calcium-imaging

There are 115 repositories under calcium-imaging topic.

  • flatironinstitute/CaImAn

    Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

    Language:Python64047775370

  • flatironinstitute/CaImAn-MATLAB

    Complete Matlab pipeline for large scale calcium imaging data analysis

    Language:MATLAB2525868147

  • flatironinstitute/NoRMCorre

    Matlab routines for online non-rigid motion correction of calcium imaging data

    Language:MATLAB144322889

  • HelmchenLabSoftware/Cascade

    Calibrated inference of spiking from calcium ΔF/F data using deep networks

    Language:Jupyter Notebook123104232
  • ciatah

    bahanonu/ciatah

    CIAtah (pronounced cheetah): a software package for calcium imaging analysis of one- and two-photon imaging datasets. Documentation: https://git.io/ciatah_docs. Formerly known as calciumImagingAnalysis (ciapkg).

    Language:MATLAB8384422

  • NICALab/SUPPORT

    Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.

    Language:Python7161816

  • kushalkolar/MESmerize

    Platform for Calcium Imaging analysis. DEPRECATED.

    Language:Python61106914

  • nel-lab/mesmerize-core

    High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn

    Language:Python61520215

  • bahanonu/imaging_tools

    A table containing imaging analysis tools for biology, with a focus on calcium imaging.

    45613

  • oist/optinist

    calcium imaging pipeline tool

    Language:TypeScript37925513

  • AllenInstitute/neuroglia

    a Python machine learning library for neurophysiology data

    Language:Python3619467

  • alexklibisz/deep-calcium

    Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks (https://arxiv.org/abs/1707.06314)

    Language:Python28639

  • vazirilab/SID

    Seeded Iterative Demixing (SID) of neuronal activity recordings made using Light Field Microscopy (LFM)

    Language:MATLAB27937

  • phflot/flow_registration

    Flow-Registration toolbox for 2P motion compensation

    Language:MATLAB217232

  • samuroi/SamuROI

    SamuROI - Structured analysis of multiple user-defined ROIs, an open source Python-based analysis environment for imaging data.

    Language:Python175217
  • BEAR

    NICALab/BEAR

    Official code for BEAR. "Efficient neural network approximation of robust PCA for automated analysis of calcium imaging data", MICCAI 2021.

    Language:Jupyter Notebook15305

  • delunapaolo/calipy

    Real-time, interactive exploration of 3D image stacks

    Language:Python13311

  • adamshch/GraFT-analysis

    This repository contains code for morphology-free analysis of functional fluorescence microscopy. The focal algorithm, Graph-Filtered Time-trace (GraFT) Dictionary Learning, is published in Charles et al. 2022 in the IEEE Transactions of Image Processing.

    Language:MATLAB12324

  • hochbaumGroup/HNCcorr

    HNCcorr algorithm for neuron identification in calcium imaging datasets.

    Language:Python12953

  • open-ephys/Bonsai.Miniscope

    Bonsai package for controlling headborne, calcium imaging miniscopes

    Language:C#126126

  • comp-imaging-sci/MVG-CNN

    Codes related to paper "Automated sleep stage classification of wide-field calcium imaging data via multiplex visibility graphs and deep learning"

    Language:Python9201

  • smu160/PvsNP

    a Python toolbox for reproducible analysis and visualization of NeuroPhysiological data.

    Language:Python9412

  • HelmchenLabSoftware/Centripetal_propagation_astrocytes

    Custom code (Python or Matlab) to compute centripetal propagation from astrocytic calcium recordings using pixel-wise correlation functions

    Language:MATLAB8920

  • inscopix/pyisx

    Python API for interacting with Inscopix data.

    Language:Python86282

  • vladscript/FinderSpiker

    Signal Processing Toolbox for Calcium Imaging Data

    Language:MATLAB8220

  • nel-lab/mesmerize-napari

    Mesmerize plugin for the napari viewer

    Language:Python63150

  • PTRRupprecht/Drawing-ROIs-without-GUI

    Drawing ROIs with a non-graphical user interface

    Language:MATLAB6333

  • danustc/Image_toolbox

    This is my toolbox for image processing and downstream analysis of calcium imaging data.

    Language:Jupyter Notebook5303

  • liang-bo/AutoStereota

    An open-source automated surgical instrument for microendoscope implantation

    Language:MATLAB5003

  • mzabolocki/fusion_org_ephys

    Electrophysiology analysis in ventral midbrain-striatal-cortical organoids (MISCOs) pre- and post- optogenetic stimulation.

    Language:Jupyter Notebook5200

  • NICALab/3DM

    Official code for "3DM: Deep decomposition and deconvolution microscopy for rapid neural activity imaging", Optics Express.

    Language:Jupyter Notebook5213

  • xiuyechen/Explore2p

    interactive analysis of two-photon calcium imaging data

    Language:MATLAB5300
  • pvbs

    flosfor/pvbs

    PVBS (Prairie View Browsing Solution) - General-purpose GUI for electrophysiology (patch clamp) and calcium imaging

    Language:MATLAB4100

  • IPMI-ICNS-UKE/TDEntropyDeconvolution

    Spatio-temporal image restoration with entropy-based regularization for application to low-SNR fluorescence microscopy image series.

    Language:Python4211

  • Phil-An/CellMatch

    Complete Matlab pipeline for matching in vivo recorded cells post hoc in histology

    Language:MATLAB4100

  • pr4deepr/GutAnalysisToolbox

    Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.

    Language:ImageJ Macro44173