Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.
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Dec 18, 2025 - Python
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calcium-imaging
Here are 44 public repositories matching this topic...
Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.
deep-learning neural-network calcium-imaging microscopy structural-imaging denoising time-lapse-imaging self-supervised-learning voltage-imaging
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Aug 11, 2025 - Python
High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
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Sep 4, 2025 - Python
Platform for Calcium Imaging analysis. DEPRECATED.
signal-processing neuroscience plotting calcium-imaging interactive-visualizations caiman pypi-package calcium-imaging-analysis
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Nov 26, 2023 - Python
The Zebrafish Activity Prediction Benchmark measures progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain.
benchmark machine-learning time-series neuroscience forecasting calcium-imaging light-sheet-microcopy
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Nov 21, 2025 - Python
a Python machine learning library for neurophysiology data
python machine-learning scikit-learn neuroscience open-science electrophysiology nwb calcium-imaging neurophysiology
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Nov 10, 2018 - Python
Fast, Simple Calcium Imaging Segmentation with Fully Convolutional Networks (https://arxiv.org/abs/1707.06314)
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Dec 8, 2022 - Python
SamuROI - Structured analysis of multiple user-defined ROIs, an open source Python-based analysis environment for imaging data.
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Apr 9, 2019 - Python
Real-time, interactive exploration of 3D image stacks
python gui numpy exploratory-data-analysis interactive-analysis segmentation pyqt calcium-imaging microscopy pyqtgraph cell-segmentation fluorescence-microscopy-imaging exploratory-data-visualizations fluorescence-data live-microscopy fluorescence-traces
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Nov 25, 2019 - Python
HNCcorr algorithm for neuron identification in calcium imaging datasets.
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Feb 11, 2023 - Python
Python API for interacting with Inscopix data.
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Jul 7, 2025 - Python
Codes related to paper "Automated sleep stage classification of wide-field calcium imaging data via multiplex visibility graphs and deep learning"
deep-learning neuroimaging calcium-imaging visibility-graph mouse-brain video-classification cnn-classification sleep-scoring spatialtemporal sleep-stage-classification wide-field-optical-imaging
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Mar 3, 2022 - Python
Automated and reproducible analysis of multiphoton imaging datasets
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Nov 25, 2025 - Python
Preserving Spatial and Quantitative Information in Unpaired Biomedical Image-to-Image Translation
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Oct 14, 2025 - Python
a Python toolbox for reproducible analysis and visualization of NeuroPhysiological data.
visualization python neuroscience open-science electrophysiology calcium-imaging reproducible-analysis video-sync neurophysiological-data
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May 20, 2019 - Python
Derotate images acquired via multiphoton calcium imaging
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Nov 1, 2025 - Python
Mesmerize plugin for the napari viewer
neuroscience neuroimaging calcium-imaging neuroscience-methods neuroscience-data calcium-imaging-analysis
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Oct 29, 2022 - Python
Spatio-temporal image restoration with entropy-based regularization for application to low-SNR fluorescence microscopy image series.
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Dec 1, 2023 - Python
Synthesising Realistic Calcium Imaging Data of Neuronal Populations Using GAN.
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Jul 6, 2023 - Python
Calcium Imaging Analyzer (CaImAn) consists of a bunch of scripts written in python and put together to speed the analysis of calcium imaging experiments performed with the NIS-Elements Advanced Research software from Nikon.
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Jun 14, 2022 - Python
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