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33c0df8123613486144636ee70c91526f2cb68ad4c165a7a43795e316cabdd9f | Text | 100 | 1 | Data and code for "The impact of EEG preprocessing parameters on ultra-low-power seizure detection"
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bf71b2b7fdf502b7a01699acf943a099b06b233f660cb0d8ae7708e0efb1b8e8 | Text | 102 | 2 | # Cingulotomy_Vocalization
This Repository contains the codes to create figures for eLife manuscript
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0950bc2c48ffacd04f2c1c591d2d0f5fee627d71c20d0a2d7b7609b5ee7b7b8c | Text | 105 | 3 | # Experiments for line-scanning
Various experiments for projects at the Spinoza Centre for Neuroimaging
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1a3a2eddd96aba7b8fdc2402b0a224a3997c22d62f55fd7f90b986a14aee5756 | Text | 105 | 3 | # ATLAS_nature_method_2024
ATLAS: A rationally designed anterograde transsynaptic tracer (NMETH-A55446A) |
eba86e706d76e026a0f6b26c724d2dcd6b75ca2ac44c556392b06bf5d8ed1988 | Text | 121 | 2 | # digital_twin_egg_data
Datasets in "A Multi-Modal Digital-Twin for Autonomous Micro Drilling in Scientific Exploration"
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5d785cf4c80f0dbba0c0edd14c6f753b307d765c9327267e14bd72d5ce62ce7d | Text | 123 | 7 | # SnpEff
[Documentation: https://pcingola.github.io/SnpEff/](https://pcingola.github.io/SnpEff/)
Enjoy!
Pablo Cingolani
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9a3a5f80fadc0921f9e71707e34867d4788e967f5365cdd6b4a5008ee3c07f8f | Text | 126 | 2 | # Konishi_Burrone_2025
Code from the Journal of Microscopy paper by Konishi et al., (2025). https://doi.org/10.1111/jmi.13436
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9ba33403957a03aeee4b7fec83c63091705aed1d87d6575fa712d18b51d88ad8 | Text | 134 | 5 | # aimi-lung2-ct
### Downloading IDC data using big query
Run download_idc_data.ipynb
### Model perfromance
Run model_perfromance.ipynb |
01bb774c083f556e1aafd1a5d30cf924039d75e2a22a758946ab23badc7e52c9 | Text | 136 | 2 | # sc-INDC
Code for "On Learning Information Maximized and Noise-Invariant Representations for Clustering Single-cell RNA Sequence Data"
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82f2279e0449a5d7944b9dfac0104f7a29d41bee63f28afea223a37e772f712f | Text | 136 | 3 | # methylation_aalosa
Scripts used in "Adaptation to Freshwater in Allis Shad Involved a Combination of Genomic and Epigenomic Changes"
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036f18a164d2648d2e0b3164cfa9591260056fba0b32cfcedb7caf7c42ed28d3 | Text | 137 | 2 | # VENM-AMD
Analysis Code associated with the video-evoked neuromarkers of visual function in age-related macular degeneration manuscript
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a22690c2370da80e0a3d2dc7f18039b0b6943671b336ac329cb8f791260f6b84 | Text | 140 | 2 | # GaitInsight
Repository of paper "Insights into gait performance in Parkinson's disease via latent features of deep graph neural networks"
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2dbae2e5cfd4a2b606cae4b63ea3fe5004ebd0ff401f55b4ba9fdf420eca6bbd | Text | 142 | 5 | # Brain MR Segmentation
### Downloading IDC data using big query
Run download_idc_data.ipynb
### Model perfromance
Run model_perfromance.ipynb |
391ec89f06317d5a6794d5d894bbbdd8c08d1f36344a968925baf190acf2f0c4 | Text | 143 | 5 | # Breast MR Segmentation
### Downloading IDC data using big query
Run download_idc_data.ipynb
### Model perfromance
Run model_perfromance.ipynb |
4a655244ace1754592f3b680663f533644ec00d5ca58a7d04497274423f9d758 | Text | 143 | 2 | # lindsey_etal_striatal_dynamics
Code implementing models of Lindsey et al., Dynamics of striatal action selection and reinforcement learning.
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86d75f821c923138d88895d60b77fb534651cdf05d74f7fd6ea6f6c2c81f2f67 | Text | 152 | 3 | ## README
To make use of the notebooks in this folder, please download the utils.zip archive, unzip it and save the utils folder next to this folder.
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0b148d3c95bc40434c8ec05c335a3bf238028d986d1fc3f22ec74dc177637ecb | Text | 154 | 2 | # Connectome_Harmonization
Big Data, Small Bias: Harmonizing Diffusion MRI-Based Structural Connectomes to Mitigate Site-Related Bias in Data Integration
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e2e9264dc8dfb0fa729bc350e9626db77d66b148aba24ffb251bfdce8f36bea5 | Text | 157 | 1 | spike_OASIS: the number of ROIs is not match to the DFoF_median. The artifact ROIs (Judge == 0) are first removed and then the spike inference was performed. |
e184361c550d3e4394d9aa8bd5802f3b58f0108cd45dfe5ace8ed5e0a5a0eeb3 | Text | 161 | 3 | # Stokes_HFB_iNPC_Analysis
This repository cantains the code for the Gale lab single cell induced neuronal progenitor cells and human fetal brain cell analysis
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a6e84163c6347a3fae10a1fe42f0560c3918578668e6ff2ca6baa5282dbcf3f1 | Text | 163 | 9 | # somireward
This is the code repository for the paper
*Predictive goal coding by dentate gyrus somatostatin-expressing interneurons*
bei Yuan et int. Bartos
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98595dd714ddcd79a23a9aa1a334526aaf873de50c35af0dfc534fd50e18718f | Text | 168 | 2 | # handwriting trajectory decoding with DILATE loss
Xu et al., (2025) Decoding handwriting trajectories from intracortical brain signals for brain-to-text communication
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db5bc92d24e3b032173cd5ba58f420afbfd6a9d459a94bf29c8e06d61d9a5fe6 | Text | 175 | 1 | This repository contains the FiPy Colab scripts and .msh files to simulate a simple 2X2 chemically based matrix computing unit, as described in the main text of Basile et al.
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c40b823f8fc690e90678f4084cd86033b4677060588f1e6a4d8fa7afe463abf2 | Text | 180 | 6 | # swc2mesh
[Pre-release version. Work in Progress.]
Main functions: convert cellular SWC files to watertight surface meshes.
Required python packages: numpy, trimesh, pymeshlab.
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143d2747853d396b44fcb4d6a4ebe198058d84a8f5753ccf3264fc7bbb3ec078 | Text | 183 | 4 | # morphodynamics_human_brain_organoid
This repository will contain the scripts and code for the "Morphodynamics of human early brain organoid development" paper (Jain, Gut et al.).
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4e2f874d26948fbd21017bef707ea73710ae71c09dcb2cdd26304e933e19d9df | Text | 191 | 6 | # zhong-et-al-2025
code to make figures from Zhong et al, 2025
"data_process_script.ipynb" show how to process and save the intermediate results.
"Figures.ipynb" for plotting all figures.
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416b7fa5d29dafcc74a27599fa0eb2b9fa457ff72ada924b69765b81597d087a | Text | 197 | 3 | # forelimbhierarchy
Code for the paper "Hierarchy between forelimb premotor and primary motor cortices and its manifestation in their firing patterns"
Data can be found on the Miri Lab DANDI page.
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f3cda1d30b04de3621f5b89b16ec6aa4913295b48b774f1cdde89981d54c724e | Text | 205 | 2 | # spine-generic-body-size-results
Results for manuscript: Labounek et al. (2024) Body size interacts with the structure of the central nervous system: A multi-center in vivo adult human neuroimaging study
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f96b7e11b215d2f795a59107b88c11e356372fb469874deb1ccd9d7c75347449 | Text | 209 | 7 | # HEKADatConverter
Convert HEKA Patchmaster *.dat to ABF files that can be opened with Clampfit
### credits:
[pyABF](https://github.com/swharden/pyABF)
[HekaReader](https://github.com/ZeitgeberH/HekaReader)
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9d72537a6491891592139ea8e5816bbe8580b97dda5c6cb879d743063b4ed561 | Text | 228 | 2 | # vesicle_measurement
Python notebooks for the segmentation measurement part of the paper "Charting the molecular landscape of neuronal organisation within the hippocampus using cryo electron tomography" by Glynn, et al. (2024)
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9e974e7cdcb1f573b972475c691148f08eda96e744e90b319df6e25c830dbd8c | Text | 228 | 6 | # VHD-System-Paper
Code for "Functional brain mapping using whole-head very-high-density diffuse optical tomography" manuscript in Imaging Neuroscience
Manuscript: https://doi.org/10.1162/IMAG.a.54
Code will be updated soon.
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446e103edb0a9af33f44c8ed3d43359c2dcd179960025c9e59ad7fabe351a0b0 | Text | 234 | 4 | # patch_clamp_analysis
Analysis software (MATLAB-based) for the Circuits, Synapses, and Molecular Signaling Section (CSMSS) at NINDS
A collection of MATLAB scripts used to analyze patch clamp neurophysiology data collected by CSMSS.
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20650b60891e3268bd30e0ad794518c9c6dfe181647a2355de1297d1d8823c91 | Text | 247 | 2 | # Traveling Wave TMS Code Repository
This repository contains the scripts used in generating EEG-controlled TMS results pertaining to a manuscript on spatial gradients of phase preference and their relationship to traveling waves in EEG and ECoG. |
b8a2bf1f798429d3cb5a415ba852ce675fd11125c6fd5c4b06e37b569bf5dece | Text | 247 | 4 | # syndevkit
Code for data analysis and figure generation for Soliman et al. 2024. A compatible python environment can be generated using the included `requirements.txt` file.
Code depends on data deposited at Zenodo (DOI:10.5281/zenodo.10810428) |
a22e215ca418e0a25079eee45cff32ee3de4612cfa49396e1061e2bd5441b0a3 | Text | 253 | 3 | # Code for "Between Two Extremes: Tripsacum dactyloides Root Anatomical Responses to Drought and Waterlogging"
Section data is included within this repository. To download raw light microscope images, please use https://doi.org/10.5281/zenodo.14834917. |
bd9bfc650a7d861e4c8628960270f60ed593a799ce9006d7d4fd476f2a72de31 | Text | 257 | 6 | # Sensorimotor integration enhances temperature stimulus processing
Repository for the analysis of "Sensorimotor integration enhances temperature stimulus processing."
The paper which publishes this code and describes methods/analysis can be found at:
TBD |
769a816fc6b1a422c2aff0efb2c864069e42eabf5be667789d8a99ef3466eaad | Text | 261 | 1 | This is the Matlab code used in the scientific publication "Context-Dependent Modulations of Subthalamo-Cortical Synchronization during Rapid Reversals of Movement Direction in Parkinson's Disease" by Winkler et al. 2025. https://doi.org/10.7554/eLife.101769.1
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9c9b235fa30f4522c0c36fb45c661886caebc15ca16a5d6309e7dffbb3f54666 | Text | 266 | 4 | Set up an environment with `pip install -r requirements.txt` and run the two notebooks to qualitatively reproduce the figures.
To set up an environment in Windows, follow:
https://packaging.python.org/en/latest/guides/installing-using-pip-and-virtual-environments/
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dd9afb99e1e27ecd6eed04603d43408eefe5c2cd634d7851b50bd2e0c20d4f82 | Text | 272 | 6 | # QuantComps
Utilities and tools for (quantitative) metric comparisons in MRI
For research article: Assessing Quantitative MRI Techniques using Multimodal Comparisons
Code is found in jupyter notebooks and which are numerically ordered to provide results from the paper
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67d57ea24a2b9167b5a0441f150f20b688a66e3feaa22b58a2296b1ac4d59966 | Text | 279 | 6 | # Stroke Resilience
Investigation of brain network reorganisation after stroke.
Publications:
1. van Assche M, Klug J, Dirren E, Richiardi J, Carrera E. Preparing for a Second Attack: A Lesion Simulation Study on Network Resilience After Stroke. Stroke. 2022;53:2038–2047.
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612abbb84bd41eec98b70618126a30773121e5a23cc359bb208853c1f916dfea | Text | 285 | 4 | ## README for Fig.5
To make use of the notebooks in this folder, please download the file p-d-sweep.h5 from doi.org/10.5281/zenodo.15570891 and paste the file into the unpacked Fig.5 folder.
Please also download the utils.zip folder, unzip it and save it next to the Fig.5 - folder.
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1a0a1a9d395d260714ccce80835f444d0de38e310a3eeb9eaa7932fc2c629673 | Text | 293 | 2 | # CELM
This code is associated with the research manuscript titled '[Insert Paper Title],' currently under peer review for publication in [Insert Journal Name]. Users are requested to cite this work in academic use. Citation details will be added once the manuscript is accepted and published
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a539498b1fc9baf0e98927e71e78a5a85480ee3d41985357849f4550745462d6 | Text | 298 | 8 | # Spine-Generic project: Acquisition and Analysis Protocol
This repository includes the documentation and the processing scripts for the
spine-generic project.
User documentation: https://spine-generic.readthedocs.io/
Developer documentation: https://github.com/spine-generic/spine-generic/wiki
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aa4617e116af42186814cfc843d886bd6943b8e8a8729fddb05ab60c47eab8b1 | Text | 305 | 16 | # Khula EEG / Microbiome Paper
## Authors
- Kevin Bonham, PhD
- Emma Margolis
- Guilherme Fahur Bottino, PhD
- Laurel Gabard-Durnam, PhD
- Vanja Klepac-Ceraj, PhD
## About
Relationship between the developing functional potential of the infant gut microbiome
and brain development as measured by EEG. |
ea531ee6cb9f8176e03a2b18033fb4c2e4bdd72b4455b7ea909ce9a08326cee4 | Text | 310 | 4 | # SLC13A5
This repository reports data to replicate results of figures published in the article: "Large-scale experimental assessment of variant effects on the structure and function of the citrate transporter SLC13A5"
[](https://doi.org/10.5281/zenodo.15352966)
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0cb4d17a6e1e7d7bb0a1e77a7e124d67f35bece2b0aaac60a2b3865965c7e288 | Text | 321 | 6 | # Physics-constrained_GP_EOS
Data and scripts for the paper: Learning thermodynamically constrained equations of state with uncertainty by Himanshu Sharma, Jim A. Gaffney, Dimitrios Tsapetis, Michael D. Shields
Link to the paper: https://doi.org/10.1063/5.0165298
For further questions, please contact hsharm10@jhu.edu... |
5fe71626596307e0b691b5d959813c73c17df145012f1f9268dfabb76aa55b45 | Text | 323 | 6 | # exa-spim-hardware
Hardware files for the ExA-SPIM microscope system
## Description
This repository contains CAD (Solidworks) files for the ExA-SPIM microscope system. Files are organized in directories for each vendor, with subassemblies for various parts of the microscope. A bill of materials (BOM) is also provided... |
511b4237ed1701af7c0a76a2037fe87cf6ab54152899e5a276a81daef385fcd1 | Text | 338 | 20 | # Cording2025
open field analysis
## Juptyer notebook to generate Figure 5 E-I & N-P
## software dependencies:
see requirements.txt
operating systems: Windows11Pro 24H2
## Installation guide
download the repository
install keypoint-moseq
https://keypoint-moseq.readthedocs.io/en/latest/install.html
typical inst... |
85bbc5c725f02c670e322c588ce03fa9c004b37dd4b83468621043ee787bdc03 | Text | 343 | 4 | Dataset for the article Soulavie et al. Induction of host genes by nested genes during C. elegans development, 2025, iScience 28(8), 113021, https://doi.org/10.1016/j.isci.2025.113021
Raw numerical data corresponding to the figures of the article in .xlsx format. Details on data acquisition and processing are provid... |
a08e58889c5c5d2efbdad0045d499e9b974494fb895c9cbc7060fd4096919988 | Text | 344 | 4 | # Drosophila_larval_optogenetic_analysis-area_and_mobility
Codes used for analysis of data included in Neural substrates of larval cold nociception in Drosophila (2022).
Demo videos are uploaded for step-by-step instructions and additional pop-up prompts guide you through each step. If you need demo files, please cont... |
7ddfbfe4edb1ede0d639f22614822e6490ea73dd29b150cf39d2261ef7bed479 | Text | 349 | 4 | # P6_Mouse_tibia_IFITM5_vs_Ctrl
This is the R Script for some figures of the article "An inducible mouse model of OI type V reveals aberrant osteogenesis caused by Ifitm5 c.-14C>T mutation".
Raw data: The single-cell transcriptomic data from the Prx1-Cre; Ifitm5 flox c.-14C>T mouse at P6 stage were deposited on the NC... |
85267fea85cfac1a5d769d67cad116ec2e492148e20d006832d519953181e156 | Text | 352 | 7 | # mTMS-MRI Project
Data and code to reproduce the content of the following manuscript:
- A multi-channel TMS system enabling accurate stimulus orientation control during concurrent ultra-high-field MRI for preclinical applications, Souza et al., bioRxiv, DOI: https://doi.org/10.1101/2023.08.10.552401
Author and copy... |
aceb882049f41842f02656c655c3863b3e15554a272f58b8129ac00689821327 | Text | 356 | 7 | # EPd_functional_analysis
Code used for functional analysis in <br>
Manjila SB, Son S, Kline H, Betty R, Wu Y, Pi H, Parmaksiz D, Shin D, Liwang JK, Kronman FN, Paul A, Kim Y <br>
Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice, bioRxivv 2024 <br>
https://www.biorxiv.org/conte... |
2dba4d4568982fc2d46590cf6e21a5fc2d2cbc7ca25644d36e6c109e5012e72f | Text | 357 | 2 |
This repository contains processed iterative indirect immunohistochemistry imaging (4i) data in the form of AnnData objects, generated for the manuscript "Morphodynamics of human early brain organoid development." All analysis code and parameters used in the study are available on GitHub at https://github.com/quadbio/... |
5227ee0791a0f391994db7575574ed6cc26308bdc25a554ace053e5354127d81 | Text | 358 | 5 | This code is associated with the eLife publication titled: 'Neural circuit mechanisms for steering control in walking Drosophila'
Entry point to calcium imaging code is: PEN_stimulation_EB_imaging_A2_patching_analysis_automated.m
Entry point to analysis of electrophysiology of DNs is: A2_dual_patch_analysis_v2.m and ... |
2ab6e416fe7fa85fe7a3dabcd5fd6fbd1e752a4b5296eefe8ee6cb8e995a0e70 | Text | 402 | 5 | R markdown file associated with analysis and figures presented in "AAV-based delivery of RNAi targeting Ataxin-2 improves survival, strength, and pathology in TDP-43 mice" Amado et al. 2025, Nature Communications.
Raw and processed counts data is available in GEO Query Accession Number: GSE283631.
For additional inf... |
704ea0a67de263071dcb015e24e0422fa6d9b6c9110561523c833d8f1a692210 | Text | 404 | 7 | # Lipid-siRNA_scRNAseq
Analysis pipeline for scRNAseq datasets published by Sorets et al. (2025)
Associated preprint available: https://doi.org/10.1101/2024.06.09.598079
Raw sequencing data and processed Seurat objects are available at Array Express under accession number E-MTAB-13964.
Interactive versions of the dat... |
fb1fea80310422c76a1437a3673f46ccd9ef52e4e2ae9c3468afea613edd8d45 | Text | 408 | 6 | # AtlasViewer
AtlasViewer is a MATLAB application for the display of fNIRS data on atlas anatomy developed and maintained by the [Boston University Neurophotonics Center](http://www.bu.edu/neurophotonics/).
# Quick links
* [Downloading AtlasViewer](https://github.com/BUNPC/AtlasViewer/wiki/Download-and-Installation)
*... |
8bf81494a1f258ab8c71301a33a9cbca1414fb69851fafdfe37874bc2e8f13eb | Text | 411 | 6 | # exa-spim-characterization
Characterization files for the ExA-SPIM microscope system
## Description
This repository contains Python notebooks for characterizing the ExA-SPIM microscope system. Files are organized in directories for each characterization test. Due to file size limitations, certain raw dataset files ar... |
8fa8e1556e7d8ff9ee481b78b33e71b7de1ecc2c128442ddf11ce20abe393af3 | Text | 423 | 7 | # MultisiteExchange
MATLAB code to generate figures 1 through 11 in "Passive water exchange between multiple sites can explain why apparent exchange rate constants depend on ionic and osmotic conditions in gray matter", Williamson et al., Magnetic Resonance Letters (2025)
Initially used MATLAB R204a.
Add the folders ... |
b387d1b757bf420d94e0ff3b22fac6167b4d2a72dbc51ef22b6faa6205e81020 | Text | 424 | 6 | # BSICoS-globular_hearts_simulation
Supplementary material such as simulation codes, mesh models, and parameters used in the paper: Electrophysiological Characterization of Preadolescents Born with Intrauterine Growth Restriction: Insights from Clinical and Computational Data
# External Resources
[Download MEsh/Heart... |
1865778a7fbac4ca9f54ac7fd7dcb38ba8ea90d2a25958116c6057a32012dac4 | Text | 431 | 10 | # Multi-Channel-Hyperspectral-NeRF-
This is the code for paper Multi-channel Volume Density Neural Radiance Field for Hyperspectral Imaging
There are two folders inside "/code"
The single channel code is the original method while the multi channel code is the method we proposed in the paper.
All our results were trai... |
7475859bd5a1ce8241fbe73430f4b416ac48e426e55430c036aeaa567c70de3e | Text | 437 | 11 | # FL_Soil
Soil Moisture. Fourier analysis, Periodic changes, LSTM, Variable and invariant features
## Installation and Datasets
We use python version 3.10, PyTorch version 1.13.1, CUDA 11.7 and torchvision 0.14.1. More details of dataset preparation can be found in [Landbench1.0] (https://github.com/2023ATAI/LandBench... |
b07a45e155eed9f72f58fc9f84c9cd413eed5ca91778305cd298b9215ebb3d10 | Text | 445 | 9 | # ZebraTrack
Program for high-speed tracking of larval zebrafish.
Provides a user-interface and a flexible logic to integrate different types of experiments that make use of provided tracking information.
See [website](https://haesemeyer.github.io/ZebraTrack/) for more detailed information.
Depends on [MHApi](https:/... |
2f96db00c1e95bcc5f0b182ef8ef51198148360b4172c4bda718623e7dc9dc21 | Text | 457 | 5 | # AudioEphys
Analysis of electrophysiological (LFP and spike) responses to auditory stimuli during sleep, across different brain regions and behavioral states (NREM, REM, Wake). The scripts included support the generation of plots, quantifications, and statistical assessments of arousal thresholds, spike activity, and ... |
fa24d0f01ca90ec1c9f7dfd10c24fd527c079aeebf5876aab6e2cd3e725e7b65 | Text | 460 | 12 | This is the python code used to produce the figures of the manuscript
A mammalian inferior colliculus model for sound source separation using interaural time differences
by Christian Leibold and Sebastian Groß
To run the code,
1) copy all sound files from the zip archives into a directory "sounds"
mkdir sounds;... |
35d6373cec7e479cb6a3e1cacf63c66250f5f73a95391a40d87fbb2b86ba6b50 | Text | 475 | 10 | # Lipid-siRNA_scRNAseq
Analysis pipeline for scRNAseq datasets published by Sorets et al. (2025)
Associated preprint available: https://doi.org/10.1101/2024.06.09.598079
Associated publication availabe: https://doi.org/10.1093/nar/gkaf600
Raw sequencing data and processed Seurat objects are available at Array Expres... |
510fe2a5e7618271df9027d9dad1f85ef3eed2cdc26b4b6dc8c4b26dee86fb77 | Text | 477 | 3 | The Computerised Adaptive Beat Alignment Test (CA-BAT) is a new test for the ability to perceive the beat in a piece of music. It takes advantage of several modern psychometric techniques, including item response theory, adaptive testing, and automatic item generation. This compressed file contains the materials for th... |
132cdc4bab4e556cb80d80f3026251be4cedce4d891eaa306d61dd451bf8b9f4 | Text | 505 | 22 | ### NiiVue ONNX
ONNX 3D convolution test for [brainchop](https://github.com/neuroneural/brainchop) models.
### For Developers
You can serve a hot-reloadable web page that allows you to interactively modify the source code.
```bash
git clone git@github.com:niivue/niivue-onnx.git
cd niivue-onnx
npm install
npm run de... |
5237abcf31071a3129135937908857f506a2ca3fae6f7124c4813798b4747024 | Text | 515 | 10 | # exa-spim-optics
Optical files for the ExA-SPIM microscope system
## Description
This repository contains optical (ZEMAX) files for the ExA-SPIM microscope system.
Note, in order to open the detection model, a blackbox model for the VEO_JM DIAMOND 5.0X/F1.3 lens needs to be obtained from Schneider-Kreuznach after s... |
eb76f496e0a644067fe4f22c2341b97972116d008806de151312eae1a7c3a819 | Text | 515 | 4 | # Alpha_Mesh_Swc_DataSet
Dataset of surface meshes produced by Alpha_Mesh_Swc, which is available here https://github.com/SpinDoctorMRI/Alpha_Mesh_Swc_DataSet.
The meshes are saved in .ply files and in some cases we provide the log files containing information about the meshing process. In the publication associated w... |
c2bc3a0be67e652b3eb48b7c809915d7fc5649925c480a82090effb9bde707f9 | Text | 518 | 6 | # Motion_Maker_G4
A MATLAB tool for generating moving patterns for the 4th generation Reiser LED panel arena. Uses a coordinate-based pixel location system to create cylindrical gratings, edges, and starfields for all types of rotational and translational apparent motion.
Check the /support/coorindate conventions.pdf ... |
5aa7241d578dc855fc22a060f8c8556a7ae109454c0ba84e1b9ce51930d95201 | Text | 530 | 5 | # CaMPARI intensity analysis and Cold plate assay video processing
Code used for analysis of data included in Modality specific roles for metabotropic GABAergic signaling and calcium induced calcium release mechanisms in regulating cold nociception, 2022.
This code is also used in Neural substrates of cold nociception ... |
b224de1213999e2335ca725a9ecc7366b2e4ed9eba27e309584e464994f14582 | Text | 533 | 14 | # spikesort-hp-2025
My wrapper code for spike sorting with kilosort
This includes the copy of the kilosort2.0 repo that was used for spike sorting in Payne & Aronov 2025
## Instructions
First follow instructions on the kilosort2.0 github page to install kilosort 2.0
Then run the built-in kilosort gui (kilosort.m in... |
844bd93a2d71c1a2aa55083c1c09ea43cfae8772bfa25d0dc4440550610bf785 | Text | 566 | 5 | # umcuEpi_CCEP_DTI
This repository contains scripts to process CCEP and DTI data and compare both connectivities.
These codes were used to analyze the data (https://openneuro.org/datasets/ds005448) and generate all figures of this manuscript: S.B. Jelsma, M. Zijlmans, I.B. Heijink, F.W.A. Hoefnagels, M. Raemaekers, W.... |
72f3921d9b7e7cbabdc7623b7147d95697faa3a12f832b171cc5604f49d8c780 | Text | 567 | 5 | Whithin this project, we are using different modalities of genome-wide CRISPR-Cas9 screens to identify novel mono- and combination therapies efficacious in Sonic hedgehog medulloblastoma.
This repository is an addition to our publication "Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependenc... |
6f562be11b49b73ccf1c451f1485c8fb0314e7a4fbbb324ea23ccd06983d97d7 | Text | 570 | 18 | # somi_reward
Data repository for the paper
*Predictive goal coding by dentate gyrus somatostatin-expressing interneurons*
bei Yuan et int. Bartos
Data was analyzed with the code published on
https://github.com/cleibold/somireward/releases/tag/v1.0.1
further detailed documentation can be found there
- The fo... |
6968ec724c5e151428f23a41ccdd095b24c3ba147932ea6e862518bf0390df82 | Text | 579 | 18 | These scripts are meant to be used together with the alphapulldown pipeline (https://github.com/KosinskiLab/AlphaPulldown, tested for versions 0.22.3 and 0.30.7) to identify potential novel LIRs.
They generate input files, analyze the resulting structural predictions, and summarize the results.
**Requirements (Python... |
d18350d3ede91160747aa241895815a8674e93af0537b87f34f204ba7b526f0d | Text | 587 | 20 | This repository contains the C++ implementation for the agent-based simulation of cortical microtubule dynamics(CMT), as described in our paper.
---
##(Publication)
Agent-Based Simulation of Cortical Microtubule Band Movement in the Arabidopsis Zygote
Tomonobu Nonoyama, Zichen Kang, Hikari Matsumoto, Sakumi Nakagawa... |
f836b603506a138f02337c8b54671b9f857f84e121b07c91af124f1af3e91840 | Text | 604 | 9 | # DeEPsnap
This is the official repository for [DeEPsnap: human essential gene prediction by integrating multi-omics data](https://www.biorxiv.org/content/10.1101/2024.06.20.599958v1).
[main_DeEPsnap.py](https://github.com/wjxiao2020/DeEPsnap/blob/main/scripts/main_DeEPsnap.py) contains the main entrance code for tra... |
a078a130198af797207cacdf78cb6ae6ce339e2d6bdc13180e2598f8e7053b90 | Text | 611 | 21 | # DRF_Classification
This code is running under Python 3.8.19. Please create a virtual environment according to the requirements.txt file.
### 1. Download the Trained Model:
Visit https://universityofadelaide.box.com/s/2ecx8vj06vkh44w7flprtnh9mpm5c4z2 to access the trained model.
Download the model and place it in ... |
ebe397b0c3b64e5253b01e73557aa6ebfd2e49b66150ad1b00678e5b0ae3ac8c | Text | 629 | 19 | ---
title: ShimNet
emoji: 💻
colorFrom: indigo
colorTo: yellow
sdk: docker
pinned: false
license: mit
short_description: ShimNet Spectra Correction
---
# ShimNet
ShimNet is a data-driven AI solution to improve high-resolution nuclear magnetic resonance (NMR) spectra
Paper: [ShimNet: A neural network for post-acquisit... |
528e54248dca621471da653a404b0de3a1f049b6a6d1fafc59d1a9e2caa958ed | Text | 661 | 13 | # ET_connectivity
Code used to generate main figures in ET manuscript posted in https://www.biorxiv.org/content/10.1101/2023.10.18.562531v1.full
(code for some, but not all extended figures are included)
System requirements:
Language: Jutpiter Notebooks
Tested on Python version 3.10.4
Requrires aditional packages i... |
afab917134c78d1adf2ffc62e4d19e5a9c4c34fe9c778f80af1eaf9d1caa79a9 | Text | 661 | 7 | # morphodynamics_human_brain_organoid
This repository contains the scripts and code for the "Morphodynamics of human early brain organoid development" paper (Jain, Gut et al., 2025).
The corresponding raw single-cell RNA sequencing data is publicly available through ArrayExpress under accession number: E-MTAB-15057. ... |
e5ae40e13fb59c1928bfa7c2da8a6e23f2589e474ff7e951764191dd4bfd5c67 | Text | 671 | 16 | phase-precession
=================
Library for quantification of hippocampal phase precession translated to python from matlab scripts written by Richard Kempter
described in Kempter R, Leibold C, Buzsáki G, Diba K, Schmidt R (2012) Quantifying circular-linear associations: hippocampal phase precession. J Neurosci Me... |
35a11b0f110c85a4ca22866d44c0b302e92cd51b28f132127308e284f25a376f | Text | 687 | 16 | # Eelbrain
[](https://zenodo.org/badge/latestdoi/3651023)
## Latest version
| Stable | Pre-release |
| ------ | ----------- |
| [](https://anaconda.org/conda-forge/eelbrain) | [, Mahesh C. Gandikota, J. M. Schwarz
1. Place loops_and_lines_run.py and loops_and_lines.py files in same directory.
2. Create a movie_frames subdirectory.
3. To run type in a terminal: "python loops_and_lines_run.py".
4. There will... |
a4ea86094668540ec4ec819ab40f4a98984fdfa67f920299fc60b99bdea9a61a | Text | 716 | 8 | # Experimental Data --- Resolving artefacts in voltage-clamp experiments with computational modelling: an application to fast sodium current recordings
This dataset contains all the experimental data collected for the work "Resolving artefacts in voltage-clamp experiments with computational modelling: an application t... |
e07155c40034062d022c4a4ad2ee1c97dc38caa9fcf5a5f69131e1224386b270 | Text | 727 | 7 | Description of files :
fULM_Quantifications.m : matlab script to process fULM data by creating temporal-averaged stimulation pattern and display baseline speed, density, BSA and activation maps
DATA_AN2235157_control_fULM.mat : whisker fULM experiment data from a control mouse.
DATA_AN2209950_EngiKO_fULM.mat : whis... |
f06c121aca2d95ce0d76840bfae4ead9b38e9d94f00aa6be94eb74010926a259 | Text | 727 | 33 | # PhoQuKs
The data and code for Photonic Quantum KernelS.
## Installation
The simulation is performed by [discopy](https://github.com/discopy/discopy).
Note the repo was under development and all results were simulated at the branch `optics` and the commit `a0aeb6c0471440250b06807802e7e94c748b4035`.
## Files
nece... |
8a121bcbc77410035494ad1073e39dbbb4a049e5309e7da78f40480685847e46 | Text | 728 | 18 | # Code for paper "The spinal premotor network driving high-frequency flexor-extensor alternation"
Simulation of a neuromechanical model that captures the activity of spinal premotor network driving scratching behavior.
The code for joint model are build on Fink et al. (2014), see also
https://github.com/anagamori/Fink... |
fa672e713712b136ece9064f40db0b4befbadbb5347a7884db717a7161dddc74 | Text | 736 | 22 | ## Interception ringlike structure
These codes reproduce the figures in manuscript Zhang, Y., Chen, Y., Wang T. & Cui, H. Neural geometry from mixed
sensorimotor selectivity for predictive sensorimotor control. eLife (2024). https://doi.org/10.7554/eLife.100064
## Hardware requirements
All the codes only require a s... |
3e32e444ecd6a9ac6a3f49f76f159c3d208d4755b2e5e8fbde6df74190298114 | Text | 749 | 21 | # Kirschner et al. - Methamphetamine and Learning Rate Dynamics
Hello!
Here you will find data and behavioral analysis scripts for:
Kirschner et al.
*"Methamphetamine-induced adaptation of learning rate dynamics depends on baseline performance."*
# Reinforcement Learning Model Fitting
Reinforcement learning model f... |
2f38c6c2b5d4abb5cfef33d89be6b63a795795fee7442bc3935bb5214b192958 | Text | 751 | 11 | # Elovl1 inhibition reduced very long chain fatty acids in a mouse model of adrenoleukodystrophy
Owner: Jeremy Huang
Email: jeremy.huang@sanofi.com
Date: 2024-11-01
Description: Contains R script codes to generate figures for paper.
Guidelines: Running Steps I - IV would generate all code from initial seurat ... |
136eb3c66de99353f3716c441d595688ae94dca696d74804fb10cb6e64d478eb | Text | 767 | 18 | # Macro_Brain_Area
This is a Macro created in FiJi to quantify total brain slide area. In fact it can be used to quantify most objects with a certain size and circularity that differs from 0.1.
# Version data
This macro was created in FiJi version ImageJ2 version 2.16.0/1.54p build 26d66057dd
# Recommendations
To ea... |
9990127a3c849fc7a8f62f50644e5298814d74409c60b818ddcd178174f0f857 | Text | 780 | 11 | ## Datasets
**Before training or running any networks**, the training sets must be downloaded and placed in the correct directory.
Download the training data from [figshare](https://figshare.com/articles/dataset/PGML_Dataset/28439978) and unzip the file. Then move all the contained `.mat` files to `/cmlData`.
## Train... |
97514accd158b5e6dd107b93de4f3020e762c80b6139a706b0bdfd3cb3178397 | Text | 781 | 8 | # HMChannelopathies
Code associated with pre-print "H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs"
This repository is organized so that code is associated with the corresponding figure in the current pre-print (https://www.biorx... |
da0ca5113c09159dc4c9ff169a30c48acce4bc9e9e9a5c85fc777814bd10db6e | Text | 789 | 18 |
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.
TopHat2 (the current release) is a collaborative effort between the... |
871e6be6930a55f89c47c7aa5a2465840a1df93e40de88032ea699fa1695d51f | Text | 806 | 14 | 
[](https://codecov.io/gh/hchau630/chau-2024-exact)
# Source code for [Chau et al. 2025](https://doi.org/10.1073/pnas.242... |
d27bbb40e96a8854bd5ccdcaae87147355f319c74353c90a9e4acd8298b27c8f | Text | 817 | 28 | # UNITY QA example data
Phantom serial number: 137-0004
Site: Lund University, Lund, Sweden
Creator: Emil Ljungberg, Lund, Sweden
## Data structure
Image data is stored in the `DICOM` folder with subfolders indicating the date of data acquisition. Each exam contains 5 series
1. FISP: Gradient echo scan to check int... |
b0658193895f77f0e58d6cbb425a789b8740a099aa248eff5eee89720169909b | Text | 818 | 9 | # MEEG-restingstate
Contains code to extract resting state networks from MEG and EEG data
Within this repository different analysis pipelines are provided to analyse MEG and EEG data and extract resting state networks
In particular it provides a pipeline for the extraction of resting state networks based on Brookes et ... |
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