From 5628a027d520c6d26a8eecee2cc27df7510f48a9 Mon Sep 17 00:00:00 2001 From: Biafra Ahanonu Date: Thu, 14 Sep 2023 14:40:22 -0700 Subject: [PATCH] Update table and add citation file - Updated table to include more recent and older methods. - Added citation file. --- CITATION.cff | 11 + README.md | 3086 +++++++++++++++++++++++++++++++++----------------- 2 files changed, 2043 insertions(+), 1054 deletions(-) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..fba1be3 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,11 @@ +cff-version: 1.2.0 +message: If you use this software, please cite it using these metadata. +title: Table of imaging analysis methods and software +authors: + - family-names: Ahanonu + given-names: Biafra + orcid: https://orcid.org/0000-0002-2021-5848 +version: 1.1 +date-released: "2018-11-21" +license: MIT +repository-code: https://github.com/bahanonu/imaging_tools \ No newline at end of file diff --git a/README.md b/README.md index b454de1..5308d5a 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ -# Imaging tools -A table containing imaging analysis tools for biology, with a focus on calcium imaging. +# Imaging analysis tools +A table containing imaging analysis tools for biology and neuroscience, with a focus on calcium imaging. -Created by Biafra Ahanonu, PhD (Basbaum Lab, UCSF). +Created by Biafra Ahanonu, PhD (HHMI Hanna Gray Fellow, Basbaum Lab, UCSF).

@@ -13,1559 +13,2537 @@ Created by Bi The table can also be found at: - https://bahanonu.com/brain/imaging_tools/ -- https://bahanonu.com/syscarut/articles/226/ +- https://bahanonu.com/syscarut/articles/233/ _Notes_: - I use _cell extraction_ to refer to algorithms that perform cell segmentation and extract neural activity traces. +- In cases where the publication did not explicitly give the algorithm a name, made one based on the underlying method used. +- This table includes algorithms that simultaneously extract cell images/contours and reconstruct cell activity traces along with ones mainly focused on determining one or the other. +- Several calcium imaging related packages have also been included along with algorithms dealing with post-hoc handling of data or cell 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! -

Table 1: Ca2+ imaging cell extraction and trace reconstruction algorithms
- -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Method YearType Notes Source Website
Turboreg 1998Motion correction. Motion correction. Thevenaz et al. 1998 http://bigwww.epfl.ch/thevenaz/turboreg/
ROI 2005Cell extraction Matrix multiplication; in some methods neuropil/background subtraction implemented. ”Kerr et al. 2005; Kuchibhotla et al. 2014; Peron et al. 2015” -
CellProfiler 2006Cell segmentation Multi-algorithm pipeline for cell segmentation. ”Carpenter et al. 2006; McQuin et al. 2018; Lamprecht et al. 2007”https://cellprofiler.org
PCA-ICA 2009Cell extraction Cell extraction using principal component analysis (PCA) followed by independent component analysis (ICA). Mukamel et al. 2009 -
”CIRF, calcium-behavior” 2011Cell extraction Regressive model to obtain Ca2+ signal based on behavior. Miri et al. 2011 -
openBIS 2011Data handling FAIR data management. Bauch et al. 2011 https://openbis.ch
Automated ROI analysis 2012Cell extraction Automatic ellipses based ROI detection. Francis et al. 2012 -
OMERO 2012Data handling Microscopy data handling. Allan et al. 2012 https://www.openmicroscopy.org
ADINA 2013Cell extraction Sparse dictionary learning. Diego et al. 2013 -
NMF 2014Cell extraction Nonnegative matrix factorization (NMF). ”Pnevmatikakis et al. 2014; Maruyama et al. 2014” -
SIMA 2014Analysis pipeline ”Normalized cut segmentation, motion correction, etc.” Kaifosh et al. 2014 https://github.com/losonczylab/sima
DataJoint 2015Data handling Schema for data handling. Yatsenko et al. 2015 https://github.com/datajoint/datajoint-matlab
Suite2p 2016Cell extraction Generative model along with GUIs. Pachitariu et al. 2016 -
CNMF (CaImAn) 2016Cell extraction Constrained NMF (CNMF). Pnevmatikakis et al. 2016 https://github.com/flatironinstitute/CaImAn-MATLAB
CNMF-E 2016Cell extraction CNMF + background model to handle one-photon data. ”Zhou et al. 2016, 2018” https://github.com/zhoupc/CNMF_E
Apthorpe CNN 2016Cell segmentation Convolutional neural network (CNN). Apthorpe et al. 2016 -
moco 2016Motion correction Fourier-transform based motion correction. Dubbs et al. 2016 https://github.com/NTCColumbia/moco
Cytomine 2016Analysis GUI Analysis of large-scale imaging data. Marée et al. 2016 https://cytomine.be
—CELLMax (conference)2017Cell extraction Maximum likelihood. ”Ahanonu et al. 2018, 2017” -
sc-CNMF 2017Cell extraction CNMF + GMM/RNN seed cleansing. Lu et al. 2017 -
OASIS 2017Trace analysis Generalized pool adjacent violators algorithm. Friedrich et al. 2017 https://github.com/zhoupc/OASIS_matlab
ABLE 2017Cell segmentation Active contours. Reynolds et al. 2017 https://github.com/StephanieRey/ABLE
SCALPEL 2017Cell extraction ”Dictionary learning, dissimilarity, and clustering.” Petersen et al. 2017 https://cran.r-project.org/web/packages/scalpel/index.html
HNCcorr 2017Cell segmentation Combinatorial optimization (correlation space analysis). Spaen et al. 2017 https://github.com/hochbaumGroup/HNCcorr
OnACID 2017Cell extraction (online)NMF variant for online Ca2+ imaging processing. Giovannucci et al. 2017 -
EXTRACT 2017Cell extraction Robust statistical estimation. Inan et al. 2017 -
NETCAL 2017Analysis pipeline Calcium imaging analysis GUI. Orlandi et al. https://github.com/orlandi/netcal
NoRMCorre 2017Motion correction. Piecewise rigid motion correction. Pnevmatikakis and Giovannucci 2017 https://github.com/simonsfoundation/NoRMCorre
CellReg 2017Cross-session alignmentAlignment of cells across days using a probabilistic approach. Sheintuch et al. 2017 https://github.com/zivlab/CellReg
NeuroSeg 2017Cell segmentation Filtering and seed/clustering based cell segmentation. Guan et al. 2018 https://github.com/baidatong/NeuroSeg
CNMF-E+ 2017Cell extraction Shrinkage estimation to improve CNMF-E initialization. Takekawa et al. 2017 -
Toolbox-Romano 2017Analysis pipeline Full analysis pipeline with ROI-based segmentation Romano et al. 2017 https://github.com/zebrain-lab/Toolbox-Romano-et-al
SamuROI 2017Analysis GUI GUI for data visualization Rueckl et al. 2017 https://github.com/samuroi/SamuROI
KNIME 2017Analysis pipeline Workflow manager for data analysis. Fillbrunn et al. 2017 https://www.knime.com
—CLEAN (conference) 2018Cell sorting Machine learning based cell sorting of cell extraction outputs. Ahanonu et al. 2018 -
FISSA 2018Trace analysis Neuropil decontamination using local region around cell. Keemink et al. 2018 https://github.com/rochefort-lab/fissa
LSSC 2018Cell segmentation Spectral clustering; variant to find local subset of eigenvectors. Mishne et al. 2018 -
PMD - PCA 2018Denoising Spatially-localized penalized matrix decomposition for denoising; compression; and improved demixing. Buchanan et al. 2018 https://github.com/paninski-lab/funimag
MIN1PIPE 2018Analysis pipeline Pre-processing + CNMF. Lu et al. 2018 -
CaImAn (preprint) 2018Analysis pipeline CNMF + several other processing tools. Giovannucci et al. 2018 -
SEUDO (preprint) 2018Trace analysis Mixture of Gaussians + maximum likelihood; post-hoc activity trace correction. Gauthier et al. 2018 -
—CIAtah 2019Analysis 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) 2019Simulator Generative model for creating simulated calcium imaging movies. Charles et al. 2019 -
CALIMA 2019Analysis pipeline Calcium imaging analysis GUI. Radstake et al. 2019 -
STNeuroNet 2019Cell segmentation Convolutional neural network to detect and segment cells. Soltanian-Zadeh et al. 2019 -
AQuA 2019Cell extraction Astrocyte imaging focused. Non-ROI cluster and propagation based detection of events. Wang et al. 2019 -
CaImAn 2019Analysis pipeline CNMF + several other processing tools. Giovannucci et al. 2019 https://github.com/flatironinstitute/CaImAn
DL+RWL1-SF 2019Cell extraction Dictionary learning and spatial correlation based cell extraction. Mishne and Charles 2019 -
marked point processes 2020Cell extraction ”Probabilistic generative model, specifically a marked point process, to extract activity traces.” Shibue and Komaki 2020 -
LocaNMF 2020Region extraction Localized semi-nonnegative matrix factorization for extracting active regions. Saxena et al. 2020 https://github.com/ikinsella/locaNMF
EZcalcium 2020Analysis pipeline Calcium imaging analysis toolbox. Cantu et al. 2020 https://github.com/porteralab/EZcalcium
OnACID-E + ring CNN 2020Cell 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 2020Cell sorting Machine learning (AutoML) based curation of CNMF-E outputs. ”Tran et al. 2020a,b” https://github.com/jf-lab/cnmfe-reviewer
DeepInterpolation 2020Denoising Encoder-decoder architecture with 2D conv. to denoise imaging data. Lecoq et al. 2020 https://github.com/AllenInstitute/deepinterpolation
BIAFLOWS 2020Benchmarking Framework for benchmarking imaging analysis workflows. Rubens et al. 2020 https://biaflows.neubias.org
FIBSI 2020Trace 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 2021Cell segmentation Neural network and gradient-based cell segmentation. Stringer et al. 2021 https://github.com/mouseland/cellpose
NAOMi 2021Simulator Detailed model simulation for benchmarking calcium imaging algorithms. Song et al. 2021 https://bitbucket.org/adamshch/naomi_sim/src/master/
OnACID-E + ring CNN 2021Cell extraction (online)OnACID for 1P data and ring CNN background model. Friedrich et al. 2021 https://github.com/flatironinstitute/CaImAn
EXTRACT 2021Cell extraction Robust statistics based cell extraction. Inan et al. 2021 https://github.com/schnitzer-lab/EXTRACT-public
Minian 2021Analysis 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 2021Analysis 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 2021Denoising Encoder-decoder architecture with 2D conv. to denoise imaging data. Lecoq et al. 2021 https://github.com/AllenInstitute/deepinterpolation
BEAR 2021Cell extraction Neural network approximation of PCA for cell extraction. Han et al. 2021 https://github.com/NICALab/BEAR
CaPTure 2021Cell extraction ROI segmentation and activity extraction. Tippani et al. 2021 https://github.com/LieberInstitute/CaPTure
CASCADE 2021Trace analysis Spike inference based on dual ephys/calcium imaging recordings. Rupprecht et al. 2021 https://github.com/HelmchenLabSoftware/Cascade
VolPy 2021Analysis pipeline Voltage imaging analysis pipeline integrated into CaImAn. Cai et al. 2021 https://github.com/flatironinstitute/CaImAn
DeepCAD 2021Denoising Deep neural network based denoising. Li et al. 2021 https://github.com/cabooster/DeepCAD-RT
SpecSeg 2021Cell 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 2021Cell 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 2021Motion correction Affine transformation of subfields followed by stiching subfields together. Hattori and Komiyama 2021 https://github.com/ryhattori/PatchWarp
MVG-CNN 2021Region 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
- - -
Note: in cases where the publication did not explicitly give the algorithm a name, -made one based on the underlying method used. This table includes algorithms that -simultaneously extract cell images/contours and reconstruct cell activity traces -along with ones mainly focused on determining one or the other. Several calcium -imaging related packages have also been included along with algorithms dealing -with post-hoc handling of data or cell activity traces. CELLMax is our algorithm -that we have presented at Society for Neuroscience and COSYNE. © Biafra -Ahanonu 2021. +
Table 1:Ca2+ imaging cell extraction and trace reconstruction algorithms
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
# Method YearAnalysis pipeline Notes/Code Citation
1 PhaseCorrelation 1996Motion correction. •  Phase correlation for motion correction, to include translation, rotation, and scale-invariance. Reddy and Chatterji 1996
2 Turboreg 1998Motion correction. •  Motion correction.
•  http://bigwww.epfl.ch/thevenaz/turboreg/ 		Thevenaz et al. 1998
3 subPixelPhase 2002Motion correction. •  Closed-form solution to subpixel translation estimation using phase correlation. Foroosh et al. 2002
4 ROI 2005Cell extraction •  Matrix multiplication; in some methods neuropil/background subtraction implemented. Kerr et al. 2005; Kuchibhotla et al. 2014; Peron et al. 2015
5 CellProfiler 2006Cell segmentation •  Multi-algorithm pipeline for cell segmentation.
•  https://cellprofiler.org 		Carpenter et al. 2006; McQuin et al. 2018; Lamprecht et al. 2007
6 PCA-ICA 2009Cell extraction •  Cell extraction using principal component analysis (PCA) followed by independent component analysis (ICA). Mukamel et al. 2009
7 ANTs 2009Image analysis •  Suite of tools for registering and analyzing imaging data.
•  http://stnava.github.io/ANTs/ 		Avants et al. 2009
8 elastix 2009Motion correction •  A general toolbox for rigid and non-rigid image registration.
•  https://elastix.lumc.nl 		Klein et al. 2009
9 Lucas–Kanade framework2009Motion correction •  Lucas-Kanade framework for non-uniform motion image registration. Greenberg and Kerr 2009
10 CIRF (calcium-behavior) 2011Cell extraction •  Regressive model to obtain Ca2+ signal based on behavior. Miri et al. 2011
11 openBIS 2011Data handling •  FAIR data management.
•  https://openbis.ch 		Bauch et al. 2011
12 Automated ROI analysis 2012Cell extraction •  Automatic ellipses based ROI detection. Francis et al. 2012
13 OMERO 2012Data handling •  Microscopy data handling.
•  https://www.openmicroscopy.org 		Allan et al. 2012
14 ADINA 2013Cell extraction •  Sparse dictionary learning. Diego et al. 2013
15 TPP 2013Analysis pipeline •  Tool for processing two-photon calcium imaging data, e.g. finding cells with SeNeCA.
•  http://uemweb.biomed.cas.cz/tpp/ 		Tomek et al. 2013
16 NMF 2014Cell extraction •  Cell extraction using nonnegative matrix factorization (NMF). Followed by CNMF. Pnevmatikakis et al. 2014; Maruyama et al. 2014
17 SIMA 2014Analysis pipeline •  Normalized cut segmentation, motion correction, etc.
•  https://github.com/losonczylab/sima 		Kaifosh et al. 2014
18 DataJoint 2015Data handling •  Schema for data handling.
•  https://github.com/datajoint/datajoint-matlab 		Yatsenko et al. 2015
19 NWB 2015Data handling •  Neurodata Without Borders (NWB) initiative to produce a common data format for electrophysiology and imaging studies.
•  https://github.com/NeurodataWithoutBorders 		Teeters et al. 2015
20 Suite2p 2016Cell extraction •  Generative model along with GUIs. Pachitariu et al. 2016
21 CNMF (CaImAn) 2016Cell extraction •  Constrained NMF (CNMF).
•  https://github.com/flatironinstitute/CaImAn-MATLAB 		Pnevmatikakis et al. 2016
22 CNMF-E 2016Cell extraction •  CNMF + background model to handle one-photon data.
•  https://github.com/zhoupc/CNMF_E 		Zhou et al. 2016, 2018
23 Apthorpe CNN 2016Cell segmentation •  Convolutional neural network (CNN). Apthorpe et al. 2016
24 moco 2016Motion correction •  Fourier-transform based motion correction.
•  https://github.com/NTCColumbia/moco 		Dubbs et al. 2016
25 Cytomine 2016Analysis GUI •  Analysis of large-scale imaging data.
•  https://cytomine.be 		Marée et al. 2016
26 ROI clustering 2016Cell extraction •  Select high-intensity pixels then perform clustering to segment.
•  https://www.bu.edu/hanlab/files/2016/02/pfgc.zip 		Mohammed et al. 2016
27 CELLMax (conference) 2017Cell extraction •  Cell segmentation and activity trace extraction using a maximum likelihood approach. Ahanonu et al. 2018, 2017; Ahanonu 2018
28 sc-CNMF 2017Cell extraction •  CNMF + GMM/RNN seed cleansing. Lu et al. 2017
29 OASIS 2017Trace analysis •  Generalized pool adjacent violators algorithm.
•  https://github.com/zhoupc/OASIS_matlab 		Friedrich et al. 2017
30 ABLE 2017Cell segmentation •  Multiple active contours and a cost function to identify cells in 2P data.
•  https://github.com/StephanieRey/ABLE 		Reynolds et al. 2017
31 SCALPEL 2017Cell extraction •  Dictionary learning, dissimilarity, and clustering.
•  https://cran.r-project.org/web/packages/scalpel/index.html 		Petersen et al. 2017
32 HNCcorr 2017Cell segmentation •  Combinatorial optimization (correlation space analysis).
•  https://github.com/hochbaumGroup/HNCcorr 		Spaen et al. 2017
33 OnACID 2017Cell extraction (online) •  NMF variant for online Ca2+ imaging processing. Giovannucci et al. 2017
34 EXTRACT 2017Cell extraction •  Robust statistical estimation. Inan et al. 2017
35 NETCAL 2017Analysis pipeline •  Calcium imaging analysis GUI.
•  https://github.com/orlandi/netcal 		Orlandi et al.
36 NoRMCorre 2017Motion correction. •  Piecewise rigid motion correction.
•  https://github.com/simonsfoundation/NoRMCorre 		Pnevmatikakis and Giovannucci 2017
37 CellReg 2017Cross-session alignment•  Alignment of cells across days using a probabilistic approach.
•  https://github.com/zivlab/CellReg 		Sheintuch et al. 2017
38 NeuroSeg 2017Cell segmentation •  Filtering and seed/clustering based cell segmentation.
•  https://github.com/baidatong/NeuroSeg 		Guan et al. 2018
39 CNMF-E+ 2017Cell extraction •  Shrinkage estimation to improve CNMF-E initialization. Takekawa et al. 2017
40 Toolbox-Romano 2017Analysis pipeline •  Full analysis pipeline with ROI-based segmentation
•  https://github.com/zebrain-lab/Toolbox-Romano-et-al 		Romano et al. 2017
41 SamuROI 2017Analysis GUI •  GUI for data visualization
•  https://github.com/samuroi/SamuROI 		Rueckl et al. 2017
42 KNIME 2017Analysis pipeline •  Workflow manager for data analysis.
•  https://www.knime.com 		Fillbrunn et al. 2017
43 U-Net2DS 2017Cell segmentation •  Evaluated several deep learning models on Neurofinder, U-Net2DS best.
•  https://github.com/alexklibisz/deep-calcium 		Klibisz et al. 2017
44 CLEAN (conference) 2018Cell sorting •  Machine learning based cell sorting of cell extraction outputs based on image and activity trace features. Ahanonu et al. 2018; Ahanonu 2018
45 FISSA 2018Trace analysis •  Neuropil decontamination using local region around cell.
•  https://github.com/rochefort-lab/fissa 		Keemink et al. 2018
46 LSSC 2018Cell segmentation •  Spectral clustering; variant to find local subset of eigenvectors. Mishne et al. 2018
47 PMD - PCA 2018Denoising •  Spatially-localized penalized matrix decomposition for denoising; compression; and improved demixing.
•  https://github.com/paninski-lab/funimag 		Buchanan et al. 2018
48 MIN1PIPE 2018Analysis pipeline •  Pre-processing to enhance neural signals then sc-CNMF for cell extraction. Lu et al. 2018
49 CaImAn (preprint) 2018Analysis pipeline •  CNMF + several other processing tools. Giovannucci et al. 2018
50 SEUDO (preprint) 2018Trace analysis •  Mixture of Gaussians + maximum likelihood; post-hoc activity trace correction. Gauthier et al. 2018
51 ACSAT 2018Cell segmentation •  Global and local adaptive thresholding to identify neurons.
•  https://github.com/sshen8/acsat 		Shen et al. 2018
52 onlineMotionCorrection 2018Motion correction •  Tested multiple algorithms and developed an online motion correction pipeline.
•  https://github.com/amitani/onlineMotionCorrection 		Mitani and Komiyama 2018
53 CIAtah 2019Analysis pipeline •  1P and 2P Imaging analysis pipeline supporting PCA-ICA, CNMF, CELLMax, EXTRACT, etc.
•  https://github.com/bahanonu/ciatah 		Corder et al. 2019; Ahanonu 2018; Ahanonu and Corder 2022
54 NAOMi (bioRxiv) 2019Simulator •  Generative model for creating simulated calcium imaging movies. Charles et al. 2019
55 CALIMA 2019Analysis pipeline •  Calcium imaging analysis GUI. Radstake et al. 2019
56 STNeuroNet 2019Cell segmentation •  Convolutional neural network to detect and segment cells. Soltanian-Zadeh et al. 2019
57 AQuA 2019Cell extraction •  Astrocyte imaging focused. Non-ROI cluster and propagation based detection of events. Wang et al. 2019
58 CaImAn 2019Analysis pipeline •  Popular calcium imaging pipeline that includes CNMF + several other processing tools.
•  https://github.com/flatironinstitute/CaImAn 		Giovannucci et al. 2019
59 DL+RWL1-SF 2019Cell extraction •  Dictionary learning and spatial correlation based cell extraction. Mishne and Charles 2019
60 Segment2P 2019Cell segmentation •  Pre-process images and run through DeepLabV3.
•  https://github.com/NoahDolev/Segment2P 		Dolev et al. 2019
61 LANMC 2019Motion correction •  Long short-term memory non-rigid motion correction, reduce computational cost by predicting non-rigid motion. Chen et al. 2019
62 marked point processes 2020Cell extraction •  Probabilistic generative model, specifically a marked point process, to extract activity traces. Shibue and Komaki 2020
63 LocaNMF 2020Region extraction •  Localized semi-nonnegative matrix factorization for extracting active regions.
•  https://github.com/ikinsella/locaNMF 		Saxena et al. 2020
64 EZcalcium 2020Analysis pipeline •  Calcium imaging analysis toolbox.
•  https://github.com/porteralab/EZcalcium 		Cantu et al. 2020
65 OnACID-E + ring CNN 2020Cell extraction (online) •  OnACID for miniscope and new ring CNN background model to improve accuracy.
•  https://github.com/flatironinstitute/CaImAn 		Friedrich et al. 2020
66 Auto CNMF-E sorting 2020Cell sorting •  Machine learning (AutoML) based curation of CNMF-E outputs.
•  https://github.com/jf-lab/cnmfe-reviewer 		Tran et al. 2020a,b
67 DeepInterpolation 2020Denoising •  Encoder-decoder architecture with 2D conv. to denoise imaging data.
•  https://github.com/AllenInstitute/deepinterpolation 		Lecoq et al. 2020
68 BIAFLOWS 2020Benchmarking •  Framework for benchmarking imaging analysis workflows.
•  https://biaflows.neubias.org 		Rubens et al. 2020
69 FIBSI 2020Trace analysis •  Extension of Ramer-Douglas-Peucker algorithm to identify baseline that is used for signal detection.
•  https://github.com/rmcassidy/FIBSI_program 		Cassidy et al. 2020; Alles et al. 2021
70 DISCo 2020Cell segmentation •  Pixel correlation and deep learning (CNN) + graph based segmentation.
•  https://github.com/EKirschbaum/DISCo 		Kirschbaum et al. 2020
71 DeepCINAC 2020Trace analysis •  Trace analysis after human labeling followed by CNNs + bidirectional long-short term memory (LSTM) network.
•  https://gitlab.com/cossartlab/deepcinac 		Denis et al. 2020
72 NDSEP 2020Cell extraction •  Dataflow framework for real-time calcium imaging processing.
•  http://dspcad-www.iacs.umd.edu/bcnm/index.html 		Lee et al. 2020
73 DeepBrainSeg 2020Segmentation •  Dual-pathway CNN to learn local and contextual features. Tan et al. 2020
74 RT-3DMC 2020Motion correction •  Bead or soma tracking for real-time motion correction during 2P imaging.
•  https://github.com/SilverLabUCL/SilverLab-Microscope 		Griffiths et al. 2020
75 Cellpose 2021Cell segmentation •  Neural network and gradient-based cell segmentation.
•  https://github.com/mouseland/cellpose 		Stringer et al. 2021
76 NAOMi 2021Simulator •  Detailed model simulation for benchmarking calcium imaging algorithms.
•  https://bitbucket.org/adamshch/naomi_sim/src/master/ 		Song et al. 2021
77 OnACID-E + ring CNN 2021Cell extraction (online) •  OnACID for 1P data and ring CNN background model.
•  https://github.com/flatironinstitute/CaImAn 		Friedrich et al. 2021
78 EXTRACT 2021Cell extraction •  Robust statistics based cell extraction.
•  https://github.com/schnitzer-lab/EXTRACT-public 		Inan et al. 2021
79 Minian 2021Analysis pipeline •  Imaging analysis pipeline with CNMF for cell extraction, in part using Jupyter notebooks with GUI elements.
•  https://github.com/DeniseCaiLab/minian 		Dong et al. 2021
80 Mesmerize 2021Analysis pipeline •  Imaging analysis platform with CaImAn for cell extraction, import support for other cell extraction algorithms.
•  https://github.com/kushalkolar/MESmerize 		Kolar et al. 2021
81 DeepInterpolation 2021Denoising •  Encoder-decoder architecture with 2D conv. to denoise imaging data.
•  https://github.com/AllenInstitute/deepinterpolation 		Lecoq et al. 2021
82 BEAR 2021Cell extraction •  Neural network approximation of PCA for cell extraction.
•  https://github.com/NICALab/BEAR 		Han et al. 2021
83 CaPTure 2021Cell extraction •  ROI segmentation and activity extraction.
•  https://github.com/LieberInstitute/CaPTure 		Tippani et al. 2021
84 CASCADE 2021Trace analysis •  Spike inference based on dual ephys/calcium imaging recordings.
•  https://github.com/HelmchenLabSoftware/Cascade 		Rupprecht et al. 2021
85 VolPy 2021Analysis pipeline •  Voltage imaging analysis pipeline integrated into CaImAn.
•  https://github.com/flatironinstitute/CaImAn 		Cai et al. 2021
86 DeepCAD 2021Denoising •  Deep neural network based denoising.
•  https://github.com/cabooster/DeepCAD-RT 		Li et al. 2021
87 SpecSeg 2021Cell extraction •  Spectral density of pixels to identify ROIs. Also incorporates motion correction and cross-session matching.
•  https://github.com/Leveltlab/SpectralSegmentation 		de Kraker et al. 2021
88 FIOLA 2021Cell extraction (online) •  GPU- and computational graph-based speed-ups along with non-negative least squares for post-initialization signal extraction.
•  https://github.com/nel-lab/FIOLA 		Giovannucci et al. 2021
89 PatchWarp 2021Motion correction •  Affine transformation of subfields followed by stitching subfields together.
•  https://github.com/ryhattori/PatchWarp 		Hattori and Komiyama 2021
90 MVG-CNN 2021Region extraction •  Automated sleep states classification using multiplex visibility graphs and deep learning. Data URL.
•  https://github.com/comp-imaging-sci/MVG-CNN 		Zhang et al. 2021
91 Flow-Registration 2021Motion correction •  Variational optical flow for non-uniform motion correction
•  https://github.com/phflot/flow_registration 		Flotho et al. 2022
92 SUNS 2021Cell segmentation •  Cell segmentation using shallow U-Nets.
•  https://github.com/YijunBao/Shallow-UNet-Neuron-Segmentation_SUNS 		Bao et al. 2021
93 Carignan 2021Cell extraction •  Online cell extraction and triggering based on OnACID and CaImAn.
•  https://github.com/tzklab/carignan 		Taniguchi et al. 2021
94 MullenClassifier 2021Cell sorting •  Feature extraction from cell images and tracs followed by supervised learning classifier. Mullen et al. 2021
95 timeUnet 2021Denoising •  Deep learning for denoising with temporal information added in.
•  https://github.com/BoHuangLab/Transfer-Learning-Denoising/ 		Wang et al. 2021
96 EMC2 2021Motion correction •  Wavelet decomposition to detect bright spots followed by motion correction with multiple hypothesis tracking and computing elastic deformation.
•  https://icy.bioimageanalysis.org/plugin/elastic-motion-correction-concatenation-emc2-of-tracks/ 		Lagache et al. 2021
97 GraFT 2022Cell extraction •  Dictionary-based learning of activity traces followed by graph-based segmentation.
•  https://github.com/adamshch/GraFT-analysis 		Charles et al. 2022
98 CaPTure 2022Analysis pipeline •  Binary/watershed segmentation followed by ROI-based mean traces.
•  https://github.com/LieberInstitute/CaPTure 		Tippani et al. 2022
99 SpecSeg 2022Cell segmentation •  Cross spectral power-based segmentation of neurons and neurites.
•  https://github.com/Leveltlab/SpectralSegmentation 		de Kraker et al. 2022
100CITE-On 2022Cell extraction •  Online cell detection and trace extraction using CNNs.
•  https://gitlab.iit.it/fellin-public/cite-on 		Sità et al. 2022
101DL-assisted 2P fiberscope2022Denoising •  Denoising 2P fiberscope data using deep neural network (conditional generative adversarial network).
•  https://figshare.com/articles/dataset/Data/19193792 		Guan et al. 2022
1024SM 2022Cell extraction •  Generative adversarial network for image segmentation.
•  https://github.com/SharifAmit/4SM 		Kamran et al. 2022
103DeepCAD-RT 2022Denoising •  Improved version of DeepCAD for real time performance.
•  https://github.com/cabooster/DeepCAD-RT/ 		Li et al. 2023a
104SEUDO 2022Trace analysis •  Mixture of Gaussians + maximum likelihood; post-hoc activity trace correction.
•  https://github.com/adamshch/SEUDO 		Gauthier et al. 2022
105AxialMotionCorrect 2022Motion correction •  Axial motion correction via multi-plane scanning plus maximum likelihood optimization.
•  https://gitlab.com/anflores/axial_motion_correction 		Flores-Valle and Seelig 2022
106FIFER 2022Motion correction •  Feature-based motion correction, finding features using a density-based estimating and clustering algorithm and matching features with a similarity metric for registration.
•  https://github.com/Weiyi-Liu-Unique/FIFER		Liu et al. 2022
107NWB 2022Data handling •  Neurodata Without Borders (NWB) to standardize ephys and imaging data across tools.
•  https://github.com/NeurodataWithoutBorders 		Rübel et al. 2022
108DeCalciOn 2023Online analysis pipeline•  Integrate hardware and software to online decode calcium signals.
•  https://github.com/zhe-ch/ACTEV 		Chen et al. 2023
109jGCaMP8 2023Calcium indicator •  Improved calcium indicators with increased sensitivity and reduced background. Zhang et al. 2023a
110NeuroSeg-II 2023Cell segmentation •  2P cell segmentation using region-based convolutional neural network with modifications.
•  https://github.com/XZH-James/NeuroSeg2 		Xu et al. 2023
111CaliAli 2023Cross-session alignment•  Cross-session alignment using vasculature information.
•  https://github.com/CaliAli-PV/CaliAli 		Vergara et al. 2023
112DeepWonder 2023Cell extraction •  Deep-learning-based cell finding for widefield datasets.
•  https://github.com/yuanlong-o/Deep_widefield_cal_inferece 		Zhang et al. 2023b
113ASTRA 2023Cell segmentation •  Deep neural network for astrocyte segmentation.
•  https://gitlab.iit.it/fellin-public/astra 		Bonato et al. 2023
114SRDTrans 2023Denoise •  Spatial redundancy for training followed by spatiotemporal transformer architecture to reduce CNN bias/issues.
•  https://github.com/cabooster/SRDTrans 		Li et al. 2023b
115REALS 2023Motion correction •  Motion correction via simultaneous transformation and low rank and sparse decomposition with gradient-based updates.
•  https://openaccess.thecvf.com/content/WACV2023/supplemental/Cho_Robust_and_Efficient_WACV_2023_supplemental.zip 		Cho et al. 2023
116LD-MCM 2023Motion correction •  Motion correction using deep learning feature identification and control point registration.
•  https://github.com/bahanonu/ciatah 		Ahanonu et al. 2023
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References

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