., Radkani, S., Hashemi, A., Harati, A., Pourreza, H., & Goudarzi, M. M. (2023). Distributed coding of
evidence accumulation across the mouse brain using microcircuits with a diversity of timescales. eNeuro.
pipeline of the scripts:
dPCA analy... |
02254874d8a853645ac66729c9c6c3cfbfe941cfb98dc266f9b3efc3d2ab7b84 | Text | 1,549 | 22 | 
# CKD Molecular Stratification
This repository contains primary data analysis code accompanying the manuscript:
Anna Reznichenko, Viji Nair, Sean Eddy, Damian Fermin, Mark Tomilo, Timothy Slidel, Wenjun Ju, Ian Henry, Shawn S. Badal, Johnna... |
22ffe0910eebdefe23bb302d3db508a5a6ebcc77ff302292c2cf650abeded3dc | Text | 1,561 | 12 | # ET-Dopamine-manuscript
Data and code accompanying Science Advances manuscript "Sub-second fluctuations in extracellular dopamine encode reward and punishment prediction errors in humans"
Please note that users must alter the file paths in the scripts to match their local storage of this repository.
This code is rel... |
a0839b1ca5784e65816a5b0df26881f626c9b5cf8b4ded99d21e567e62d76fe3 | Text | 1,561 | 33 | # Modeling naturalistic face processing in humans with deep convolutional neural networks
## Overview
This repository contains a python implementation of the key analyses in the manuscript by Guo Jiahui<sup>†\*</sup>, Ma Feilong<sup>†\*</sup>, Matteo Visconti di Oleggio Castello, Samuel A. Nastase, James V. Haxby, & ... |
1a54ad35f9fe7cd9346ba900cb4a546f5480eb9fb0b9c6e6dbb30f64e2412b3d | Text | 1,563 | 41 | [](https://zenodo.org/badge/latestdoi/439061046)
# Background
This repository contains code for the paper found [here](https://doi.org/10.1093/brain/awad246), which used in silico analyses of publically available transcriptomic data to investigate the relationships betwee... |
857087c6fed971fa74c14df8438bdf2cbc0e1b085e7219d23166a57beffb3425 | Text | 1,567 | 20 | # BDanskin_SciAdv_2023
Code associated with the manuscript for Science Advances.
This repository contains code and processed data necessary to regenerate figures from:
> Danskin B.P. et al. Exponential history integration with diverse temporal scales in retrosplenial cortex supports hyperbolic behavior (2023). Unde... |
fddd79e5993d2945c9315d239f4632db38cc287d6a57ec52ee1ffa6a66f80ed0 | Text | 1,579 | 36 | [](https://zenodo.org/doi/10.5281/zenodo.10278287)
Data analysis repository for Kulkarni et al, [Age-associated changes in lineage composition of the enteric nervous system regulate gut health and disease](https://doi.org/10.7554/eLife.88051.1)
BioRxiv version of our [man... |
8faa55befa297af6425c9fc5c5fbc6da26f24dfb7edeafd80d5b6036de371a32 | Text | 1,590 | 35 | Status
======
This project is now discontinued.
Project DeepSpeech
==================
.. image:: https://readthedocs.org/projects/deepspeech/badge/?version=latest
:target: https://deepspeech.readthedocs.io/?badge=latest
:alt: Documentation
.. image:: https://github.com/mozilla/DeepSpeech/actions/workflows/ma... |
606102a9d8618806fa938fcfdd1be39decab785b6c8508aad1e88a341c41e459 | Text | 1,591 | 23 | # Masuda et al, 2023
[](https://doi.org/10.5281/zenodo.7903214)
Masuda, F.K., Sun, Y., Aery Jones, E.A., Giocomo, L.M. (2023, February). [Ketamine evoked disruption of entorhinal and hippocampal spatial maps](https://www.biorxiv.org/content/10.1101/... |
68489ff10dee7936585fd1721fada647fd45e53db0853b513fb32461eb19903c | Text | 1,596 | 42 | # Estimating person-specific neural correlates of mental rotation: A machine learning approach
This is the source code to reproduce the published analyses.
## Content
├── scripts # Source files
├── estimate_neural_correlates.py # Script to estimate neural correlates
├── require... |
769d02e2bac937760b12af16fdf3ff8748a876507e4a94bf0e29bdda2188ed2c | Text | 1,610 | 13 | # PostnatalMouseHypothalamus_SingleCellTranscriptome
This repository includes the codes used for the analysis of the postnatal hypothalamus of CRH-IRES-Cre mice that were sequenced using single nuclei RNA sequencing (snRNA-seq), by employing a retrograde nuConnect-seq approach. We investigate the properties of the hyp... |
344bd742832ff6c986ab1c1d7070c0a57146f26744caa00dfbf44e06d522fd62 | Text | 1,616 | 28 | ### DePTH: Deep learning Prediction of TCR-HLA association
---
[](https://www.python.org/downloads/release/python-390/)
DePTH is an open source software for sequence-based TCR (T cell receptor) and HLA (Human Leukocyte Antigen) association prediction.
... |
f02817176f11d28a956b4445815fefa953b6e71536682d70bd360ad7e7d31745 | Text | 1,618 | 24 | # Semi-2DCAE
Under the "data" directory, we have provided a link to the raw dataset used in this paper.
Furthermore, under the root directory, we have included our training and testing programs.
1 Purpose:
"train.py": This script is used to train the Semi-2DCAE model on the ISCX-VPN2016 dataset.
"test.py": The test sc... |
4d266a47bf4d4581c1624bf2c7cff724e7573b0b0f9d96704d3c90513c613bfa | Text | 1,626 | 34 | find_denovo
===========
A simple tool for identifying *de novo* variants from a VCF/BCF file.
### Installation
```
git clone git://github.com/DonFreed/find_denovo.git
cd find_denovo
make HTSDIR=/path/to/htslib/
```
### Usage
```
find_denovo [options] [-O <v|z|b|u>] [-i <in.vcf|in.vcf.gz|in.bcf>] -p in.ped [-o <out.v... |
cdd059ed93f09e4873999eb8ac5bd2c5598ee17c57767ec5068e53fcc1e1d4ab | Text | 1,633 | 38 | # Trialhistory_lapses_EA
[](https://doi.org/10.5281/zenodo.10161052)
## Overview
This repository contains the code necessary for generating figures related to the manuscript titled "Trial-history biases in evidence accumulation can give rise to apparent... |
11958fc5fc3a1380f9d75986820beced0582f836e96f3fade43167e2d9800428 | Text | 1,635 | 29 | ## Resolving inter-regional communication capacity in the human connectome
This repository contains code written in support of the work presented in
[Resolving inter-regional communication capacity in the human connectome](https://www.biorxiv.org/content/10.1101/2022.09.28.509962v1),
as well as data necessary to rep... |
1f2de14735b1ee9d3a342fa7c5d5e87b95727276c0a56c8a9d77221f37880602 | Text | 1,639 | 53 | <div align="center"><img src="https://raw.githubusercontent.com/pallets/flask/refs/heads/stable/docs/_static/flask-name.svg" alt="" height="150"></div>
# Flask
Flask is a lightweight [WSGI] web application framework. It is designed
to make getting started quick and easy, with the ability to scale up to
complex applic... |
609f0d547d875a2453d4ceea227f8e5879d412ddd62e26e809550027b4e5d701 | Text | 1,642 | 29 | ## Repository for Cancer Disease Response Inference
This repository contains code implementation of experiments in the paper **Inferring cancer disease response from radiology reports using large language models with data augmentation and prompting**. [[JAMIA](https://doi.org/10.1093/jamia/ocad133)]
### Experiment of... |
d83285e5ca399d5b9181973d720c2ec6f80a2c1ce598001be9a4610defb69f24 | Text | 1,648 | 38 | # Code repository for locus coeruleus (LC) data analyses
This repository contains code scripts to reproduce analyses and figures in our manuscript:
- Weber and Divecha et al. (2023), *The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics.* [eLife ... |
2054b98c31af3d1fef74503c82c3aaa3eb7f2fbfef70ca8cbbdf3c9fc77f7f74 | Text | 1,649 | 53 | # Installation guide
1. Download and unzip [Celeb-A.zip - Aligned&Cropped Images](http://mmlab.ie.cuhk.edu.hk/projects/CelebA.html) dataset to ```data/```
1. Install PyTorch - https://pytorch.org/get-started/locally
2. Install dependencies
```
pip install tqdm scikit-learn pandas seaborn scikit-image
```
3. Setup di... |
7b3f28aa2a628fd47bf32422bde640c12995297b1678bd3afa6c429e83ae2542 | Text | 1,650 | 44 | # DeepMID
Nuclear magnetic resonance (NMR) is an unbiased, reproducible, and non-destructive detection method widely used to analyze and characterize complex systems. However, it is challenging to perform mixture identification because of the offset and peak overlap of chemical shifts that often exist in mixtures. Con... |
207d5a56effc41b281cd18fe5e35b1504a68e32f8e5bae633a21baa4c69bc0f0 | Text | 1,653 | 9 | ## Goldfish_Telencephalon_scRNAseq: This repository contains MATLAB files for diffrent processing and analysis tasks that were built and customized for the “A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types” article by Muhammad Tibi and Stav Biton et. a... |
d2769f84f2555555a22be9dfc81cd02ef9fac03023b95926e0886e232c5c4f5f | Text | 1,672 | 16 | # Domain-adaptation-DOA-prediction
A Deep Learning Framework for Anesthesia Depth Prediction from Drug Infusion History
Abstract:
In target-controlled infusion (TCI) of propofol and remifentanil intravenous anesthesia, accurate prediction of the depth of anesthesia (DOA) is very challenging. Patients with different phy... |
64736dea2ed6d7b3d245a5874be20c52c44f4c97e3328417705f22a318258de2 | Text | 1,674 | 57 | [](https://github.com/ipa/pymc-survival/actions/workflows/python-package.yml)
# PyMC Survival
## Overview
PyMC Survival is a collection of Bayesian parametric survival models written in Python using the scikit-learn... |
20ad1464c124fbf6cb977a76f98f8bf0b34a457bea138d2c504b334105c3b9b1 | Text | 1,683 | 41 | # SonoNet weights
This repository contains pretrained weights and model descriptions for all of
the SonoNet variations described in our recent submission:
Baumgartner et al., ["Real-Time Detection and Localisation of Fetal Standard Scan Planes in 2D
Freehand Ultrasound"](https://arxiv.org/abs/1612.05601), arXiv prepr... |
2a4ee923c1169ae33adb84520f36b5dcc33fa5636d26a4db1d157b9b0045a6a4 | Text | 1,692 | 35 | # TcellsInBrain
Data/HeathLabData.xlsx contains data from Ghazanfari 2021.
Data from Harris 2012 is are freely available from Dr. Harris on request.
The provided bash files provide the commands and sequence used for this project. Use as examples.
Note: Data to be used with scripts is to be in the following format... |
17b4d0ccf6111b4074dba72ad80fcb0e6b254409737c6e7720fc1c7e4d6cbb0f | Text | 1,699 | 16 | # Welcome to the Open Toolbox for Behavioral Research (OTBR)
Our toolbox helps scientists to take care of their experiments without worrying too much about the technical implementation of the tools. In addition to the help provided by our tools, our toolbox also offers the possibility of graphical representation, which... |
4b97f3430616dd44ee351379b2ebb3b94c938d25c795c9065257601ac282da35 | Text | 1,699 | 21 | This repository and the folders therein contain the code and data required to reproduce the figures that illustrate data and results in the manuscript by Petousakis et al., 2023.
The manuscript has been accepted and published in eLife: https://elifesciences.org/articles/91627
The reproduction of the figures requires A... |
efd14f624d1610909caebcc6ec662652791b3a1de8d0cb342258d5b9141a44a9 | Text | 1,705 | 31 | # EEG microstate analysis
[](https://zenodo.org/badge/latestdoi/90614948)
Python 2.7.x module containing functions to perform EEG microstate decomposition and information-theoretic analysis.
Based on the publications:
[1] von Wegner F, Tagliazucchi E, Laufs H. Information-theoretical anal... |
2ca9b655ab02ce2277dcd609de163d38e387d191f6e30230fafcf37fc6178618 | Text | 1,708 | 56 | Aligner
=======
### What it does well
**Stitches together any mode of serial section image data:**
- TEM
- Block-face SEM
- Fluorescence Array Tomography
**Fast and scalable:**
- Runs on linux cluster using Sun Grid Engine API
- Align 2 to billions of images
- Approx. linear time/volume & mem/volume scaling
- Two ... |
939ff544531935a5a487bf4448165aef774da7137ae227875cc01e59824a0120 | Text | 1,708 | 42 | [](https://doi.org/10.5281/zenodo.6821322)
# BISS - Bio image segmentation service
This software performs the segmentation of blood vessels in MRI-Volumes of mural brains.
A combination of a neuronal net (UNet) and various image processing steps is used... |
37275f6c78071808852c091add0da6140e96bd089b7d905d38088125ed449edb | Text | 1,709 | 5 | Data and analysis for Taylor et al. (in prep): *Molecular signatures of alternative fitness strategies in a facultatively social hover wasp*. Analyses are collated into a single R markdown file, *LF_2020.Rmd*. Note that this file also contains a number of ancillary analyses which appeared in my PhD thesis but which are... |
f303da04c59211249b60bfa50d76c8a1f52ae141faabcf270b003467303d4215 | Text | 1,709 | 21 | KrausData : .mat files containing the data from each of the trials
AnalyzeAllData.m : matlab function running analysis of all session and creates 'AnalyzedData.mat'
RunAllSessionsTimeVsDistance.m : matlab script running the analysis of all trials (called from AnalyzedAllData.m)
NeuronFiringTimeVsDistance.m : matl... |
73b53fd2c50cd3a82e87e221eb3097228aae2d9029df9826f7cdc9f8eb0cf060 | Text | 1,712 | 43 | # Deep learning reduces data requirements and allows real-time measurements in Imaging Fluorescence Correlation Spectroscopy
This repository contains the training code of FCSNet and ImFCSNet models.
## Create the conda environment
Create a conda environment called *tf25_gpu* with the *environment.yml* file. The envir... |
77c56238f54309ff029bb738161b37ad9daaa54b813c6c5afa9af95ef568308d | Text | 1,717 | 16 | # Comparing machine learning approaches for Danish Trauma Care
Code accompanying by study: "Assessing optimal methods for transferring machine learning models to low-volume and imbalanced clinical datasets: experiences from predicting outcomes of Danish trauma patients" available at:
https://www.frontiersin.org/journa... |
fda5cefccb52aeddf287a9ce24a9bfb3e5cad748542958915c5d4fab969927f3 | Text | 1,720 | 27 | # Phys_Seg
Physics-informed segmentation algorithm packaged in an easy-to-use fashion. This software is based on the following publications:
Borges, P., Sudre, C., Varsavsky, T., Thomas, D., Drobnjak, I., Ourselin, S., Car-doso, M.J.: Physics-informed brain MRI segmentation. Lecture Notes in ComputerScience11827 LNCS... |
f66219f4ce9982bfccc95616256f96ab0b98887d2f90067e29e4dad706a01dda | Text | 1,728 | 19 | # Research Template
[](http://ethoscope.readthedocs.org/en/latest/?badge=latest)
[](http://ethoscope.readthedocs.org/en/dev/?badge=dev)
Ethoscope
============
This ... |
386730317275fb0832f634833301151c65c9bf35844758dc53365fd708fbac80 | Text | 1,740 | 37 | This dataset belongs to the following publication:
Interaction of human keratinocytes and nerve fiber terminals at the neuro-cutaneous unit
Christoph Erbacher, Sebastian Britz, Philine Dinkel, Thomas Klein, Markus Sauer, Christian Stigloher, Nurcan Üçeyler
FILE OVERVIEW
1. List of provided files:
model ... |
dc7dc55c3e011f364175f69742d2cd03139bd2dbfa51ea6963c48cc90e89649a | Text | 1,740 | 50 | |BMicro|
========
|PyPI Version| |Build Status Unix| |Coverage Status| |Docs Status|
This is a Python library for the post-measurement analysis of
Brillouin microscopy data.
Documentation
-------------
The documentation, including the code reference and examples, is available at
`bmicro.readthedocs.io <https://bmi... |
61126b1d0c801ba6c0aa9cca989fa6ffad4277c1b413d72e4ded6fd4aa9d4f1e | Text | 1,742 | 42 | *This repository is passively maintained: issues will be addressed -- especially if they come with a suggested solution -- but there is no active updates to the data or code. Contributions are welcome.*
# Machine Learning's CO2 Impact
Checkout the [**online GPU emissions calculator**](https://mlco2.github.io/impact)!... |
69ce8a1edf83d4c42cd8595870610096bd0828d6767f1df36dff2c55ea1bda21 | Text | 1,745 | 32 | [](https://travis-ci.org/NREL/nfp)
[](https://badge.fury.io/py/nfp)
[](https://zenodo.org/badge/latestdoi/158466097)
# Neural fingerprint (nfp)
Keras layers f... |
bbfcad7537286dc21b44efabc66880b9dfe0cdd66e1dd9dbf31167abb0bf5a91 | Text | 1,750 | 25 | # Eelbrain
[](https://zenodo.org/badge/latestdoi/3651023)
[](https://github.com/christianbrodbeck/Eelbrain/wiki/Installing)
| Stable | Pre-release |
| ------ | ----------- |... |
7975b158b2a1ed132d1e0049395b4b774499c94cd7318451325ddbb275c08815 | Text | 1,753 | 19 | # MetaRL-PRL
A demo code to train a Meta-RL network in a probabilistic reversal learning task (dynamic foraging task). The code trains a recurrent neural network using the method proposed in [Wang et al., arXiv, 2016]. The network updates its synaptic weights using advantage actor critic (A2C) algorithm across training... |
6107fe62743ee8c46b4f666bdca6e07f292b5c0180975260803b029817cff1ee | Text | 1,771 | 40 | i3S Annotated Datasets on Digital Pathology
WELCOME
In an effort to contribute and push forward the field of Digital Pathology, Ipatimup and INEB, two major research institutions in Portugal, have joined forces in the construction of histology datasets to support grand Challenges on automatic classification o... |
ec16b04755fb9765c72eb84d49dd729a25e1647b6f3d7b5aa877cb693683b114 | Text | 1,772 | 30 | # interpretable-splicing-model
Scripts for preprocessing and training the interpretable splicing model.
# Installation
No special hardware or GPU is required. A recent version of Python is required (version 3.8 tested). The following packages should be installed using "pip install", preferably under a virtual enviro... |
4c32f1a0e2034fdf74cdc464be41703a658ae6e71fa9441f7640e25271d3f94e | Text | 1,781 | 60 | # LN Metastasis Prediction using Deep Learning
Lymph node metastasis prediction from ultrasound images using deep learning
If you use this code in your research, consider citing:
```
@article{
title={xxxx},
author={xxxx},
journal={xxxx},
year={xxxx},
publisher={xxxx}
}
```
## Prerequisites
- Ubuntu 18.04 ... |
3b86d2d814284561e4db9039c852a5f72664f168cf15f8e42448230ede673446 | Text | 1,795 | 32 | # STAGATE
[](https://zenodo.org/badge/latestdoi/398185411)
## News
2022.03.05 STAGATE based on pyG (PyTorch Geometric) framework is availble at [STAGATE_pyG](https://github.com/QIFEIDKN/STAGATE_pyG).
... |
f16f3b9164e5989cea269ada95880cb9087daf1aad8122a8f651858c2ed1d540 | Text | 1,796 | 39 | # Self versus Change (versus Y) = SvCvY
This task is a generalizable implementation of the self versus change task used in the DSN lab. Users respond 'Yes' or 'No' to a series of words.
In the default task, they are asked to judge whether a word describes them (Yes or No), and in other blocks, whether the word descri... |
39541b3be49612fb3947b8777434ab396be39c5bef2755286847b449ff748b1e | Text | 1,799 | 19 | # MetaRL-PRL
A demo code to train a Meta-RL network in a probabilistic reversal learning task (dynamic foraging task). The code trains a recurrent neural network using the method proposed in [Wang et al., arXiv, 2016]. The network updates its synaptic weights using advantage actor critic (A2C) algorithm across training... |
5feb2255ee426b93d317c4fc88ef8bfd6e83f2c08379a25d566087ff5513c826 | Text | 1,809 | 48 | # Demo of CRF code used in:
#### Identification of Pattern Completion Neurons in Neuronal Ensembles using Probabilistic Graphical Models
#### Luis Carrillo-Reid^, Neurobiology Institute UNAM
#### Shuting Han^, Columbia University
#### Darik O'Neil^, Columbia University
#### Ekaterina Taralova, Columbia University
####... |
0798d9866b211f9b2eb51899526c8e3f0416a8d8bcd83e343524135158bd4cb8 | Text | 1,814 | 43 | # Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity
The `notebooks` folder contains a jupyter notebook that downloads all calcium-dependent fluorescence traces used in the paper and generates the data panels of figures 3 to 5.
### Colab
The notebook contains code t... |
43a0fa0abf2df4765e2d75636d72c210c7a4789a463438eb3b408367ad28e06e | Text | 1,819 | 51 | # axtToSyn
Detect synteny blocks and synteny breakpoints from pairwise genome alignment file.
axtToSyn.py is a python script that performs synteny block detection using a pairwise genome alignment fileq (.axt format) output by the UCSC pairwise genome alignment pipeline our [lastz-pipeline](https://github.com/carbone... |
96a976c8119ab2a997c57ae69f884268c26a030468667cafca3dfe1a4c5005ec | Text | 1,827 | 37 | This repository contains the Granger Causality (GC) and Synchrony analysis scripts and codes for the results reported in:
Time-dependent homeostatic mechanisms underlie Brain-Derived Neurotrophic Factor action on neural circuitry
K. M. O'Neill, E. D. Anderson, S. Mukherjee, S. Gandu, S. A. McEwan, A. Omelchenko, A... |
0e47362ec87041a918ba562cbef5ec459f2a1142e48bf3ff4140069cd9d3359b | Text | 1,829 | 16 | ## Code for "Interpretable Spatial IDentity Neural Network-based Epidemic Prediction"
### Abstact
Focusing on epidemic infectious number forecasting, in this paper, we streamlines the well-known Spatio-Temporal IDentity model (STID) and retains the optional spatial identity matrix for learning the contagion relations... |
0532b78a0c69bd14ac0412296d2c4eebea132620c9ff5b3ad503af493524c592 | Text | 1,830 | 28 | # Code for _A Synaptic Corollary Discharge Signal Suppresses Midbrain Visual Processing During Saccade-Like Locomotion_ by Ali, Lischka, Preuss, Trivedi, Bollmann 2023
This repository contains calcium signal detection code used for Ali, Lischka et al. 2023. The corresponding author is [Johann H. Bollmann](http://bollm... |
cf5b3a5b17e6a9fa3fbf2258291b2d108073ecc6a7ad0490f5812591c4ccc6ea | Text | 1,835 | 36 | # Differentiable Rotamer Sampling with Molecular Force Fields #
## Congzhou M Sha, Jian Wang, Nikolay V Dokholyan ##
Copyright 2023.
Permissions for usage and reproducing this work are found in LICENSE.
We implemented differentiable rotamer sampling (RotamerSampler.py, RotamerSamplerParallel.py) as well as the AMBER... |
fa65523bc91d5493709bc9bc8a8e79fdb8a7588665deed39c6fd98e72c3ffa08 | Text | 1,841 | 68 | |pypi| |docs| |coverage|
===========
ome-zarr-py
===========
Tools for multi-resolution images stored in Zarr filesets, according to the `OME NGFF spec`_.
See `Documentation <https://ome-zarr.readthedocs.io/>`_ for usage information.
Documentation
-------------
Documentation will be automatically built with `readt... |
8aec34d103d20372ade6835f54612b7ed6017d9fb99456045575615ec66fa2f0 | Text | 1,845 | 16 | # CamCAN-dMRI-study
This repository contains the code used for the following research paper:
Henriques, RN, Henson, R, Cam-CAN, Correia, MM. Unique information from common diffusion MRI models about white-matter differences across the human adult lifespan. 2023 (currently under revision)
# Content
- Folder "proces... |
f1313cd7c3572d604c05eb0a4591e2fc6c4a35ffaddd46ea29dc2d4d47316f18 | Text | 1,850 | 41 | # ORION
Here you can find the code for the BMVC 2017 version of "Orientation-boosted Voxel Nets for 3D Object Recognition", a.k.a ORION.
If you use this code for research please cite:
@InProceedings{SZB17a,
author ... |
cedd195adbe8dc464cb37a6959aee7837392eec345ea7959f449a48d7cc42855 | Text | 1,852 | 53 | # CMKN
Implementation of the Convolutional Motif Kernel Network (CMKN). This method allows to build neural network models that
incorporate learning within the reproducing kernel Hilbert space (RKHS) of the position-aware motif kernel into simple
end-to-end learning. This approach results in artificial neural networks... |
cc442367224719e34b99e84f0885cb5ae1caa79c78629e36e4d177ec2447114d | Text | 1,853 | 32 | [](https://doi.org/10.5281/zenodo.8380003)
# Neural functional theory for inhomogeneous fluids: Fundamentals and applications
This repository contains code, data sets and models corresponding to the following publication:
**Neural functional theory for ... |
21db20a46a073e3179d8c63d2e03eb9865c8ca2b26d45263b68186342fda27bc | Text | 1,860 | 36 | # PFC - Basal-ganglia network model
[](https://zenodo.org/doi/10.5281/zenodo.10079814)
This repository contains code used to generate the neural network model figure from the [manuscript](https://www.nature.com/articles/s41593-023-01542-x):... |
a0dc36e4307bf38b840df642c2aca077cfbe19dccd9e7fd4d916be14ed2a20fb | Text | 1,870 | 30 | # Domain adaptive neural networks for population genetic inference
This repository contains code to implement the domain adaptation framework for population genetic inference using TensorFlow as proposed in:
> Mo Z, Siepel A. 2023. Domain-adaptive neural networks improve supervised machine learning based on simulated... |
f674e7f2fd8a18b8aacf093c65c8f680fe9a407dd23386df4593e474f249c567 | Text | 1,875 | 17 | # Deep Embedded Clustering
This package implements the algorithm described in paper "Unsupervised Deep Embedding for Clustering Analysis". It depends on opencv, numpy, scipy and Caffe.
This implementation is intended for reproducing the results in the paper. If you only want to try the algorithm and find caffe too di... |
28e6eb0bbf121a518d26c46acc276cd4da19ad57893fa7923bae106688421287 | Text | 1,878 | 29 | # Multimap targeted free energy estimation
This is a repository including code and input files to reproduce the work of the paper:
Andrea Rizzi, Paolo Carloni, Michele Parrinello. *Free energies at QM accuracy from force fields via multimap targeted estimation*. PNAS [DOI: 10.1073/pnas.2304308120](https://www.pnas.or... |
1c76e9323db52d41a627c74c9fe69061d3d2ae9fd01e03ec40b39dbf0105e7d0 | Text | 1,884 | 27 | > ***Trajectories through semantic spaces in schizophrenia and the relationship to ripple bursts***
>
> **PNAS**, October 2023
>
> **Matthew M Nour**, Daniel C McNamee, Yunzhe Liu, Raymond J Dolan
matthew.nour@psych.ox.ac.uk
# Main scripts
To reproduce paper results (within tolerance of stochastic procedures like agg... |
189b1326556b5dcda5935bbb6b6e638848644e52f2496da5db2263c684c50812 | Text | 1,886 | 58 | # DeepCID
Raman spectra contain abundant information from molecules but are difficult to analyze, especially for the mixtures. Deep-Learning-Based Components Identification for Raman Spectroscopy (DeepCID) has been proposed for the problem of components identification. Convolution Neural Network (CNN) models have been ... |
a605a4bb3939ef81d2908108757907f5600f66a4d4cd8c5f478100cbf63d32b8 | Text | 1,892 | 55 | ============================================
Topographic axonal projection at single-cell precision
supports local retinotopy in the mouse superior colliculus
Dmitry Molotkov, Leiron Ferrarese, Tom Boissonnet, Hiroki Asari
asari@embl.it
2023-Sep-15
============================================
This zip fil... |
491ffc5456df341de6c82d11d326bc31cb656bda95f52863832bf722b635741b | Text | 1,898 | 20 | Data repository for "Immediate neural impact and incomplete compensation after semantic hub disconnection"
Abstract: The human brain extracts meaning using an extensive neural system for semantic knowledge.
Whether broadly distributed systems depend on or can compensate after losing a highly interconnected hub is ... |
c63a9a1fd2033362133e26207c6ae1ebfc509a3555a903759f111bfbfb454512 | Text | 1,899 | 38 | <p align="center"><img width=300 src="https://bdd100k.com/images/bdd100k-logo.svg" /></p>
---
BDD100K is a diverse driving dataset for heterogeneous multitask learning.
[**Homepage**](https://www.bdd100k.com/) |
[**Paper**](https://arxiv.org/abs/1805.04687) |
[**Doc**](https://doc.bdd100k.com) |
[**Questions**](http... |
755f3fe311768951f9626eeb85873b4437bad1e1449fee25368aa1e38022992e | Text | 1,912 | 25 | # MEG-MASC: a high-quality magneto-encephalography dataset for evaluating natural speech processing.
Laura Gwilliams, Graham Flick, Alec Marantz, Liina Pylkkänen, David Poeppel, Jean-Rémi King
- [Paper](https://arxiv.org/abs/2208.11488)
- [Data](https://osf.io/ag3kj/)
- [Code](https://github.com/kingjr/meg-masc)
## ... |
249e99054c2b4e6ce1e327cdf46d12d302c95c0cefc71623a590329407660aad | Text | 1,914 | 69 | # Code for the paper Predicting enzymatic function of protein sequences with attention
## How to use it
1- First clone this repository:
```
git clone git@gitlab.inria.fr:nbuton/tfpc.git
```
2 (optional)- Install python3.7 if you don't have this python version (Maybe other version are possible but not tested):
```
... |
08e22bcafc14796c25703f9559d1b7ff993a46436530b2c9151f1e9286645e03 | Text | 1,925 | 34 | # Automated-RGS
Automated-RGS is a machine learning approach for the Rat Grimace Scale (RGS). Currently machine learning approaches exist for the capturing of rodent facial images and the grading for the Mouse Grimace Scale (MGS). However, depsite their widespread useage in pain research, no current systems have been d... |
b904c73553693728687ceaaeacc06c80007b366ff1b4232295f62080313b5fef | Text | 1,928 | 60 | # clustering
Python GUI scripts for molecular trajectory clustering analysis.
### Files
* nastic_gui.py: cluster using R-tree based spatio-temporal indexing of trajectory bounding boxes
* nastic2c_gui.py: two color version of nastic
* segnastic_gui.py: cluster using R-tree based spatio-temporal indexing of all traje... |
8e6bd699e0c25a787907da6f4891a23d7a563ac220508bac0fd411b1825dbc27 | Text | 1,937 | 53 | =====
Pysam
=====
|build-status| |docs|
Pysam is a python module for reading and manipulating files in the
SAM/BAM format. The SAM/BAM format is a way to store efficiently large
numbers of alignments (`Li 2009`_), such as those routinely created by
next-generation sequencing methods.
Pysam is a lightweight wrapper o... |
0a8a788ae63e84a38e21c52924daf25be138bfefe7291fc3b69f274afd5e30d8 | Text | 1,956 | 7 | # Xception_ornithopod
PLOS ONE: Classification of large ornithopod dinosaur footprints using Xception transfer learning
The trained data is downloadable from **https://doi.org/10.5281/zenodo.10056871**
## Abstract
Large ornithopod dinosaur footprints have been confirmed on all continents except Antarctica since the ... |
4a9e29c6ac72d3a0613b414483f3b169a2b590c3bac4b40400ed28ab94a3c50a | Text | 1,962 | 37 | # HorovodPINNs
Data-based parallel acceleration for physics-informed neural networks (PINNs) via Horovod. Its code comes with the preprint entitled:
$h$-analysis and data-parallel physics-informed neural networks, P. Escapil-Inchauspé and G. A. Ruz.
We apply data-based Horovod acceleration to pioneer [PINNs](https:/... |
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