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06c87e5f59b65bc8865a0a1cd181ec7d8ea5046387ffb014e4fb071d7ca23a61 | Text | 242 | 10 | # nails-segmentation-dataset
Small dataset for nails segmentation
### Context
This small dataset can be used as a start point for nails segmentation model.
### Content
In nails_segmentation.zip you can find folders with images and masks.
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843b8087d4d3e9f4b0aa87564e3fc07feb0d73b9a335c36745d955e6c0fecb77 | Text | 243 | 4 | # Sapkal_et_al_2024
- Collection of all code to be published with Sapkal et al, 2024, Nature.
- All data organized in the format acceptable for analysis scripts shared here, is made available at [edmond.de
](https://doi.org/10.17617/3.OIX8RZ)
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78129406c4d9abec750ad77bd5b09085f350932cd6a931b5ef3d8f75a8a2079e | Text | 245 | 4 | # Brain_HORS
Code and scripts for replicating the figures and analyses of the paper: https://www.biorxiv.org/content/10.1101/2023.12.04.569913v1.abstract
Original python and julia code can be found here: https://github.com/andresantoro/RHOSTS
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d2d85a49f7fc7d6ac43624491125a7549f98b992cdd78cddd10a3286e7425a78 | Text | 245 | 4 | # MSCAP
MSCAP is an epigenetic clock based on multi-scale convolutional neural networks.
# Mlp-DDR
Mlp-DDR is a multilayer perceptron-based disease risk prediction model, which includes six additional models trained by machine learning methods.
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af03fd1a0db9df992797ce4549de26c97f6ae2b681ccc01ceae354a8ba1dd916 | Text | 251 | 3 | ## License
This repository is licensed under the [Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License](https://creativecommons.org/licenses/by-nc-nd/4.0/). Please read _Academic Use EULA.pdf_ before using these files.
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f6d711f8b59cdedd3d516f3a041420064e0ace2d57dbc6baa4980011408e8b6d | Text | 252 | 2 | # Synaptic-connectome-of-the-Drosophila-circadian-clock_Reinhard-and-Fukuda-et-al.-2024
Code to replicate the analyses in Reinhard, Fukuda et al., (2024) Synaptic connectome of the Drosophila circadian clock. https://doi.org/10.1038/s41467-024-54694-0
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fc4994c5e133251ca21bc943a1ff05eafce5abd380ad523f4e6db5e96a26a709 | Text | 254 | 8 | # Engram *eLife*
This is the repository with modeling code and data for:
O’Leary J. D., Bruckner, R. Autore, L., and Ryan, T. J. (2024).
Natural forgetting reversibly modulates engram expression. *eLife*. Link:
https://doi.org/10.7554/eLife.92860.1
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f046966ff0f09d8d6d9d431c22354ec253a6423b5bae11e63d7e98164c586544 | Text | 256 | 12 | The statistical analyses are performed by running the Rmarkdown file `prems_ant_data_analysis_.Rmd`.
Christophe Pallier 2024/02/05
License
--------
Attribution-ShareAlike: CC BY-SA 4.0
<https://creativecommons.org/licenses/by-sa/4.0/legalcode.txt>
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b57e6ac2cd4c1806bf7643f9e931683da053635f1f99c10b04bd88cf5ab99818 | Text | 258 | 5 |
Whenever citing or using these scripts, please cite
Di Plinio, S, Northoff, G, Ebisch, SJH. 2024. The Degenerate Coding of Psychometric Profiles through Functional Connectivity Archetypes. Frontiers in Human Neuroscience, DOI: 10.3389/fnhum.2024.1455776
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d5b046ad51707457ebdac8d3dcc07b63cb83e64a257d878a247d12db34d89321 | Text | 263 | 6 | # 2024_motorconnectivity
Data deposition for Areshenkoff et al. 2024 (PLoS Biology).
The file `generateFigures.R` sources the R files needed to generate several of the figure panels reported in Areshenkoff et al.
Dependencies: `plyr`, `ggplot2`, `patchwork`.
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ebaf18fcdbb88bc81dfa3995e72d607ee0e776ffec2f6c4eb9a6d1c71083857c | Text | 269 | 6 | # calc_ENLwFC
Code utilized for the paper "Networks extracted from nonlinear fMRI connectivity
exhibit unique spatial variation and enhanced sensitivity to differences
between individuals with schizophrenia and controls" (Kinsey et al.)
skinsey8@gsu.edu
airaji@gsu.edu
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b0c3282ba1c1a552cbd5888b51421bb5cf7e3c5e161f2ddba8ea03900095748d | Text | 271 | 6 | pydcemri
========
Python module for processing dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data. Given a T1-weighted, dynamic, contrast-enhanced data set, a multiflip data set, and either an AIF or blood curves, produce maps of Ktrans, ve, and vp.
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1f9ef7768bfc7fc9a18516871cd7ac6f9b2256f074ce03394bec97c87d555639 | Text | 272 | 5 | # MQuad_paper_reproduced_results
Reproducable jupyter notebooks and data files for MQuad paper
Due to file size limitation on github, raw cellsnp data for large datasets is available on SourceForge:
https://sourceforge.net/projects/mquad-paper-reproduced-results/files/
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20d732e7c421f9d310fcdbc5eb5f20f7c0337f89d5d3641b3db25a0b24234076 | Text | 279 | 5 | # Tomato-leaf-disease-detection-
This project aims to find a rapid, accurate approach to tackle the necessity of automated detection of tomato disease by using a TNet model.
The data can be accessed from the https://www.kaggle.com/datasets/amreenbatool/plant-leaf-disease-data
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936e2c0ef94889a453b52f597526bb0dde5ecf168fcd902d7d039c7e045f53f0 | Text | 279 | 8 | # Scripts for analyses in m6ATM manuscript
Scripts can be found in the **analysis** folder, and data is in the **data** folder.
<br>
Large files were compressed in the ```tar.gz``` format, please use ```tar``` command to decompress the files.
```shell
$ tar zxvf ***.tar.gz
```
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ae30fe5ae85de12b39e2c1ac5beeea7423d46df7c5239e0f719da94754f73174 | Text | 280 | 3 | ## Deep Learning-Based Correction and Unmixing of Hyperspectral Images for Brain Tumor Surgery
#### David Black, Jaidev Gill, Andrew Xie, Benoit Liquet, Antonio Di leva, Walter Stummer, Eric Suero Molina
[DOI: 10.48550/arXiv.2402.03761](https://doi.org/10.48550/arXiv.2402.03761)
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0b359030741547ae7fa67732f448f1e052b87b27e663486b14e2528750bcc299 | Text | 283 | 6 | Trinotate is an extension of the Trinity project (http://trinityrnaseq.github.io/)
Documentation is provided at http://trinityrnaseq.github.io/
For questions, comments, etc., contact us through the Trinity user group (https://groups.google.com/forum/#!forum/trinityrnaseq-users).
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07a323a9275645919e08725c6eeee7c86ee091ec8d2b91fefa6db4ed0ca77e5d | Text | 285 | 2 | Data and Scripts used in the implemented workflow for analysis of repeated ASL measurements.
If using any of these data or scripts, please reference: Tapper et al., Method for detection of cerebral blood flow in neurointensive care using longitudinal arterial spin labeling MRI, 2024
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5c57c97015c72d03374f147d3bbc9cbb5536e59c5ba6b4ddbfe811d2a3e8121b | Text | 287 | 4 | ## Multi-level efficiency/clustering coefficient
This provides the code for the multi-level efficiency and clustering coefficient method used to quantify integration-segregation balance of the brain network.
This also provides code for metastability and pattern complexity calculation.
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c6f3c795ec59e8cc8efac2f6ae70b85d868eb7035dae8f2ad8724196088663b7 | Text | 287 | 7 | ## Lung Cyto
### **Automated recognition and segmentation of lung cancer cytological images based on deep learning**
* `ultralytics.zip`: YOLOV8 model with SEAttention, unzip it before running the following code.
* `train.py`: Training code.
* `predict.py`: Testing code.
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ab7b23376dce46eee465daff8c218dca66b6f92397b3edff77a982cf31f82ada | Text | 292 | 7 | # Forman_elife_2024
Processing scripts related to "PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking"
Thomas E Forman, Marcin P Sajek, Eric D Larson, Neelanjan Mukherjee, Katherine A Fantauzzo
https://doi.org/10.7554/eLife.98531.2.sa3
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ef554229b8d63f1a7b3450e377fa979efec8966c83d57673b82a96e01921e402 | Text | 293 | 9 | # anurogryllus-resonance
Code and data for Mann et al. 2024
## Installation
```shell
conda create -n resonance python=3.12 matplotlib jax metpy numpy pandas scipy numba ipykernel pyyaml matplotlib-scalebar xlrd
conda activate resonance
pip install -e . --force --upgrade --no-dependencies
``` |
7ab6948ee6510b0b8a3416eb5e87f3f0d41994dda7da7b5a4a2a8a0c858a6e14 | Text | 295 | 7 | # OilSpillDataset_Analysis
This repository contains the analysis code for the Oil Spill Dataset.
The dataset can be found at: Zenodo https://doi.org/10.5281/zenodo.10555314
The repo consists of 2 folders, one to recreate the analysis found in the paper and one for the segmentation analysis.
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8fec5e8d4e8946a3aecc655eba9a4dfce99b1be4ad07ef18db84abbb150a4fc3 | Text | 296 | 1 | This repository contains the analysis code for ["Enhancing Cognitive Performance Prediction through White Matter Hyperintensity Disconnectivity Assessment: A Multicenter Lesion Network Mapping Analysis of 3,485 Memory Clinic Patients"](https://academic.oup.com/brain/article/147/12/4265/7821065)
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76c4e0ed4a2dc05f4256c9eb67e660f0cf1fa17ac294ec42f9d230f06ee66367 | Text | 297 | 4 | # orientation_tuning_drift
Data repository for Bauer et al., 2023: https://doi.org/10.1101/2023.09.22.558966
data.zip contains two files (data_orientation_deprivation.mat and data_stability.mat) which contain the data used in the https://github.com/Joel-Bauer/orientation_tuning_drift reposetory. |
b4e9bba9c09e8e4ff7c403712fc3a9c0dd6e75369176ba9347c46ddfb59ef49b | Text | 303 | 4 | # Brain_HORS
Code and scripts for replicating the figures and analyses of the Nature Communications paper: [https://www.nature.com/articles/s41467-024-54472-y](https://www.nature.com/articles/s41467-024-54472-y)
Original python and julia code can be found here: https://github.com/andresantoro/RHOSTS
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c8e638d7863abc523d902d67dc2dc0aea6014be6b3857ce9ae2380e36d6436fa | Text | 304 | 3 | # MAP-MRI-based Cortical Cytoarchitectonic Segmentation
This code uses Gaussian Mixture Modeling clustering to directly segment cortical voxels from high-resolution MAP-MRI parameters.
NIFTI volumes of MAP-MRI microstructural parameters used can be downloaded at https://doi.org/10.5061/dryad.1c59zw45n
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796dcd02d6c6bfc814c5968493c28cac360405148495740a2bad3aaf2a25cbf5 | Text | 309 | 9 | # Notes
Scripts for "Hippocampal volumes in UK Biobank are associated with APOE only in older adults" by Chaloemtoem et al.
doi: https://doi.org/10.1101/2024.06.05.24307704
<br/>
Adapted from [ukbio_pipeline](https://doi.org/10.5281/zenodo.11100675) v1.0.0 by [verathor14](https://github.com/verathor14).
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d18bf5093c59251b937506c7fb79d74654483f0eeb960343bca00297433078cf | Text | 310 | 3 | # EchoLocator
Package for cleaning echographic images. It provides a watermark removal strategy and an adaptive cropping methodology.
The details on the implementation are reported in the paper "EchoLocator: an Open Source Python Package for the Standardisation of Echographic Images in Multicentre Analysis".
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f4d191051390f2730e6c323d105f6b3a08b922bfba83697d4c003e098672d376 | Text | 313 | 3 | For the code used to plot figures in Nguyen et al., The Medial Entorhinal Cortex Encodes Multisensory Spatial Information, Cell Reports, 2024:
Due to the large size of the raw data, we are unable to upload it to GitHub. Please reach out to the lead author to obtain the processed data needed to run these codes.
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18d8b271882e5659d6b106eec7684a556a19e050ac2638b414d04859f4e7efbb | Text | 323 | 2 | This code is based on the origional tools build by Nate Zuniga to analyze the data for the publication "Quantitative and Kinetic Proteomics Reveal ApoE Isoform-dependent Proteostasis Adaptations in Mouse Brain" PLOS: Computational Biology 2024
Each script contains commented information at the top regarding how to use i... |
6671487783e7ca9309e98d6675d6766a160c47885f5fbf967e3a4c87216e074b | Text | 323 | 3 | This repository includes code for: "Population encoding of observed and actual somatosensations in the human posterior parietal cortex" PNAS 2024 S Chivukula* T Aflalo*,CY Zhang, E Rosario, A Bari, N Pouratian, RA Andersen.
These authors contributed equally to this work ‡ Correspondence to srinivas.chivukula@gmail.com... |
daf4a75e4da0a17c5507dc9fac1ea568c7948c032b0f5abd67829244442a94c1 | Text | 327 | 2 | # DRG-model-data2024
This folder contains data associated with the paper: Farooqui J, Nanivadekar AC, Capogrosso M, Lempka SF, Fisher LE. The effects of neuron morphology and spatial distribution on the selectivity of dorsal root ganglion stimulation. J Neural Eng. 2024 Sep 4. doi: 10.1088/1741-2552/ad7760. PMID: 392... |
df22209cee27f6c62ddc01d0b4ae0596fa2e6be2e476161bdb1250e90f568c65 | Text | 327 | 11 | # HPRO package
HPRO is a python module for Hamiltonian Projection and Reconstruction to atomic Orbitals.
Author: Xiaoxun Gong (xiaoxun.gong@berkeley.edu)
## Installation guide
1. You should have Python 3.8+ for installing this package.
2. Go to `src/` directory and use the command `pip install .` to install the pac... |
5776dae6ab8d22046b743eaa08f4ca0628c96598057d28e3c2f0699ae0a8a666 | Text | 339 | 4 | # SOP-dynamics
Codes for the paper 'Structural origin of relaxation in dense colloidal suspensions'
Folder SOP contains the python codes to calculate the structural order parameter both in 2d and 3d. The folder dynamics contains the matlab codes to find the relative displacements in 2d and non-affine displacements in ... |
79b5a26fc8f85e355c43076cccc5fe8831bfe94388348ea780d327e72511baa0 | Text | 344 | 7 | Sex differences in functional cortical organization reflect differences in network topology rather than cortical morphometry
Bianca Serio*, Meike D. Hettwer, Lisa Wiersch, Giacomo Bignardi, Julia Sacher, Susanne Weis, Simon B. Eickhoff, Sofie L. Valk*
* Correspondence to:
Bianca Serio (b.serio@fz-juelich.de)
Sofie L.... |
e707ceac91284e776413815d11d37d9f6f3d165776bceae43e2d7537f51a512e | Text | 348 | 8 | - Data access needs approval from the Dominatly Inherited Alzheimer Network (DIAN)
- https://dian.wustl.edu/contact/
- Please contact the corresponding author Dr. Muriah D. Wheelock for data access.
Notes of the name of the data files loaded:
- MRI_subjectlist_N207_221213.xlsx
- regression_covariates.csv
- HDI_individ... |
d0f8335d2fa9cd23ff9a39dff165f1f81fe0b31e6ec492f9b23ca0567eefb531 | Text | 351 | 5 | # Syntactic_Semantic_Specialization_9_10_yo
The excel shows all the subjects and their corresponding runs used for this project. All the original data is on [OpenNeuro.org ](https://openneuro.org/datasets/ds003604)https://openneuro.org/datasets/ds003604
All the scripts used are the same as the ones used in Syntactic_... |
5dca2285541b5bebeed7e333cd0da9f707400a0bf5921e9dce9d6bd3d5ce5e9a | Text | 356 | 5 | # Surface tools
Welcome to Surface tools! a collection of tools for surface-based operations
- equivolumetric surfaces: creates equivolumetric surfaces based on the ratio of areas of the mesh surfaces, without the trouble of dealing with volumetric operations. Built together with Alexander Huth at a Brain Hack, a vers... |
8b850b4169d4a6828b327741095a59fc3a7c8ea7d87cfdc753b27cea4a1ea31e | Text | 356 | 9 | # MEA_signal_predictor
This repository was used to predict MEA signals in neuron-astrocytes co-cultures.
The methods are explained in this publication: https://doi.org/10.1098/rsos.240839
The original dataset used with this code can be found at: https://zenodo.org/record/7741379
Please, if you reuse this code, c... |
fdbeef8459a42520b4be3c969c5eadae565660f397355ca9944fc485cde5c190 | Text | 358 | 8 | # Dynamic-tuning-of-neural-stability-RNN
Code accompanying the paper: "Dynamic tuning of neural stability for cognitive control."
Muyuan Xu, Takayuki Hosokawa, Ken-Ichiro Tsutsui, Kazuyuki Aihara
https://www.pnas.org/doi/10.1073/pnas.2409487121
Code used to train a recurrent neural network on the reversal-learning... |
582e2bc66856ee34a306f5b542f9a5066c79214948d0ba997582bca2594e1be9 | Text | 365 | 10 | # eeg_removal_memprage
will remove eeg electrode artifact from an memprage/most anatomical images.
nina fultz 2021: please message nfultz@mgh.harvard.edu if you run into any problems
biasfieldcorrection script is from daniel gomez 2021
Usage:
will remove eeg electrode artifact from an memprage/most anatomical imag... |
910d1a2dbe4caab8c30648e3828f94c83086176aae27045b1bc33bc3cf24e627 | Text | 370 | 2 | # LIP_single_trial_decision_variable
This repository contains the code required to reproduce all figures and results of the paper "Direct observation of the neural computations underlying a single decision" by Natalie A Steinemann*, Gabriel M Stine*, Eric M Trautmann, Ariel Zylberberg, Daniel M Wolpert & Michael N ... |
ca670f98379164cc71d8354c91ad315f01e9b4668ec59b46fa151b3c07c0801c | Text | 374 | 6 | # README
This repository contains the code used in the genome-wide association study of eleven neuropathology endophenotypes performed by Shade et al. (forthcoming). Any questions can be directed to lincoln.shade@uky.edu or david.fardo@uky.edu.
DOI generated using Zenodo: [![DOI](https://zenodo.org/badge/374730412.s... |
e1a4c3e8cfaf77fcca5031bd1bc2120041215774ab67c365aaa7c74dae1a5694 | Text | 374 | 5 | # GridCellTorus
This repository contains code for topological analysis of grid cell population code as in "Toroidal topology of population activity in grid cells" by Gardner and Hermansen et al. https://www.nature.com/articles/s41586-021-04268-7#Sec42
Data is found in https://figshare.com/articles/dataset/Toroidal_t... |
f4a983e1b60a72a100cca9cec06e1e5f2a51d9820b3c8c21b7d377deb78b05c5 | Text | 384 | 8 | # Data repository for Van der Plas**, Tubiana** and colleagues, 2023 eLife
Data that was used for cRBM analysis of zebrafish spontaneous activity recordings. Contains neural recordings and trained cRBM models.
For further information, please see our paper at:
https://elifesciences.org/articles/83139
**We welcome to... |
c64d7e056f2812c648cddda7f08d526514e994ebf708763a6d8490d438a911fa | Text | 387 | 9 | [](https://doi.org/10.1002/jnr.70008)
All the R scripts created for the analysis on the differentially expressed genes between male and female mouse spinal cords using single-nucleus RNA sequencing data.
Scripts are ordered for result reproduction purpo... |
afa69644271cbbff9c22c83396f1d2d0479c4ea5f5fdab5a0fafbbf7bcc109aa | Text | 397 | 7 | # StableAndPreciseICMS
Repository to accompany:
"Intracortical microstimulation of somatosensory cortex evokes stable and precise tactile sensations"
Greenspon, et al. Nature Biomedical Engineering (2024)
To run this code you will need to update the 'HelperFunctions\DataPath.m' script to the location of the data.
The ... |
77ece4fabfba5e8a372cd675890032396397111169d7e261b67b0f2aba7e897d | Text | 401 | 6 | # flexible_decision_making_training
Training code for the rat flexible decision-making task
>Marino Pagan, Vincent D Tang, Mikio C Aoi, Jonathan W Pillow, Valerio Mante, David Sussillo, Carlos D Brody (2022)
>A new theoretical framework jointly explains behavioral and neural variability across subjects performing flex... |
1e3f5660ff2dbe9b245152fc25ea2104c2c33424a13d9cf60d02463c7f4f0a08 | Text | 405 | 3 | # Hr38_eLife
Code for Watanabe et.al., eLIFE 2024
This is a repository of code for analyzing 2 photon calcium imaging data and to generate figures (Figure2 , Figure 2- figure supplement 1, and Figure 3- figure supplement 1) associated with the manuscript "Whole brain in situ mapping of neuronal activation in Drosophila... |
0f505ca38bc9454e58c9f9554c11029a2fc389fdb59736f1209c4b78c23d9bd7 | Text | 411 | 11 | # metamers
code for generating visual metamers as described in
> freeman and simoncelli, metamers of the ventral stream, nature neuroscience, 2011
> http://www.nature.com/neuro/journal/v14/n9/abs/nn.2889.html
see `contents.m` for what's in here and `metamerTest.m` for testing basic functionality.
written in matlab... |
a89eab11ba19cda11045fd7dcfd19f8f5b3f0c7f7b2155bce14d42c899e67cd4 | Text | 412 | 15 | # Agglomeration
[](https://magnum.travis-ci.com/seung-lab/Agglomeration)
## Installation
```
- Pkg.clone("git@github.com:seung-lab/Agglomeration.git")
- Pkg.build("Agglomeration")
- Pkg.resolve()
```
## Us... |
74094891fc519536b8ba2024502ea39a84ed24cf19af498b3ddbdfd3d45ebd56 | Text | 424 | 5 | # MIMIC-CXR
MIMIC-CXR is a publicly available database of chest x-rays with free-text radiology reports. You can read more about the dataset on [the PhysioNet project page](https://physionet.org/content/mimic-cxr/).
This repository is intended to support use of the data by providing code, documentation, and a central... |
b292987369fdf2587bb89a28c74f7a165fa2f758fc7b835f71188017aa55afd7 | Text | 430 | 9 | # NetworkLevelAnalysis_v1.0
DEPRECATION WARNING!
This toolbox will become deprecated in Spring 2025, and replaced by a new GUI based version!
This toolbox also does not properly handle multiple comparisons FDR corrections, which will be addressed in new Spring 2025 release
Planned URL of new version will be (curren... |
0303093e081039e8e909b59917f4f53f3a2c4572b271778660dbe6dc428d3f50 | Text | 434 | 15 | Code used for "Low-power scalable multilayer optoelectronic neural networks enabled with incoherent light"
Folder structure:
data_analysis_and_plotting:
MATLAB and Python Code used in generating and analyzing data for figures in article
experimental_control:
Python code used to run experiments
network_tra... |
5b5d3070415a5fc5efc1dd6550f09bea3c7fb8051628fcdda4e9c0f8a59c335b | Text | 440 | 10 | # Tools for bioimage analysis
## Annotated data
An annotated high-content fluorescence microscopy dataset with Hoechst 33342-stained nuclei and manually labelled outlines
[https://zenodo.org/record/6657260](https://doi.org/10.5281/zenodo.6657260)
## C01_conversion tool
This folder contains code and instructions to ... |
b56203fa041f90ff77a8e7271a652dd81f9288cae223c710c473d25b70f0a86b | Text | 445 | 9 | # 3D_Printed_Skull_Cap
Design Files for Digitally Designed and 3D Printed Skull Caps
3D-printed microdrive mouse headcap design for multiple targeted location silicon probe implantation.
The .stl files are adjusted for Formlabs Form3B printer with Clear-V4 Resin. Clearance has taken into account with the 3D-printing... |
acf13c632f9bedb2d58e9fc33607e3547665b67d50f5adaf719bc9bd881fc7a4 | Text | 447 | 1 | The csv files contain tabular data used to generate charts and analyse statistical significance shown in figures. Each file represents the raw data in the figure panel and is named by the figure number and panel, as well as the description of the analysed parameter. E.g., ÒFig 3d hASYN_hASYN PLA dots (number)Ó contains... |
da841398e4b961a3021eb82bc97815fc81afedb92cf042182f19470030e3e32d | Text | 447 | 12 | Data and code for:
A neural algorithm for computing bipartite matchings.
(c) 2024 Saket Navlakha, navlakha@cshl.edu
To reproduce results, simply run "src/run.sh". This will run all the experiments on the random and real-world networks.
Panels for Figure 2 will be placed in "figs/" and can be compiled into ... |
c6be8470b1a0f3b616a1d3989c210c209dd5fa757481812c203a9f45bc592a12 | Text | 448 | 12 | Data and code for:
A neural algorithm for computing bipartite matchings.
(c) 2024 Saket Navlakha, navlakha@cshl.edu
To reproduce results, simply run "src/run.sh". This will run all the experiments on the random and real-world networks.
Panels for Figure 2 will be placed in "figs/" and can be compiled into ... |
6623bcdf4d428d36af68b7c49ff8e2cadb08b02258061a9c4769a1d680a810b8 | Text | 455 | 8 | # PRE_VIS_DA_CURR_BIO
Pre-existing visual responses in a projection-defined dopamine population explain individual learning trajectories
* **bioRxiv link:** https://www.biorxiv.org/content/10.1101/2024.02.26.582199v1.abstract
* See `README.md` in the pipeline directory for instructions on how to run the analysis from... |
b6b78d02dcbc76d6ed350e1be4b432c3dbd89a01181ef6e3d5694bd44c0ebc5c | Text | 462 | 9 | # multistateAvalanches
Code and data used in the paper ["Criticality and universality in neuronal cultures during ‘up’ and ‘down’ states"](https://www.biorxiv.org/content/10.1101/2024.01.10.575061v1)
Complete code and data will be released upon journal publication
## Contents
- neurongen: code used to generate the si... |
b17584a0468a877d777014c38c6702911e34bf620c383e73def792d342b221ec | Text | 470 | 4 | # DiscreteRingAttractor
MATLAB code for Noorman et al. (2024), Maintaining and updating accurate internal representations of continuous variables with a handful of neurons.
All related data can be downloaded from Janelia Figshare (https://doi.org/10.25378/janelia.26169355). The function main.m contains instructions fo... |
4cd47328f9501febae7e44a4f50cfcfe5e53687fa36b43843f2689674444983c | Text | 473 | 10 | ## README
Codes from the manuscript [Bocchio, Vorobyev et al 2023](https://www.biorxiv.org/content/10.1101/2023.09.18.558335v1)
Here you will find:
- MATLAB Codes used to analyse spontaneous 2-photon calcium imaging data (Figs 1 and 4a)
- Python Codes used to analyse 2-photon imaging + holographic optogenetic stimula... |
a505927cd488ad9f4119d0bc0bc0147cb7e47fe37401bfa3fdfc245d4791276b | Text | 482 | 2 | # Newman_QuaSOR_2021
Quantal Synaptic Optical Reconstruction (QuaSOR) Matlab pipeline for analysis of synaptic transmission and corresponding Matlab scripts for the analysis of synaptic nanostructures at the Drosophila neuromuscular junction. Includes scripts largely authored by Zachary Newman in the Isacoff Lab at UC ... |
23da4ccaf5c41d34beb3c99d5b3dd563882bf482aa0a3c55be66e267a503e85e | Text | 483 | 25 | # Neurocognitive dynamics of preparatory and adaptive cognitive control
## Setting up programming environment
### Install Anaconda / Miniconda
See [here](https://docs.anaconda.com/free/anaconda/install/index.html).
### Install MNE
```shell
conda create --strict-channel-priority --channel=conda-forge --name=mne-1.5... |
a6a95e103d4aff5f0f1b46e67f2741b93150ecc4f71056f03c96ece32ad5527a | Text | 486 | 2 | # CNNs-lightning-prediction
This codebase was developed for the manuscript entitled "Predicting Cloud-to-Ground Lightning in the Western United States from the Large-Scale Environment using Explainable Neural Networks" by Kalashnikov et al. (2024). The associated datasets which this code uses are stored in the followin... |
80c4e5ae22269919b36b43eec843652b607059c636997a8e293477eae7f2286c | Text | 488 | 5 | ## This is a dynamic clamp README for Kv3.4
The dynamic clamp code has been modified off of Niraj Desai 2017 "A Dynamic Clamp on Every Rig" https://www.eneuro.org/content/4/5/ENEURO.0250-17.2017.
This has been adapted for Hodgkin Huxley modeling of Kv3.4-PM and Kv3.4-PN based on a previously published paper in _J Neu... |
17af4588d8b951b4b48798281f4ebe7daca4d838a6b1121bc24be4497a21b2bf | Text | 489 | 16 | # electron-tvmc
This is code related to the paper:
```text
@article{nys2024ab,
title={Ab-initio variational wave functions for the time-dependent many-electron Schrödinger odinger equation},
author={Nys, Jannes and Pescia, Gabriel and Sinibaldi, Alessandro and Carleo, Giuseppe},
journal={arXiv preprint arXiv:24... |
5c06995042ba8e2034a6db2387500ed1f61f076e43804648b8d617e7f873563d | Text | 491 | 12 | # Fly Behavior analysis
### Contact: [kkwon@unist.ac.kr](mailto:kkwon@unist.ac.kr)
In this repository,
- Calculate centroid of each DGRP flies
- Walking distance in whole experiment times
## Reference
If you found this code useful, please cite :
Jiwon Jeong, Kujin Kwon, Terezia Klaudia Geisseova, Jongbin Lee, Taej... |
3388cbf42343d26893d270b1d1dda5bda6398637585dbab970023a0d4a426ebc | Text | 495 | 9 | # Intrinsic dynamics of randomly clustered networks generate place fields and preplay of novel environments
This repository contains all code necessary to create the figures of the paper:
> Breffle J, Germaine H, Shin JD, Jadhav SP, Miller P. 2024. Intrinsic dynamics of randomly clustered networks generate place fiel... |
cd1053d782711ef1b3fa514e61da20341782c32fa0f9a3e5029a05bbdc0c4445 | Text | 510 | 10 | ABFUN is a python library for extracting actions potentials and
classify them based on temperature information within an *.abf file.
This work is protected with a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
To view a copy of this license, visit http://creativecommons.org/lice... |
5b9dee167871e85e7a3e575b6644c6d06657813c3fdb147e693478f894441284 | Text | 511 | 8 | # SEM2
This the current model development code spinned off from the *Structured Event Memory* (SEM) model, originally presented in Franklin et al., 2019 [[pdf](http://gershmanlab.webfactional.com/pubs/Franklin20.pdf)].
This repository contains modifications described in https://psyarxiv.com/pt6hx/. This repository is... |
03c286a72ff0d8ce41a6599988ea423f227909072da7f4a78aea2c7842203488 | Text | 514 | 9 | ## Multivariate-GWAS and evolutionary analysis of reading/language- and rhythm-related traits
This repository includes all scripts written for the manuscript [The shared genetic architecture and evolution of human language and musical rhythm](https://www.biorxiv.org/content/10.1101/2023.11.01.564908v1).
## Contact
G... |
ed7697e9d1b6a73e1fddaadc4952b6b4f3715114dae8bd4e2c598f2b6edf85f5 | Text | 515 | 6 | # BilingualBrainNet
Data and code for analysing functional connectivity data from bilingual samples.
[Data](https://github.com/zchuri/BilingualBrainNet/tree/main/Data) contains all the preprocessed brain and phenotypic data.
[Code](https://github.com/zchuri/BilingualBrainNet/tree/main/Code) contains all the scripts t... |
32ae80e4f2e2eb5c6ebd791ae8b102fd72dad47fe1589225e25650dea80dd0a4 | Text | 517 | 7 | # GF_mouse_primate_23
Code for analysis of physiology and gene expression data from GF mouse experiment: The primate gut microbiota contributes to brain-body energetic trade-offs in host metabolism
Code for microbiome data analysis can be found here: https://github.com/Mallott-Lab/PrimateMicrobiomeandBrainGrowth
Ama... |
f74853d77a045fd6ebfc72119622cb802b146162d018bb3cd96de1434bd177e4 | Text | 529 | 10 | # SubdiffusionDKI
An implementation of the algorithms in [Farquhar et al., (submitted) 2023]
To run these files, you will need ml (the Mittag-Leffler function by Roberto Garrappa, available at https://www.mathworks.com/matlabcentral/fileexchange/48154-the-mittag-leffler-function)
Originally developed by Megan Farquha... |
fc6089f5d5911d5c10b8b57ef842eb8dc56504c81678bb80b7ba6886de30892a | Text | 530 | 9 | # SytSim
**Author:** Chris Norman
**Contact:** chris.alex.norman@outlook.com
Toolbox for simulating neurotransmitter release from synaptic vesicles under 'release of inhibition' models in response to arbitrary calcium stimuli. Currently under development, see the *example* notebook for basic implementation.
... |
4a9e692b33faf276dd9393e0bd730d35cd9c122e359048032007d5bf48f1dd9d | Text | 534 | 12 | # PROTEAS
PROTein Expression AnalysiS
Protein microarray expression analysis
The analysis was performed on raw data collected after microarray image analysis. The raw intensity values for each receptor/protein was recorded automatedly via image recorder software or manually using ImageJ software.
# DOWNLOAD
To down... |
2a7fa5311d7134375536d313e2ab6d386732c5d5615aee75ef5131e58c28d7f4 | Text | 541 | 4 | Figures and Tables presented in the journal article "Hazarika, D., Vishnu, K. N., Ransing, R., & Gupta, C. N. (2024). Dynamical Embedding of Single-Channel Electroencephalogram
for Artifact Subspace Reconstruction. Sensors, 24(20), 6734. https://doi.org/10.3390/s24206734 " can be generated by downloadeding data and so... |
7d7187f3211acdc06a12778dcdd168c7694e3acd0ffe2e38c140741515474319 | Text | 544 | 19 | This dataset (0-14260s) includes timestamps of 55 CA1 units, 58 BLA units, one CA1 local field potential (LFP), one band-pass filtered CA1 LFP (100-250Hz; ripple), and one BLA LFP.
Below is a list of event timestamps.
1) Pre-training sleep: 0-3530s; 5615-7500s
2) Contextual fear training: 7521-9272s
(10x f... |
70bcb9d30259193bf3db3be124f67ab4ca9a23bde614a775bbd62bec358a2fed | Text | 549 | 11 | # axonal AP
NEURON (and some python) scripts associated with the manuscript:
János Brunner, Antónia Arszovszki, Gergely Tarcsay and János Szabadics
Axons actively compensate for biophysical constraints of variable size to uniformize their action potentials (2024)
...................................................... |
ba8dd89846350ec934942c4b1bc94e70f38a4dd54ab4e29ec89372b53965b6f5 | Text | 565 | 29 | # README #
This README would normally document whatever steps are necessary to get your application up and running.
### What is this repository for? ###
* Quick summary
* Version
* [Learn Markdown](https://bitbucket.org/tutorials/markdowndemo)
### How do I get set up? ###
* Summary of set up
* Configuration
* Depe... |
22a65e671018dd4e8f21c79c6c8369b25750ae877900c9c1a634dfb36d89fe01 | Text | 568 | 7 | # BEBE-datasets
These are notebooks which format datasets for use in the Biologger Ethogram Benchmark (<https://github.com/earthspecies/BEBE>).
If you would like to format a new bio-logger dataset for use in the BEBE pipeline, it needs to be done in a specific way. We have annotated one of these notebooks (`format_HA... |
97872249fddaf32d18cf96b79ae4a1c5240390f027e0d66a6341662203bd152b | Text | 569 | 4 | # Auditory-GAN-
This code is for our article titled"Auditory-GAN: Deep Learning Framework for Improved Auditory Spatial Attention Detection"
The proposed auditory-GAN system consists of a spectro-spatial feature extraction (SSF) module and an auditory generative adversarial network auxiliary (AD-GAN) classifier. The S... |
4a4cc41ac50d36081ceef2e711ccaca374b4d4a7f69ff0d9ed62cbe6a7c06902 | Text | 575 | 17 | Tempo [](http://www.janelia.org)
=====
Tempo is a MATLAB GUI for browsing, analyzing and annotating time-synchronized media files.
[Documentation](https://cdn.rawgit.com/JaneliaSciComp/tempo/7f37ebcbed08cfa0d746ad5baa3901ed4a986187/Documentation/index.html)
=============
Authors
=... |
65058960f41c308d36f576d36d2a6cb75ee6d627ee72e63c16b44442d914ba47 | Text | 576 | 7 | # Codebase supporting *"Hyperspectral unmixing for Raman spectroscopy via physics-constrained autoencoders"*
This repository contains the codebase associated with the paper:
Georgiev, D., Fernández-Galiana, Á., Pedersen, S., Papadopoulos, G., Xie, R., Stevens, M., & Barahona, M. (in press). *Hyperspectral unmixing f... |
3e8ba64da4a67fe19125ddc7d777e2aa23493148fee92f6fde110d2eb80faf62 | Text | 579 | 15 | # This kit will launch a docker container to run wmhkit and exit when done.
# Use the releases tag to first install the docker container image of wmhkit.
# Running (Can launch any number of instances):
# 1. To check the usage of the script:
sudo bash run_ucdwmhkit.sh
# 2. Example run command:
sudo bash /path/run_... |
641a0f121e25312b693475dca89ea058fc33e195874111496a0f01460fddf295 | Text | 581 | 11 | # Spot-Spine
This ImageJ plugin allows to detect and count dendritic spines, to segment spine heads, to trace spine necks, to obtain quantitative morphological measurements.
Spine detection and spine heads segmentation use algorithms from the plugin [3D ImageJ Suite](https://mcib3d.frama.io/3d-suite-imagej/).
Spine ... |
aebebe0ab0ec013c68ae2c79a663c84d61a3bb61bcf1a93e88ee1ff275d45854 | Text | 584 | 7 | [](https://github.com/eippertlab/spinal-lep1/releases/tag/v1.0)
[](https://zenodo.org/doi/10.5281/zenodo.12658842)
[](https:/... |
f6941e33ed5160f976c0a28806106eb38f4f48dfb5da62af4724344de1876fb6 | Text | 584 | 7 | [](https://github.com/eippertlab/spinal-lep1/releases/tag/v1.1)
[](https://zenodo.org/doi/10.5281/zenodo.12658842)
[](https:/... |
d4149e2611375fa1cc0aeb6f652d23cc0c93aa3c26e70d1a6409dd0be2e8a7d1 | Text | 586 | 7 | # **MRI feature extraction and KPS prediction**
### This repository hosts the code for our study, "Postoperative Karnofsky Performance Status Prediction in Patients with IDH Wild-Type Glioblastoma: A Multimodal Approach Integrating Clinical and Deep Imaging Features." Specifically, it contains the variational autoenco... |
45ad63bce7f76495443434c32456d5a45de0893533bf3dcc1fab68a80a3dff77 | Text | 590 | 14 |
# OptMRL
Interpreting Deep Neural Networks for the Prediction of Translation Rates - Frederick Korbel, Ekaterina Eroshok, Uwe Ohler
## Overview
This repository contains analysis code and data necessary to reproduce findings from the manuscript and training code for the OptMRL model. MPRA data from Seelig et. al us... |
e8d1234a0fe1fb65207504926b73600d8a47bbd213cceb33b1f76346eec91c51 | Text | 591 | 15 | # tre-tVMC
Taylor-Root Expansion time-dependent Variational Monte Carlo
Please cite our work if you use this code
```
@article{nys2024ab,
title={Ab-initio variational wave functions for the time-dependent many-electron Schr$\backslash$" odinger equation},
author={Nys, Jannes and Pescia, Gabriel and Sinibaldi, Ales... |
f0c8bc17c1029d793ea2171c0ec3d0d4c88192e2e5b28b3534e50b2f30b1da38 | Text | 595 | 5 | ### Replication of Sex-Dependent Alterations of Apoptotic Processes in Alzheimer's Disease Revealed by Large-Scale Single-Cell Transcriptomics
- `gender_analysis_seurat.R` is used to perform the differential expression analysis using Seurat (version 5.1.0, RRID:SCR_016341)
- `biological_analysis.R`is used to visualize... |
92158b335d635e221163ac32d2c49a613f87bebccf551563c6402901f5af04fb | Text | 600 | 8 | 'get_ndRMS.m' is a MATLAB function to get the ndRMs,
'script_run_ndRMS.m' is an example script to call the function.
Please cite the following paper when you used the ndRMS in your study:
** Geukes, S.H., Branco, M.P., Aarnoutse, E.J., Bekius, A., Berezutskaya, J., & Ramsey, N.F. (2024). Effect of Electrode Distance... |
2f653a75a8248578f794c325fcb67247fe89b160cdec0446539901445a6ae618 | Text | 610 | 20 | # Electrodiffusive network model
This repository contains an implementation of the model presented in
[Sætra MJ, Mori Y (2024) An electrodiffusive network model with multicompartmental neurons and synaptic
connections, PLoS Comput Biol 20(11): e1012114](https://doi.org/10.1371/journal.pcbi.1012114).
## Installation... |
0d581de7ca501669f8fa53e47d9f044345a6ae2257fc836820a62a17ab1d9fea | Text | 614 | 8 | # MultipleCoherentSubnetworks
Analysis and Figures scripts for 'Emergence of multiple spontaneous coherent subnetworks from a single configuration of human connectome coupled oscillators model'
The simulations and several utilities are dependent on [AnilloVibrain/KuramotoNetworksPackage](https://github.com/AnilloViBr... |
6bc18274577d3d3bced5f807e1e96c66b4a01f2493bcbfa5f143295c4d2ce977 | Text | 618 | 29 | # Functional Genomics in a Genome-Wide Assocation Study of Progressive Supranuclear Palsy
Jack Humphrey, Ashvin Ravi & Kurt Farrell
Icahn School of Medicine at Mount Sinai, New York
2023-2024
## Manuscript
Currently preprinted on [MedRxiv](... |
315c77b946b768822f464b0c4a3104b99544012692bd7ee5409b6a18d5c6aa8b | Text | 633 | 7 | # ATRT_project
This repository contains all code that has been used to analyse CRISPR-Cas9 screens in ATRT cells performed with the genome-wide knockout library Brunello.
These analyses include correction for gene-independent effects in CRISPR/Cas9 knockout screens (CRISPRcleanR), hit calling using the gene essential... |
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