Imaging tools
A table containing imaging analysis tools for biology, with a focus on calcium imaging.
Created by Biafra Ahanonu, PhD (Basbaum Lab, UCSF).
Calcium imaging analysis with CIAtah (https://github.com/bahanonu/ciatah).
The table can also be found at:
Notes:
- I use cell extraction to refer to algorithms that perform cell segmentation and extract neural activity traces.
- Future versions of the repository will include table file (e.g. CSV) and basic LaTeX code so others can import or modify the table more easily going forward.
- Depending on monitor size and browser, scroll horizontally to see right-most table columns (e.g. websites/URLs).
- Any additional papers or algorithms that should be added or suggested updates to the table, leave a comment on the associated blog post or open an issue on the GitHub page, I want to make sure everyone’s brilliant work is acknowledged!
| Method | Year | Type | Notes | Source | Website |
| Turboreg | 1998 | Motion correction. | Motion correction. | Thevenaz et al. 1998 | http://bigwww.epfl.ch/thevenaz/turboreg/ |
| ROI | 2005 | Cell extraction | Matrix multiplication; in some methods neuropil/background subtraction implemented. | ”Kerr et al. 2005; Kuchibhotla et al. 2014; Peron et al. 2015” | - |
| CellProfiler | 2006 | Cell segmentation | Multi-algorithm pipeline for cell segmentation. | ”Carpenter et al. 2006; McQuin et al. 2018; Lamprecht et al. 2007” | https://cellprofiler.org |
| PCA-ICA | 2009 | Cell extraction | Cell extraction using principal component analysis (PCA) followed by independent component analysis (ICA). | Mukamel et al. 2009 | - |
| ”CIRF, calcium-behavior” | 2011 | Cell extraction | Regressive model to obtain Ca2+ signal based on behavior. | Miri et al. 2011 | - |
| openBIS | 2011 | Data handling | FAIR data management. | Bauch et al. 2011 | https://openbis.ch |
| Automated ROI analysis | 2012 | Cell extraction | Automatic ellipses based ROI detection. | Francis et al. 2012 | - |
| OMERO | 2012 | Data handling | Microscopy data handling. | Allan et al. 2012 | https://www.openmicroscopy.org |
| ADINA | 2013 | Cell extraction | Sparse dictionary learning. | Diego et al. 2013 | - |
| NMF | 2014 | Cell extraction | Nonnegative matrix factorization (NMF). | ”Pnevmatikakis et al. 2014; Maruyama et al. 2014” | - |
| SIMA | 2014 | Analysis pipeline | ”Normalized cut segmentation, motion correction, etc.” | Kaifosh et al. 2014 | https://github.com/losonczylab/sima |
| DataJoint | 2015 | Data handling | Schema for data handling. | Yatsenko et al. 2015 | https://github.com/datajoint/datajoint-matlab |
| Suite2p | 2016 | Cell extraction | Generative model along with GUIs. | Pachitariu et al. 2016 | - |
| CNMF (CaImAn) | 2016 | Cell extraction | Constrained NMF (CNMF). | Pnevmatikakis et al. 2016 | https://github.com/flatironinstitute/CaImAn-MATLAB |
| CNMF-E | 2016 | Cell extraction | CNMF + background model to handle one-photon data. | ”Zhou et al. 2016, 2018” | https://github.com/zhoupc/CNMF_E |
| Apthorpe CNN | 2016 | Cell segmentation | Convolutional neural network (CNN). | Apthorpe et al. 2016 | - |
| moco | 2016 | Motion correction | Fourier-transform based motion correction. | Dubbs et al. 2016 | https://github.com/NTCColumbia/moco |
| Cytomine | 2016 | Analysis GUI | Analysis of large-scale imaging data. | Marée et al. 2016 | https://cytomine.be |
| —CELLMax (conference) | 2017 | Cell extraction | Maximum likelihood. | ”Ahanonu et al. 2018, 2017” | - |
| sc-CNMF | 2017 | Cell extraction | CNMF + GMM/RNN seed cleansing. | Lu et al. 2017 | - |
| OASIS | 2017 | Trace analysis | Generalized pool adjacent violators algorithm. | Friedrich et al. 2017 | https://github.com/zhoupc/OASIS_matlab |
| ABLE | 2017 | Cell segmentation | Active contours. | Reynolds et al. 2017 | https://github.com/StephanieRey/ABLE |
| SCALPEL | 2017 | Cell extraction | ”Dictionary learning, dissimilarity, and clustering.” | Petersen et al. 2017 | https://cran.r-project.org/web/packages/scalpel/index.html |
| HNCcorr | 2017 | Cell segmentation | Combinatorial optimization (correlation space analysis). | Spaen et al. 2017 | https://github.com/hochbaumGroup/HNCcorr |
| OnACID | 2017 | Cell extraction (online) | NMF variant for online Ca2+ imaging processing. | Giovannucci et al. 2017 | - |
| EXTRACT | 2017 | Cell extraction | Robust statistical estimation. | Inan et al. 2017 | - |
| NETCAL | 2017 | Analysis pipeline | Calcium imaging analysis GUI. | Orlandi et al. | https://github.com/orlandi/netcal |
| NoRMCorre | 2017 | Motion correction. | Piecewise rigid motion correction. | Pnevmatikakis and Giovannucci 2017 | https://github.com/simonsfoundation/NoRMCorre |
| CellReg | 2017 | Cross-session alignment | Alignment of cells across days using a probabilistic approach. | Sheintuch et al. 2017 | https://github.com/zivlab/CellReg |
| NeuroSeg | 2017 | Cell segmentation | Filtering and seed/clustering based cell segmentation. | Guan et al. 2018 | https://github.com/baidatong/NeuroSeg |
| CNMF-E+ | 2017 | Cell extraction | Shrinkage estimation to improve CNMF-E initialization. | Takekawa et al. 2017 | - |
| Toolbox-Romano | 2017 | Analysis pipeline | Full analysis pipeline with ROI-based segmentation | Romano et al. 2017 | https://github.com/zebrain-lab/Toolbox-Romano-et-al |
| SamuROI | 2017 | Analysis GUI | GUI for data visualization | Rueckl et al. 2017 | https://github.com/samuroi/SamuROI |
| KNIME | 2017 | Analysis pipeline | Workflow manager for data analysis. | Fillbrunn et al. 2017 | https://www.knime.com |
| —CLEAN (conference) | 2018 | Cell sorting | Machine learning based cell sorting of cell extraction outputs. | Ahanonu et al. 2018 | - |
| FISSA | 2018 | Trace analysis | Neuropil decontamination using local region around cell. | Keemink et al. 2018 | https://github.com/rochefort-lab/fissa |
| LSSC | 2018 | Cell segmentation | Spectral clustering; variant to find local subset of eigenvectors. | Mishne et al. 2018 | - |
| PMD - PCA | 2018 | Denoising | Spatially-localized penalized matrix decomposition for denoising; compression; and improved demixing. | Buchanan et al. 2018 | https://github.com/paninski-lab/funimag |
| MIN1PIPE | 2018 | Analysis pipeline | Pre-processing + CNMF. | Lu et al. 2018 | - |
| CaImAn (preprint) | 2018 | Analysis pipeline | CNMF + several other processing tools. | Giovannucci et al. 2018 | - |
| SEUDO (preprint) | 2018 | Trace analysis | Mixture of Gaussians + maximum likelihood; post-hoc activity trace correction. | Gauthier et al. 2018 | - |
| —CIAtah | 2019 | Analysis pipeline | ”1P and 2P Imaging analysis pipeline supporting PCA-ICA, CNMF, CELLMax, EXTRACT, etc.” | Corder et al. 2019 | https://github.com/bahanonu/ciatah |
| NAOMi (bioRxiv) | 2019 | Simulator | Generative model for creating simulated calcium imaging movies. | Charles et al. 2019 | - |
| CALIMA | 2019 | Analysis pipeline | Calcium imaging analysis GUI. | Radstake et al. 2019 | - |
| STNeuroNet | 2019 | Cell segmentation | Convolutional neural network to detect and segment cells. | Soltanian-Zadeh et al. 2019 | - |
| AQuA | 2019 | Cell extraction | Astrocyte imaging focused. Non-ROI cluster and propagation based detection of events. | Wang et al. 2019 | - |
| CaImAn | 2019 | Analysis pipeline | CNMF + several other processing tools. | Giovannucci et al. 2019 | https://github.com/flatironinstitute/CaImAn |
| DL+RWL1-SF | 2019 | Cell extraction | Dictionary learning and spatial correlation based cell extraction. | Mishne and Charles 2019 | - |
| marked point processes | 2020 | Cell extraction | ”Probabilistic generative model, specifically a marked point process, to extract activity traces.” | Shibue and Komaki 2020 | - |
| LocaNMF | 2020 | Region extraction | Localized semi-nonnegative matrix factorization for extracting active regions. | Saxena et al. 2020 | https://github.com/ikinsella/locaNMF |
| EZcalcium | 2020 | Analysis pipeline | Calcium imaging analysis toolbox. | Cantu et al. 2020 | https://github.com/porteralab/EZcalcium |
| OnACID-E + ring CNN | 2020 | Cell extraction (online) | OnACID for miniscope and new ring CNN background model to improve accuracy. | Friedrich et al. 2020 | https://github.com/flatironinstitute/CaImAn |
| Auto CNMF-E sorting | 2020 | Cell sorting | Machine learning (AutoML) based curation of CNMF-E outputs. | ”Tran et al. 2020a,b” | https://github.com/jf-lab/cnmfe-reviewer |
| DeepInterpolation | 2020 | Denoising | Encoder-decoder architecture with 2D conv. to denoise imaging data. | Lecoq et al. 2020 | https://github.com/AllenInstitute/deepinterpolation |
| BIAFLOWS | 2020 | Benchmarking | Framework for benchmarking imaging analysis workflows. | Rubens et al. 2020 | https://biaflows.neubias.org |
| FIBSI | 2020 | Trace analysis | Extension of Ramer-Douglas-Peucker algorithm to identify baseline that is used for signal detection. | ”Cassidy et al. 2020; Alles et al. 2021” | https://github.com/rmcassidy/FIBSI_program |
| Cellpose | 2021 | Cell segmentation | Neural network and gradient-based cell segmentation. | Stringer et al. 2021 | https://github.com/mouseland/cellpose |
| NAOMi | 2021 | Simulator | Detailed model simulation for benchmarking calcium imaging algorithms. | Song et al. 2021 | https://bitbucket.org/adamshch/naomi_sim/src/master/ |
| OnACID-E + ring CNN | 2021 | Cell extraction (online) | OnACID for 1P data and ring CNN background model. | Friedrich et al. 2021 | https://github.com/flatironinstitute/CaImAn |
| EXTRACT | 2021 | Cell extraction | Robust statistics based cell extraction. | Inan et al. 2021 | https://github.com/schnitzer-lab/EXTRACT-public |
| Minian | 2021 | Analysis pipeline | ”Imaging analysis pipeline with CNMF for cell extraction, in part using Jupyter notebooks with GUI elements.” | Dong et al. 2021 | https://github.com/DeniseCaiLab/minian |
| Mesmerize | 2021 | Analysis pipeline | ”Imaging analysis platform with CaImAn for cell extraction, import support for other cell extraction algorithms.” | Kolar et al. 2021 | https://github.com/kushalkolar/MESmerize |
| DeepInterpolation | 2021 | Denoising | Encoder-decoder architecture with 2D conv. to denoise imaging data. | Lecoq et al. 2021 | https://github.com/AllenInstitute/deepinterpolation |
| BEAR | 2021 | Cell extraction | Neural network approximation of PCA for cell extraction. | Han et al. 2021 | https://github.com/NICALab/BEAR |
| CaPTure | 2021 | Cell extraction | ROI segmentation and activity extraction. | Tippani et al. 2021 | https://github.com/LieberInstitute/CaPTure |
| CASCADE | 2021 | Trace analysis | Spike inference based on dual ephys/calcium imaging recordings. | Rupprecht et al. 2021 | https://github.com/HelmchenLabSoftware/Cascade |
| VolPy | 2021 | Analysis pipeline | Voltage imaging analysis pipeline integrated into CaImAn. | Cai et al. 2021 | https://github.com/flatironinstitute/CaImAn |
| DeepCAD | 2021 | Denoising | Deep neural network based denoising. | Li et al. 2021 | https://github.com/cabooster/DeepCAD-RT |
| SpecSeg | 2021 | Cell extraction | Spectral density of pixels to identify ROIs. Also incorporates motion correction and cross-session matching. | de Kraker et al. 2021 | https://github.com/Leveltlab/SpectralSegmentation |
| FIOLA | 2021 | Cell extraction (online) | GPU- and computational graph-based speed-ups along with non-negative least squares for post-initialization signal extraction. | Giovannucci et al. 2021 | https://github.com/nel-lab/FIOLA |
| PatchWarp | 2021 | Motion correction | Affine transformation of subfields followed by stiching subfields together. | Hattori and Komiyama 2021 | https://github.com/ryhattori/PatchWarp |
| MVG-CNN | 2021 | Region extraction | Automated sleep states classification using multiplex visibility graphs and deep learning. Data URL. | Zhang et al. 2021 | https://github.com/comp-imaging-sci/MVG-CNN |
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