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0b225e1b6f1fd1ad45169bb0f9971e224cdc0b649137fcd8f24e9440a6c70344 | Text | 85 | 2 | # MLCD
Codes used to create ANN-based machines to predict properties for Carbon Dots
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731daffaa17f3ba0311dcdad36e0b5898aae591c4ed233c0e69f22c2bbcbc315 | Text | 92 | 3 | meta_models
=======================
Python package with common meta-models building blocks.
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dd163e3a1b97e7a7fe59a6d3f4b431c8196f2b24742743a90ec2b88cc3a3a126 | Text | 92 | 2 | # egly-driver-network
Code for https://www.biorxiv.org/content/10.1101/2021.02.18.431872v2.
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b09bd8da21997c1d6d32d176e4f0926a3b079ddb2c5a9e0ac02b2f1cff2504fc | Text | 98 | 2 | # BiologicalImageProcessing
Repository for biological image processing and analysis using Matlab
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d41d60b835c97a0fd202501338bb82ac1796d0cdb896f2c90096210af64d821d | Text | 100 | 2 | # Adult_WM_vs_GM_hGPC_2020
Analysis of white and grey matter tissue and GPCs from adult human brain
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88f23578539b73f394a46b22090350693072e33f0a7f99b4ea1ef9c6f2201021 | Text | 109 | 5 | # Wang2022Data
Data and example analysis code for Wang NComm 2022
See explanation of files in Read_me.txt.
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1555e8da00bc2e3f32b285599816e1fb41f8c786236afe5ecaac8424a0ffe6f2 | Text | 113 | 2 | # multistep_replay
Example scripts for analysis of the MEG 'multistep' data from Wimmer, Liu, McNamee, and Dolan
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1d0ecb364c53922a817716e465ff71729b6a1f9b296dbf2bdf72692cf6505f6f | Text | 115 | 3 | # ICuRuS
genes.fpkm_tracking: gene level FPKM of D1 and D2; the original data come from Kronman, H. et al., 2019.
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4511d14ff195ebc758593a88c50bb83a3d099cfb591eebccccbb3a485c252042 | Text | 118 | 2 | # fMRI_QC
Code (MATLAB and Python) to QC preprocessed + postprocessed fMRI scans for functional connectivity analyses
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70ad3e6d8305f99b251d376187b86f87a8d6ceb3bb6c6745ec677a0b8242da76 | Text | 139 | 2 | # fMRI_connectivity_processing
Code for processing resting state fMRI data, using SPM and BioImageSuite, for connectivity/network studies.
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b9c02cf1c1317dc01d8e179c4e16ff5c2c358739c43763e675720f3ee8e859c6 | Text | 150 | 2 | # warfarin_prediction_kscpt_tutorial
Machine learning dose prediction tutorial for Korean Society for Clinical Pharmacology and Therapeutics (KSCPT)
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fb4546efc6ae883fbdf72cb69b0bbd4fc9a08d40f04230877f4ebbe05d3a24d2 | Text | 171 | 4 | # GSFSF
A New Decoding Approach with Goal Selection and Feedback for Solving Math Word Problems
Dataset Ape210k can be downloaed in https://github.com/Chenny0808/ape210k
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c8752b64bfccbf1d0b8f6b37b201022a37c77117ee8e943784b996c3a1777f38 | Text | 175 | 4 | # MageeLab-Public
MageeLab-Public.
The files contained within are data, figures, and associated analysis code found in publications from the Laboratory of Jeffrey C. Magee.
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b5c695a9cfab39819380c5d3e75e2bb0504b4c043e2fa3d8f22bdf7c8958a61a | Text | 178 | 3 | # SMARTPHONES-AND-COGNITIVE-CONTROL
Data, protocol, and other study info to promote scientific transparency
Includes behavioral and ERP data sets and R scripts for data analysis
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4346dd895a95facd604e2a4d4b0fb3e70203c73cdd09da1e01c2263bc4f91bc7 | Text | 181 | 9 | # EpiNano
Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads
##
This repository is now located here: https://github.com/novoalab/EpiNano
Thanks!
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53b0abcc69346e813436b7d884db6e6501c58281febfe2794e7f0c31818eba7c | Text | 187 | 2 | # bkms-data
Processed data files based on the [BKMS](http://bkms-react.tu-bs.de/) database, usable in the [ASKCOS synthesis planner](https://github.com/itai-levin/chemoenzymatic-askcos).
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c27e5cd66649e4d435c7182da6013b6932913b9d51922219b68ed7bfe2a1fd67 | Text | 189 | 2 | # umcuEpi_MRI_and_ioECoG
Code used for the paper: Straumann et al (2022) - The spatial relationship between the MRI lesion and intraoperative electrocorticography in focal epilepsy surgery
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4ea281f3c3bfc60bdffc33f043afc0128e5132090f3afd6b75255c3508877a78 | Text | 239 | 9 | # Hierarchical deployment of Tbx3 dictates the identity of hypothalamic KNDy neurons to control puberty onset
### Analysis Scripts
* 1-5 Single cell data pre-processing
* 6 Correlation-Analysis
* 7 Cell composition analysis
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216d5cd09295c27be13c178e55a385ab5c3d766a781bd7a151e65ba05594e7ba | Text | 253 | 1 | This is an example code for analyzing TCF4 levels using short-read RNA-seq splice-junction data from Sirp at al. (2022), "Expression of alternative Transcription factor 4 mRNAs and protein isoforms in the developing and adult rodent and human tissues".
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75a364699cb13e743986567d1576efb0175e577ee4454c6f96ed5d0a16459d07 | Text | 260 | 2 | # Hierarchical_Bootstrap_Analysis_RB
This repository contains the code to perform the hierarchical bootstrap analyses for testing the effects of Munc13 on synaptic transmission by comparing it in RIM+ELKS knockout neurons and RIM+ELKS+Munc13 knockout neurons.
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c676818a82c3d016683721ce7d68c66fb561778bec8ded3d659cc8718a388dfa | Text | 266 | 1 | This repository contains code that were used to produce the main data in the paper entitled:"Neural representations of naturalistic events are updated as our understanding of the past changes", eLife 2022 (link to the paper:https://elifesciences.org/articles/79045)
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0e89805e38bb803fe15af5adbd7dcd229f99be79e2033adfa9ba633af7462f16 | Text | 269 | 5 | # Cerebrovascular impairment after COVID-19
Data and code supportting "Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study"
https://pubmed.ncbi.nlm.nih.gov/36451358/
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e079105ebb0e73fa40d43c8cf428b60b461f35d8df23035a78e12a223b211e83 | Text | 273 | 13 | # cmplx-syn
First, download VGGFace2 and corresponding face networks, and run image_preprocessing.py.
Second, use main.py to run and analyze complex synaptic models.
Usage:
python main.py -t exp_name
python main.py -a exp_name
python main.py -p exp_name
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7e7c6e4cbe32f78df82c27c6cf8ad1763201c57e1213c58a5b9152dad94df14b | Text | 274 | 9 | # YAS_HD
Contains code used for analysis of YAS_HD cohort
Permutations folder
- contains files and code to perform sphere permutations of the chosen parcellations
PLS_permutations
- contains jupyter notebook with code to perform PLS on spatial nulls and empirical data
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2193593261298a6791e18fa5ff7959aebc27e4c821f1e9c1cd0f3f58d3fc05fb | Text | 290 | 7 | > [!NOTE]
>
> This repository has moved and is now maintained as a part of the [BSB monorepository](https://github.com/dbbs-lab/bsb).
# Glia: NMODL asset manager
View the online documentation at [https://nmodl-glia.readthedocs.io/en/latest/](https://nmodl-glia.readthedocs.io/en/latest/)
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31855b2bad6f86e7903720fafd90fbf4990d79f9e66bfe290fe29329d40e3c65 | Text | 301 | 5 | # MVCS
Corresponding to paper "Persistence of Hippocampal and Striatal Multivoxel Patterns
During Awake Rest after Motor Sequence Learning" by King, Gann, Mantini, Doyon & Albouy
Output of Scrubbing_precheck MATLAB script is necessary for the main pipeline script IF scrubbing option is implemented
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8f012f1407f2c630b7d2fb140471471ae73b08e132923eed13840e3703c2f1fd | Text | 333 | 8 | # Cell Representation and Segmentation with Shape Priors
This repository contains the source code for the article "A Cell Segmentation Framework with Shape Representations". You can start using the library and run the example notebooks by installing the requirements from the *requirements.txt*:
pip install -r require... |
6730bd2fb9065668759ffc387280ed63f000286a982d7980289b0a28932f541d | Text | 339 | 6 | # ALLCools
[](https://github.com/lhqing/allcools/actions/workflows/test.yml)
[](https://lhqing.github.io/ALLCools/intro.html)
Please see [documentation](https://lhqing.github.io/ALL... |
1ed0da84b156756c6799694d037b531056598e60af4cfff2637e6c2569a8557a | Text | 353 | 6 | # Jasek_et_al
This repository holds code used to analyse data, generate images, figures and videos for the following paper:
Desmosomal connectomics of all somatic muscles in an annelid larva
Sanja Jasek, Csaba Verasztó, Emelie Brodrick, Réza Shahidi, Tom Kazimiers, Alexandra Kerbl, Gáspár Jékely
Dec 20, 2022 https://... |
31f4372735d78a649443fd24e30f433247b317cf56fe8596a7bb6f474db953b2 | Text | 364 | 3 | # Transparency and open science standards in the policies of medical and health science journals
This repository contains the data and code used to analyse TOP scores (using OSF's Transparency and Openness Promotion Guidelines) for 20 high-ranking journals in health and medical sciences. More details are available on ... |
5bc0329a9eeebe2fbf26f5237ffe99b19ca4540f533e1237aa090894165cdc87 | Text | 374 | 8 | > [!NOTE]
>
> This repository has moved and is now maintained as a part of the [BSB monorepository](https://github.com/dbbs-lab/bsb).
# arborize
A framework to package NEURON cell models following a clear separation between
cell model description and its implementation in NEURON. Cell models described
using this frame... |
97a89f7ee775a6417beadbc0e9825b5e28eb3ada68ea3ee4382f9b623698d424 | Text | 376 | 8 | # POViT
Source code and data of POViT.
Instuctions of different folders:
Dataset: Input, the features, is raw data of air holes of L3 PC nanocavities, which needs to be normalized before fed into POViT.
Output, the target, is raw data of simulated results of FDTD.
ViT: Our POViT models. Results in Paper is ba... |
9b70538c926027d863154928e61d2e767977090e42822f0e7649580c42fe3a53 | Text | 408 | 12 | # Thalamocortical contribution to cognitive task activity
code repository for: Hwang, K., Shine, J.M., Cole, M.W., Sorenson, E. (In Press). Thalamocortical contributions to cognitive task activity. eLife.
Most analyses in main_analysis.py, FC calculations in create_FCmat.py
## raw data can be downloaded at:
MDTB: h... |
7ba9eb124737b0afaf9d0e3567181dd26f5815c38760ab3f24bc5746865a4b06 | Text | 416 | 4 | # Code for Vandrey et al. eLife, 2022
Data and analysis code used to generate figures and statistical ouputs for https://elifesciences.org/articles/83008, previously avaialable as preprint here: https://www.biorxiv.org/content/10.1101/2022.08.25.505296v1
To use the code, clone the analysis scripts and data and specify... |
2bcd63365e7488b21b821f87bca2e3f2a3ca24848774d5a25468a664e07b7410 | Text | 422 | 7 | # Snakemake workflow: 3D RNA-FISH cell type-specific analysis
This workflow combines AIRLOCALIZE (Lionnet et al.) and a minimal U-Net segmentation model to realize cell type-specific 3D RNA-FISH data analysis.
Our published work demonstrates this workflow with Drosophila clock neurons in vivo.
If you use this workfl... |
a3506410de6439c9eef9d5cd5b73528dd64e15dcb256a5a7f988edcafbe5e846 | Text | 422 | 11 | # qccCorpus
Repository for the Quechua Collao corpus baselines for automatic dimensional emotion recognition:
- Support Vector Regressor (SVR)
- K-Nearest Neighbor Regressor (KNR)
- Random Forest Regressor (RFR)
- Multilayer Perceptron (MLP)
- Convolutional Neural Network (CNN)
- Long short-term Memory (LS... |
8d2b0d56bc66721a8fe52f15519c436da5c4fa185bd66a949b51942e1480b14d | Text | 453 | 3 | # Nearlab sEMG dataset
The dataset used in the paper "Transfer learning in hand movement intention detection based on surface electromyography signals". Please refer to the paper about the processing detail. If you use this dataset in your analysis please cite the paper.
The EMG dataset is currently available at follow... |
b84dcdc390532ef34d9aaf44fb88cddbe3ccc62c6b1f7caf0150941f8247fb2b | Text | 461 | 4 | # hierarchical_regression
Python code for hierarchical multiple linear regressions. This code has been checked and validated against the same analysis conducted in SPSS.
This code was used for an analysis in the following paper: Boyle et al. (2021). Verbal intelligence is a more robust cross-sectional measure of cogni... |
d85c264438d6243dedb0f92528e451ddfc83b27de859ac4b8d9a478f0b4ee16d | Text | 462 | 6 | # Spongy-bone-segmentation
The supplementary algorithm to: Vascular accident risk factors in ALGS paper
This algorithm an extension for the Skull analysis described in the paper: Sex differences and risk factors for bleeding in Alagille syndrome
The input data are already pre-processed in the VG Studio Max software ac... |
d06ea96a9d88f46772c3628994cc89488e77599e637f4f6e71ec3a9d5736e620 | Text | 464 | 9 | # Diffusion_PNN_CGMD
Scripts for setting up and performing the simulations are in the 'Scripts'-folder.
Scripts for analyzing the results are in the 'Analysis'-folder.
Some example data are in the 'Example_data'-folder. Note that the data sets are not complete, and that different system types may have different form... |
04fda9f44a173dadc98846bde9fe9603610b736daef8bee7bf1fe4c96331226b | Text | 468 | 8 | # SingleCellModeling
Code for the publication "Generation and analysis of context-specific genome-scale
metabolic models derived from single-cell RNA-Seq data"
Important: For this code to work, the files in the "ChangesToRAVEN" folder may need to
replace the corresponding files in RAVEN, depending on the RAVEN versi... |
7a49a6a7618003c74cfb7d39ecc653b3584fba8077e299c225c46fe15e2c81d7 | Text | 486 | 9 | # Validate_ComBat
This is the Code for our paper "Validation of cross-sectional and longitudinal ComBat harmonization methods for magnetic resonance imaging data on a travelling subject cohort" in NeuroImage: Reports. https://doi.org/10.1016/j.ynirp.2022.100136
The code should be run as follows:
1. Cross-sectional_ana... |
6e17e330b1e2885529a9debb97971ae088ca4f597f0d71d0b1ab6f74743e8320 | Text | 532 | 11 | # CATHARSiS
CAlcium Transient detection HARnessing Spatial Similarity
Reference:
Jürgen Graf, Vahid Rahmati, Myrtill Majoros, Otto W. Witte, Christian Geis, Stefan J. Kiebel, Knut Holthoff, Knut Kirmse. (2022)
Network instability dynamics drive a transient bursting period in the developing hippocampus in vivo. eLife20... |
6f5e877b029d4ed8d29a6d67ac36d36320f9c9bbc1514362e9ca3d43ee5a3d94 | Text | 537 | 25 | .. _readme:
README
******
Description
===========
The Iterative Alternating Sequential (IAS) algorithm is based on an iterative scheme that alternatively updates the dipole
moments Q by solving a linear least squares problem using a priorconditioned CGLS algorithm with sutable
stopping condition and updating the hy... |
0ea2eedaa1f1b1a9d36bb0ef6f15eee329f66c32191a105f3b9eea1640dbe642 | Text | 538 | 6 | Flinazr_train7_2.pb:
A neural network interatomic potential (NNIP) developed for LiF-NaF-ZrF4 molten salt. This NNIP was used to generate results for the following manuscript:
https://arxiv.org/abs/2209.09924
Please cite the mentioned manuscript when publishing results generated using this NNIP:
Chahal R., Roy S., Ban... |
adc078f277e11dfb2194e3544ac903dfd2990a39bc5aeb435b50bd3c143e2605 | Text | 544 | 15 | # Utils for the Brian2Loihi emulator
The utils repository provides background information for the Loihi emulator written in Brian2 which is available on this repository:
https://github.com/sagacitysite/brian2_loihi
## Parts of the utils repository
### Algorithm
The *algorithm* folder provides the algorithms in pur... |
a00c1cc90ad816980005c7f4b897b1dbf10cd42b594c72259fd38f986801e687 | Text | 558 | 15 | # pyNeurite
A computer vision package that traces and analyzes neurites fully automated. Optimized for time-lapse videos.
Used in Schelski and Bradke 2021
# Installation
1. Open a terminal, navigate to the folder where you want to put the repository and clone it:
> git clone https://github.com/maxschelski/py... |
9da367aea9e8faffefdda2feb6cc37754072314012254071dfba83de8963ff3e | Text | 563 | 27 | # DRPreter (Drug Response PREdictor and interpreTER)
DRPreter: Interpretable Anticancer Drug Response Prediction Using Knowledge-Guided Graph Neural Networks and Transformer
## 1. Create cell-line data
`... |
38e3158148d4d1008ac39b92427134798a599933249ae11592aa0b5f49c5d27d | Text | 568 | 11 | # CortexRelease
## Executing the Cortex
Cortex.exe and configTrain.txt should be either in the same folder or config file should be given as a second command line argument.
##Configuring Train Config
- window size: Depth of the Cortex tree.
- epoch: Training count
- base string: the name for log and output files.
- ran... |
b02fa41d737479a28f77c947af116a93bdb486c3a097386dbb1881b7318d6470 | Text | 572 | 7 | # Eye Movement Detector Evaluation
Contains the annotation tool, used stimuli, and data labelled by two annotators. Code and data are in Matlab formats. Analysis code is not entirely complete as it was done interactively do an extent, but should give a good clue to what was done.
This was the data used in:
Andersson, ... |
982d406032cf692dac564631f5bf0c0f67b85e4032676d0773dea2614e9c4476 | Text | 610 | 13 | # Event-detection
EPSC and IPSC event detection in Igor
This file was taken directly from SpAcAn, created by Charly Rousseau and Guillaume Dugue.
Citation: https://pubmed.ncbi.nlm.nih.gov/22457509/
Very few changes have been made by our lab; the exceptions are better detection of events occurring in rapid succession ... |
4de8dc443402c9902e457d89401d54a5649322e8184156151a6e72525a34516e | Text | 617 | 16 | # snakebids
Snakemake + BIDS
This package allows you to build BIDS Apps using Snakemake. It offers:
* Flexible data grabbing with PyBIDS, configurable solely by config file entries
* Helper function for creating BIDS paths inside Snakemake workflows/rules
* Command-line invocation of snakemake workflows with BIDS ... |
b1fc0e7c2c74ad3ca67ff2c1808619ee8a9809b52424f6e929240b2dcdd6ec42 | Text | 618 | 2 | # CoroNet
CoroNet is a Deep Convolutional Neural Network model to automatically detect Covid-19 infection from chest X-ray images. The deep model called CoroNet has been trained and tested on a dataset prepared by collecting Covid-19 and other chest pneumonia X-ray images from two different publically available databas... |
6da9baa13d8ec10893d9c1773ba3b6966b1f353e0455276b61565b0a78fec76e | Text | 629 | 11 | # GABAergicOlfactoryFeedback
Codes used for the analysis of the 2P data in Mazo et al., 2022 Nature Communication
Processed (registered and sorted by trial type) data can be found here:
'XXexp' structures are ChRmison-expressing mice. Data is organized as: trial repetitions x time (30 fps) x Cell
'CL' is continuous l... |
9e78e2610279f2f0bc19b325bc7ed673e63a9d0860cffd746010c8f7b97e5d05 | Text | 631 | 34 | # Through the looking glass: Deep interpretable dynamic directed connectivity in resting fMRI
# DICE model
Usman Mahmood, Zengin Fu, Satrajit S. Ghosh, Vince D. Calhoun, Sergey M. Plis
Accepted at NeuroImage
Paper : https://www.sciencedirect.com/science/article/pii/S1053811922008588?via%3Dihub
#### Dependencie... |
b4d1c895ccc8221807ad7f95916bfa3ef1992d9305319ac0cecdf9530aec7db4 | Text | 643 | 13 | # Behavioural signatures of memory resources for language: looking beyond the lexicon/grammar divide
<br>
This repository contains the `R` code for the analyses reported in
> Divjak, D., Milin, P., Medimorec, S., and Borowski, M. (2022). Behavioural signatures of memory resources for language: looking beyond the lex... |
9217a2e43df624b631d2fbc82156d60c42e382e586b427f0e50c663d861f4bed | Text | 653 | 14 | # Adaptation Manifolds
This repo contains the accompanying code for the preprint "[Distinct patterns of cortical manifold expansion and contraction underlie human sensorimotor adaptation](https://www.biorxiv.org/content/10.1101/2022.06.09.495516v1)", which explores changes in cortical functional architecture during sen... |
8eaf45f6dbf3c54b950782e45a2bb3b6cf4d918d26f91b2bff3ab08c751e9d4a | Text | 670 | 15 | funlib.evaluate
===============
.. image:: https://travis-ci.com/funkelab/funlib.evaluate.svg?branch=master
:target: https://travis-ci.com/funkelab/funlib.evaluate
Popular metrics and reporting tools for volume evaluation. Currently includes
RAND, VOI, expected run length, and a metric to measure the number of spli... |
d2e7979b4a28534b32f4fea7a726519d5b8db70b6cf5e8df8b5dad1193548376 | Text | 691 | 27 | ==============================
PAC desensitization eLife 2022
==============================
This repository contains code to reproduce MD-related figures for
James Osei-Owusu*, Zheng Ruan*, Daniel S Matasic, Wei Lu, Zhaozhu Qiu. (2022) Molecular
mechanism underlying desensitization of the proton-activated c... |
84e2e4ea65b4090c548ab369fb0cfbc8152aa1d462c134de25efcf135c27bcaf | Text | 698 | 14 | # Description
This repository contains data and code to reproduce the findings reported in: Schevenels, K., Gerrits, R., Lemmens, R., De Smedt, B., Zink, I., Vandermosten, M. Early white matter connectivity and plasticity in post stroke aphasia recovery. NeuroImage: Clinical. https://doi.org/10.1016/j.nicl.2022.10327... |
d43645b43c5d62759b3eaae4582b03dc3d90020d7a493b817283859c05631df8 | Text | 701 | 10 | # A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo
### Katrin Möller, Max Brambach, Ambra Villani, Elisa Gallo, Darren Gilmour and Francesca Peri
This repository contains the code used for parts of the analysis of the paper "A role for the centrosome in regulating the rat... |
bf8f4a50069c354e970f22de82ecb659a0bab137c9586695e2c5aa12b7ab6cc1 | Text | 710 | 30 | # BCI_V1
Codes used in the V1 BCI manuscript
Includes code used to perform k-nearest neighbor (KNN) decoding, permutation test for testing the 2D Gaussian fit, and 2-sample proportions Z-test.
--List of standard Matlab statistical test functions used within the paper--
Linear regression:
[b,bint,r,rint,stats] = re... |
2977907618af463cc9ae60cbb1a589b9c48c3dae6ddf507d7b067098c08ea27e | Text | 737 | 35 | # cifar.torch
**Newer version of this code is included in https://github.com/szagoruyko/wide-residual-networks**
The code achieves 92.45% accuracy on CIFAR-10 just with horizontal reflections.
Corresponding blog post: http://torch.ch/blog/2015/07/30/cifar.html
Accuracies:
| No flips | Flips
--- | --- | ---
VGG+BN... |
18a08ef71410039eff410bc3856fd1563d1b527a7b77b51070ff54bdb3ca7d33 | Text | 739 | 27 | # X-ray age
- Predict biological age from frontal CXR image.
## supported file type
- jpeg
- png
## usage
- Download pre-trained model
- https://riken-share.box.com/s/pe202pcmhx7idymve2x3xfu7nu6gfbrt
```python
python predict.py path_to_cxr_image
```
**TorchXRayVision**
- X-ray age model is also available in [Torch... |
dc2ca8d52864f98900dcd4c2255778d22b730cf91d8201d0a79d05af86ff4d51 | Text | 741 | 12 | # BRIAN
A computational platform for extracting and reconstructing single neurons in 3D from multi-colour labelled populations
* **BBSTATIC.py** is a small standalone utility for testing the method.
* **XTBBFilter.py** is the Imaris XTension that pre-filters the images.
* **XTBB.py** is the main Imaris XTension used f... |
e9d776185958ce5b89b50f23fd951a9858876727f3615f86afc8eeb7d1d4f807 | Text | 742 | 11 | # Conserved_structures_cortex
Code for Paper "Conserved structures of neural activity in sensorimotor cortex of freely moving rats allow cross-subject decoding"
by Svenja Melbaum, Eleonora Russo, David Eriksson, Artur Schneider, Daniel Durstewitz, Thomas Brox, Ilka Diester.
This repository contains code with the most ... |
53adb24691f78fce4e9925e7311a42a17f21857c1334009b3751c477a5800274 | Text | 755 | 7 | GitHub repository associated to the paper: M. Celotto, S. Lemke, and S. Panzeri ["Inferring the Temporal Evolution of Synaptic Weights from Dynamic Functional Connectivity"](https://braininformatics.springeropen.com/articles/10.1186/s40708-022-00178-0). Brain Informatics, 2022.
In this work, we estimated the performa... |
2aa5407782edb8fb2dcf0b781383abbe4f444f45cc33c6072d7a63e53056c0d3 | Text | 783 | 11 | # 50-percent-tracked
Custom python script used to process .TXT files derived from wrMTrck Plugin in ImageJ for analysis of swimming behaviour in C. elegans.
1. Analyze your videos of swimming C. elegans using the ImageJ Plugins wrMTrck (https://www.phage.dk/plugins/wrmtrck.html)
2. Validate tracking (remove non-worm o... |
ec3dbe012ef3f7583ba45e83749be6bc05e6936767f406e4256a14ea4dfddb9f | Text | 795 | 17 | # meso_stp
Code for our manuscript "Mesoscopic description of hippocampal replay and metastability in spiking neural networks with short-term plasticity"
To run the Julia codes, open your terminal and type:<br />
a) for simulating the microscopic model: "julia microscopic_model.jl"<br />
b) for simulating one of the ... |
0a55ee2a9cb06ec317de65b30505e09ca02f16f2859e5146884e05b81d2d49dd | Text | 798 | 22 | # GlaucomaML
Various Glaucoma related machine learning and computer vision projects done with Caprioli lab at Stein Eye.
## Projects
### RimNet
A model for generating rim segmentations from images of the optic nerve head. We strove to achieve good performance even in instances where the rim is incomplete.
Paper ... |
648604668d1b8f4655c551ae2a489ba7e02d3f08947cc1161534fa263025178d | Text | 801 | 35 | To convert and C01 images to tiff or png format (with and without normalization)
# 1. Download and install bftools:
cd ~/bin
wget http://downloads.openmicroscopy.org/latest/bio-formats/artifacts/bftools.zip
unzip bftools.zip
rm bftools.zip
export PATH=$PATH:~/bin/bftools
# 2. Install required python packages:
pip... |
216feabed95a88e90a9a2c1fc12b6a4db337e563ae0f76f0b575ab8842842043 | Text | 815 | 23 | [](https://travis-ci.com/nicholasturner1/Synaptor) [](https://badge.fury.io/py/synaptor) [](https://www.python.org/download/release... |
d0c0f1cc013d86a032f56ffac0137d185f0f071d039a83a1e3cdc56f67b65101 | Text | 823 | 9 | # learnMSA analysis
This repository contains materials suitable to reproduce the comparative experiments with learnMSA. In particular:
- scripts to automatically download HomFam, BaliFam and our ultra large datasets
- scripts to run learnMSA as well as Clustal Omega (http://www.clustal.org/omega/#Download), MAGUS (ht... |
a35a59ea442e634e66613a728276348d8a161adf1ed57de3766dc64031774c55 | Text | 826 | 36 | # edbo
Experimental Design via Bayesian Optimization: *edbo* is a practical implementation of Bayesian optimization for chemical synthesis.
**Reference:** Shields, Benjamin J.; Stevens, Jason; Li, Jun; Parasram, Marvin; Damani, Farhan, Janey, Jacob; Adams, Ryan P.; Doyle, Abigail G. "Bayesian Reaction Optimization as... |
410c89524a297f3b02c86cdc69d610a6a3b7381d3e775ef6871ad1f569e61403 | Text | 834 | 12 | # GNNs_fields_prediction
Machine learning (ML) code used in the paper "Predicting stress, strain and deformation fields in materials and structures with graph neural networks"
published in Scientific Reports.
December, 2022
Each folder contains the ML code for the corresponding mechanics example reported in the pap... |
04e28072065921dde6c5d26aa85f0eca27ca9e3353c9f1ef7381f3ab2f373861 | Text | 838 | 13 | # Copolymer Machine Learning
A machine-learning (ML) implementation that incorporate the information of both **molecular composition** and **sequence distribution** of copolymers including **random, block, and gradient** copolymers. Please refer to our work "Machine Learning Strategies for the Structure-Property Relati... |
4f3f852dab40bd268b1536dabbe69b1fc380cb2d6c4675c438f90e9927ae9e67 | Text | 840 | 18 | SingleCellToolbox:
SingleCellToolbox is a matlab toolbox for single-cell RNA-Seq data.
Installation:
The only installation needed is to clone the git repo and set the path. Recommended file structure:
SingleCellToolbox
SingleCellToolbox - this is the repo
ImportableData - This is where all the existing public datas... |
ea747fa935a651b0ec5fe468f9ce92a6bd7f8eed4b0f2c644a355f283437b5f7 | Text | 876 | 11 | # Brian2Loihi implementation of the SpreizerNet
This is an implementation of the [Spreizer network](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007432) in the [Brian2Loihi Emulator](https://github.com/sagacitysite/brian2_loihi). It is based on [Leo Hiselius's Brian2 implementation of the Sp... |
4a69348cb3ca6e7802731a96e096f8ce60cb188e46a9a11e936426f2d917c91a | Text | 881 | 17 | # General Information
This Zenodo upload contains the data and analysis code required to reproduce the analysis and figures in the publication entitled "MyD88-TLR4-dependent choroid plexus activation precedes perilesional inflammation and secondary brain edema in a mouse model of intracerebral hemorrhage". DOI:[___add_... |
de739f906bdb45d3cd77cdddd4bb53847db8a966d019295fb207d26123c29f52 | Text | 882 | 11 | # Frequency and Phase Correction of MRS signals Using Cross-Correlation
The algorithm is based on the "Automatic frequency and phase alignment of in vivo J-difference-edited MR spectra by frequency domain correlation" paper. The authors of the paper find the maximum using manual grid search. But here, the problem is c... |
1f756010f69b2385cb5a2854116d7bf4a97ef36c73e53d69d21841cf5b5ddf65 | Text | 888 | 13 | # PyTorchUtils
Some utilities for working with PyTorch and torms3's DataProvider for connectomics data
This package is meant to be EXTREMELY lightweight. It represents a notetaking system rather than a stable updated codebase. This decision was motivated by observing that different experiments often require tweaks tha... |
4a7b8cbd2641e85b9ab8e7e820c242f4c648faf2852e88281903997b27e32a36 | Text | 897 | 16 | Matlab (www.mathworks.com) or GNU Octave (https://www.gnu.org/software/octave/) and Brain Connectivity Toolbox (https://sites.google.com/site/bctnet/) are required for most. Additional requirements are listed in the comments for each script and some of these are included in the Resources folder.
DTI_nets/: Scripts f... |
b82927d76098ea9796f13399bb100cbb6b8ec6edc5f5c68e7d77b3b96f8d5146 | Text | 899 | 41 | # SimTune
This is the code repository that supplements the work: "SimTune: Simulator Tuning to Bridge the Reality Gap for Resource Management in Edge Computing".
<a href="https://gitpod.io/#https://github.com/imperial-qore/SimTune/">
<img src="https://gitpod.io/button/open-in-gitpod.svg" alt="Open in gitpod">
<... |
5198ef14a9359f29851a25f099cc7944873991a34b324f7ca1237d2c4432b3ab | Text | 900 | 19 | # GLADC
This is the code of "Deep Graph Level Anomaly Detection with Contrastive Learning".
# Data Preparation
Here, we give three example experiment datasets including BZR, COX2 and DHFR. Other datasets can be obtained according to the link in the paper.
# Experiment Environment
The required packages are shown in the... |
3c576eb80b9c10c6069bf12e393abb3b60bccae978b0f139827e8323001036f8 | Text | 911 | 29 | ### Tactile braille letters dataset
This dataset contains all letters of the braille alphabet (A - Z) and 'Space' recorded with the iCub fingertip mounted to an Omega.3 robot.
## Requierments
pandas
pickle
## Information
sampling frequency (in Hz) = 40
number of samples = 51
time per record (in seconds) = 1.275
repet... |
b0b154fc31936bd953a438e050216bfce7510830c189799c25d5c37703639a96 | Text | 916 | 24 | # neuriteMT
The package analyzes microtubule (MT) orientation in neurites based on the output from utrack / plustiptracker (Danuser lab; https://github.com/DanuserLab/u-track).
# Installation
1. Open a terminal, navigate to the folder where you want to put the repository and clone it:
> git clone https://github... |
4ede60d714a36cfbed45ca9b0463adf3435a8acfc966dc131ffe319a50e35049 | Text | 925 | 50 | # Deep Neuronal Filter (DNF)
## Prerequisites Libraries and packages:
1) Install the Fir1 library from _https://github.com/berndporr/fir1_ by running:
` sudo add-apt-repository ppa:berndporr/dsp `
` sudo apt-get install iir1`
` sudo apt-get install iir1-dev`
2) Install openCV library by running:
` sudo apt insta... |
f73a829aec7b9d29fa696c851bfe98acdcf3836807a7bd6e297746e1b5bdb415 | Text | 934 | 17 | # Machine Learning to Predict Overall Short-term Mortality in Cutaneous Melanoma
## Code
This repository contains
* `cleaning_and_ML_models.ipynb`, the Python notebook with all the code produced for the data cleaning, analysis, model definition, training and testing
* `DNNs trained.h5`, the H5 file containing the tra... |
53401f63ce29ca70476495da12991d470e1ad1a19a7d69cc4028fe7ab27689d6 | Text | 940 | 15 | # DVS-Attacks: Adversarial Attacks on Dynamic Vision Sensors for Spiking Neural Networks
This repository provides the source codes for applying DVS-Attacks on Dynamic Vision Sensors for Spiking Neural Networks, and for applying event-noise filters. If you used these results in your research, please refer to the paper
`... |
2f1c67618358c6768a75f90d951c8efece75753a075f77d0fc4b8f426a9b40bc | Text | 949 | 15 | # Placenta_Sex_Diff
Sex differences in full-term, >= 36 weeks, uncomplicated human placentas
## Sex differences in placenta expression
#### Step 1: Process RNA sequence data
- FastQC, MultiQC, and bamstats for visualizing quality. bbduk to trim reads and remove adaptors.
- Reads aligned to a GRCh38 sex chromosomome... |
21b2185c12b2598c711227a90fd188986f512263d422045dff80bdae8af6520d | Text | 951 | 22 | # Description of data
Files are STC-formatted, ready to be processed using `mne_read_stc_file1`.
They contain source-localised EMEG recordings for each subject and condition, restricted to data within a bilateral STC mask.
The files are grouped into directories, which have been compressed using `7zip` and segmented ... |
80ad12ba2cc2653af4e6cccdc4920a4641a7ea87750af7ffe5df2204d065e1d6 | Text | 975 | 21 | # Notebook examples for reproducing two usecases using GPU-enabled Jupyterlab in Galaxy Europe
1. Notebooks 1-6: Reproduce analysis from paper https://www.sciencedirect.com/science/article/pii/S2666990021000069 using notebook itself and via remote training
Citation:
```
Narges Saeedizadeh, Shervin Minaee, Rahele Kafi... |
cd2d845e6bb566b96ac93b0740122ea2cb8d9c22dd9ab43a2fa25d76a35bd496 | Text | 976 | 25 |
### Environment Setup
> base environment: python 3.7, cuda 10.2, pytorch 1.6, torchvision 0.7.0, tensorboardX 2.1 \
pytorch-geometric: \
pip install torch-scatter -f https://pytorch-geometric.com/whl/torch-1.6.0+cu102.html \
pip install torch-sparse -f https://pytorch-geometric.com/whl/torch-1.6.0+cu102.html \
pip in... |
c9420fe0bae9e0553a71fe4e8dae099b53a441c4441f7573ed8670eb15dcc1cc | Text | 977 | 21 | # Evolutionary learning of interpretable decision trees
This repo hosts the code of the paper [Multi-objective automatic analysis of lung ultrasound data from
COVID-19 patients by means of deep learning and decision trees].
``@misc{custode2022multiobjective,
title={Multi-objective automatic analysis of lung ult... |
76bebf0b33ca1c5e122b67ddddc74b21e0506615b117ac6787e784a7942ab1a5 | Text | 988 | 19 | # ANNSCGP
Supervised Artificial Neural Network with Selective Connection based on Gene Patterns
ANNSCGP proposes a supervised Artificial Neural Network with Selective Connection based on Gene Patterns (ANN-SCGP) model using Omics-data
To start ANNSCGP, you can download Binary package named "ANNSCGP_1.0.0.zip" for Win... |
c6869af65dc05b3ebed376303545ee61adab657c6ba8cfb5174a21b9b074966a | Text | 988 | 24 | # NonstationaryDynamicMeanFieldTheory
Code for calculating the autocorrelation and Lyapunov exponent of recurrent rate network
The provided script nonstationaryDMFT.jl calculates autocorrelations and largest Lyapunov exponent using DMFT of Gaussian relu network with common sine input.
When using, please cite the foll... |
9384abcc1b0624aacb62889f77076644b0ba11fb62a0f30097e52f2238c4c7ef | Text | 998 | 32 | # spatial-factorization-py
Probabilistic factor models for spatially correlated data. Includes nonnegative and real-valued versions.
## Installation
Many people find it convenient to install everything in a conda environment. We recommend installing the [miniforge](https://conda-forge.org/miniforge/#latest-release) ve... |
1c48a1f0e1fe198d4bf1a1e761a071ca3f35b72cfb9b0895688852642179637a | Text | 1,007 | 23 | # Legacy Repository: Commonality Analysis for Neuroimaging Toolbox
This repository is now **archived** as a legacy reference.
All development has moved to the **new toolbox**:
➡️ [Voxel-Based Analysis Toolbox](https://github.com/kamentsvetanov/vba-toolbox)
The new repository includes:
- All functionality from this... |
1a7b05419eda50ec60cb28dddd15b8dbc7235533c350234bebd18ab0bea762f4 | Text | 1,038 | 54 | # mri-classification
Cardiac MRI classification using Recursive Neural Networks
## Getting Started
1. Install requirements
2. Copy `data` folder to root directory
```
mri-classification
├── data <-- this one
├── data.py
├── labeler.py
├── LICENSE
├── notebooks
├── project.py
├── README.md
├── requirements.txt
├── s... |
67109d59739a9cc38705b514d6efae9e8b37e1c32527dc020c0a279976bdcfe6 | Text | 1,041 | 7 | # Conserved_structures_cortex
This repository contains example data for the paper “Conserved structures of neural activity in sensorimotor cortex of freely moving rats allow cross-subject decoding” (Melbaum et al. 2022).
We used the freely available tool MuViLab for the behavioral labeling of the videos from 48 recor... |
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