Neuroscience imaging analysis tools

in neuroscience on 08 November 2021

Summary

Provide new and existing researchers a central location for methods and URLs for calcium imaging data processing and analysis tools.

This table also includes imaging data handling and analysis tools beyond calcium imaging and will be updated going forward.

The table can be sorted by column by clicking each header.

Also found as part of the Brain Initiative Notes post imaging analysis tools or https://github.com/bahanonu/imaging_tools.

Calcium imaging analysis with CIAtah (https://github.com/bahanonu/ciatah).

Imaging analysis tools, a table by Biafra Ahanonu, PhD

Imaging analysis tools

Biafra Ahanonu, PhD

Updated: 13 September 2023 | Started: 01 December 2018

Methods for calcium imaging cell identification and fluorescence activity trace reconstruction

Imaging analysis with CIAtah (https://github.com/bahanonu/ciatah ).

With the increased use of calcium (and voltage) imaging for a plethora of research purposes, the need for tools that can accurately, quickly, and efficiently process this data is needed. As a graduate student in Mark Schnitzer's lab , I built and furthered new tools (e.g. CELLMax and CLEAN) and software packages (see CIAtah, https://github.com/bahanonu/ciatah ) to improve analysis of calcium imaging data. While there are existing reviews covering calcium imaging analysis, I decided to expand upon the table in my dissertation to include more recent and additional older algorithms, tools, and analysis pipelines. Those interested in a brief overview of calcium imaging, see the return of the brain initiative notes .

The table below is primarily focused on tools for calcium imaging, but some of them also include tools for voltage imaging, data handling for biology, and more. The goal will be to expand this to include additional imaging analysis tools going forward and I might make it more dynamic akin to my Nobel Prize Browser .

This is a part of the brain initiative notes and can also be found at neuroscience imaging analysis tools or https://github.com/bahanonu/imaging_tools .

Table updates
Below is a changelog of updates to the table, such as adding new methods.

2021.11.14 - Added FIBSI, SpecSeg, FIOLA, and PatchWarp.
2021.11.29 - Added MVG-CNN.
2023.09.12 - Updated online table to include additional papers (added throughout 2022-2023).

Table note

I use cell extraction to refer to algorithms that perform cell segmentation and extract neural activity traces.
Any additional papers or algorithms that should be added or suggested updates to the table, leave a comment below or open an issue on the GitHub page, I want to make sure everyone’s brilliant work is acknowledged!
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.

Table 1:Ca²⁺ imaging cell extraction and trace reconstruction algorithms


#	Method	Year	Analysis pipeline	Notes/Code	Citation

1	PhaseCorrelation	1996	Motion correction.	• Phase correlation for motion correction, to include translation, rotation, and scale-invariance.	Reddy and Chatterji 1996
2	Turboreg	1998	Motion correction.	• Motion correction. • http://bigwww.epfl.ch/thevenaz/turboreg/	Thevenaz et al. 1998
3	subPixelPhase	2002	Motion correction.	• Closed-form solution to subpixel translation estimation using phase correlation.	Foroosh et al. 2002
4	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
5	CellProfiler	2006	Cell 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	2009	Cell extraction	• Cell extraction using principal component analysis (PCA) followed by independent component analysis (ICA).	Mukamel et al. 2009
7	ANTs	2009	Image analysis	• Suite of tools for registering and analyzing imaging data. • http://stnava.github.io/ANTs/	Avants et al. 2009
8	elastix	2009	Motion correction	• A general toolbox for rigid and non-rigid image registration. • https://elastix.lumc.nl	Klein et al. 2009
9	Lucas–Kanade framework	2009	Motion correction	• Lucas-Kanade framework for non-uniform motion image registration.	Greenberg and Kerr 2009
10	CIRF (calcium-behavior)	2011	Cell extraction	• Regressive model to obtain Ca²⁺ signal based on behavior.	Miri et al. 2011
11	openBIS	2011	Data handling	• FAIR data management. • https://openbis.ch	Bauch et al. 2011
12	Automated ROI analysis	2012	Cell extraction	• Automatic ellipses based ROI detection.	Francis et al. 2012
13	OMERO	2012	Data handling	• Microscopy data handling. • https://www.openmicroscopy.org	Allan et al. 2012
14	ADINA	2013	Cell extraction	• Sparse dictionary learning.	Diego et al. 2013
15	TPP	2013	Analysis 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	2014	Cell extraction	• Cell extraction using nonnegative matrix factorization (NMF). Followed by CNMF.	Pnevmatikakis et al. 2014; Maruyama et al. 2014
17	SIMA	2014	Analysis pipeline	• Normalized cut segmentation, motion correction, etc. • https://github.com/losonczylab/sima	Kaifosh et al. 2014
18	DataJoint	2015	Data handling	• Schema for data handling. • https://github.com/datajoint/datajoint-matlab	Yatsenko et al. 2015
19	NWB	2015	Data 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	2016	Cell extraction	• Generative model along with GUIs.	Pachitariu et al. 2016
21	CNMF (CaImAn)	2016	Cell extraction	• Constrained NMF (CNMF). • https://github.com/flatironinstitute/CaImAn-MATLAB	Pnevmatikakis et al. 2016
22	CNMF-E	2016	Cell extraction	• CNMF + background model to handle one-photon data. • https://github.com/zhoupc/CNMF_E	Zhou et al. 2016, 2018
23	Apthorpe CNN	2016	Cell segmentation	• Convolutional neural network (CNN).	Apthorpe et al. 2016
24	moco	2016	Motion correction	• Fourier-transform based motion correction. • https://github.com/NTCColumbia/moco	Dubbs et al. 2016
25	Cytomine	2016	Analysis GUI	• Analysis of large-scale imaging data. • https://cytomine.be	Marée et al. 2016
26	ROI clustering	2016	Cell 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)	2017	Cell extraction	• Cell segmentation and activity trace extraction using a maximum likelihood approach.	Ahanonu et al. 2018, 2017; Ahanonu 2018
28	sc-CNMF	2017	Cell extraction	• CNMF + GMM/RNN seed cleansing.	Lu et al. 2017
29	OASIS	2017	Trace analysis	• Generalized pool adjacent violators algorithm. • https://github.com/zhoupc/OASIS_matlab	Friedrich et al. 2017
30	ABLE	2017	Cell 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	2017	Cell extraction	• Dictionary learning, dissimilarity, and clustering. • https://cran.r-project.org/web/packages/scalpel/index.html	Petersen et al. 2017
32	HNCcorr	2017	Cell segmentation	• Combinatorial optimization (correlation space analysis). • https://github.com/hochbaumGroup/HNCcorr	Spaen et al. 2017
33	OnACID	2017	Cell extraction (online)	• NMF variant for online Ca²⁺ imaging processing.	Giovannucci et al. 2017
34	EXTRACT	2017	Cell extraction	• Robust statistical estimation.	Inan et al. 2017
35	NETCAL	2017	Analysis pipeline	• Calcium imaging analysis GUI. • https://github.com/orlandi/netcal	Orlandi et al.
36	NoRMCorre	2017	Motion correction.	• Piecewise rigid motion correction. • https://github.com/simonsfoundation/NoRMCorre	Pnevmatikakis and Giovannucci 2017
37	CellReg	2017	Cross-session alignment	• Alignment of cells across days using a probabilistic approach. • https://github.com/zivlab/CellReg	Sheintuch et al. 2017
38	NeuroSeg	2017	Cell segmentation	• Filtering and seed/clustering based cell segmentation. • https://github.com/baidatong/NeuroSeg	Guan et al. 2018
39	CNMF-E+	2017	Cell extraction	• Shrinkage estimation to improve CNMF-E initialization.	Takekawa et al. 2017
40	Toolbox-Romano	2017	Analysis pipeline	• Full analysis pipeline with ROI-based segmentation • https://github.com/zebrain-lab/Toolbox-Romano-et-al	Romano et al. 2017
41	SamuROI	2017	Analysis GUI	• GUI for data visualization • https://github.com/samuroi/SamuROI	Rueckl et al. 2017
42	KNIME	2017	Analysis pipeline	• Workflow manager for data analysis. • https://www.knime.com	Fillbrunn et al. 2017
43	U-Net2DS	2017	Cell segmentation	• Evaluated several deep learning models on Neurofinder, U-Net2DS best. • https://github.com/alexklibisz/deep-calcium	Klibisz et al. 2017
44	CLEAN (conference)	2018	Cell 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	2018	Trace analysis	• Neuropil decontamination using local region around cell. • https://github.com/rochefort-lab/fissa	Keemink et al. 2018
46	LSSC	2018	Cell segmentation	• Spectral clustering; variant to find local subset of eigenvectors.	Mishne et al. 2018
47	PMD - PCA	2018	Denoising	• Spatially-localized penalized matrix decomposition for denoising; compression; and improved demixing. • https://github.com/paninski-lab/funimag	Buchanan et al. 2018
48	MIN1PIPE	2018	Analysis pipeline	• Pre-processing to enhance neural signals then sc-CNMF for cell extraction.	Lu et al. 2018
49	CaImAn (preprint)	2018	Analysis pipeline	• CNMF + several other processing tools.	Giovannucci et al. 2018
50	SEUDO (preprint)	2018	Trace analysis	• Mixture of Gaussians + maximum likelihood; post-hoc activity trace correction.	Gauthier et al. 2018
51	ACSAT	2018	Cell segmentation	• Global and local adaptive thresholding to identify neurons. • https://github.com/sshen8/acsat	Shen et al. 2018
52	onlineMotionCorrection	2018	Motion correction	• Tested multiple algorithms and developed an online motion correction pipeline. • https://github.com/amitani/onlineMotionCorrection	Mitani and Komiyama 2018
53	CIAtah	2019	Analysis 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)	2019	Simulator	• Generative model for creating simulated calcium imaging movies.	Charles et al. 2019
55	CALIMA	2019	Analysis pipeline	• Calcium imaging analysis GUI.	Radstake et al. 2019
56	STNeuroNet	2019	Cell segmentation	• Convolutional neural network to detect and segment cells.	Soltanian-Zadeh et al. 2019
57	AQuA	2019	Cell extraction	• Astrocyte imaging focused. Non-ROI cluster and propagation based detection of events.	Wang et al. 2019
58	CaImAn	2019	Analysis 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	2019	Cell extraction	• Dictionary learning and spatial correlation based cell extraction.	Mishne and Charles 2019
60	Segment2P	2019	Cell segmentation	• Pre-process images and run through DeepLabV3. • https://github.com/NoahDolev/Segment2P	Dolev et al. 2019
61	LANMC	2019	Motion 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	2020	Cell extraction	• Probabilistic generative model, specifically a marked point process, to extract activity traces.	Shibue and Komaki 2020
63	LocaNMF	2020	Region extraction	• Localized semi-nonnegative matrix factorization for extracting active regions. • https://github.com/ikinsella/locaNMF	Saxena et al. 2020
64	EZcalcium	2020	Analysis pipeline	• Calcium imaging analysis toolbox. • https://github.com/porteralab/EZcalcium	Cantu et al. 2020
65	OnACID-E + ring CNN	2020	Cell 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	2020	Cell sorting	• Machine learning (AutoML) based curation of CNMF-E outputs. • https://github.com/jf-lab/cnmfe-reviewer	Tran et al. 2020a,b
67	DeepInterpolation	2020	Denoising	• Encoder-decoder architecture with 2D conv. to denoise imaging data. • https://github.com/AllenInstitute/deepinterpolation	Lecoq et al. 2020
68	BIAFLOWS	2020	Benchmarking	• Framework for benchmarking imaging analysis workflows. • https://biaflows.neubias.org	Rubens et al. 2020
69	FIBSI	2020	Trace 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	2020	Cell segmentation	• Pixel correlation and deep learning (CNN) + graph based segmentation. • https://github.com/EKirschbaum/DISCo	Kirschbaum et al. 2020
71	DeepCINAC	2020	Trace 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	2020	Cell extraction	• Dataflow framework for real-time calcium imaging processing. • http://dspcad-www.iacs.umd.edu/bcnm/index.html	Lee et al. 2020
73	DeepBrainSeg	2020	Segmentation	• Dual-pathway CNN to learn local and contextual features.	Tan et al. 2020
74	RT-3DMC	2020	Motion 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	2021	Cell segmentation	• Neural network and gradient-based cell segmentation. • https://github.com/mouseland/cellpose	Stringer et al. 2021
76	NAOMi	2021	Simulator	• 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	2021	Cell extraction (online)	• OnACID for 1P data and ring CNN background model. • https://github.com/flatironinstitute/CaImAn	Friedrich et al. 2021
78	EXTRACT	2021	Cell extraction	• Robust statistics based cell extraction. • https://github.com/schnitzer-lab/EXTRACT-public	Inan et al. 2021
79	Minian	2021	Analysis 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	2021	Analysis 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	2021	Denoising	• Encoder-decoder architecture with 2D conv. to denoise imaging data. • https://github.com/AllenInstitute/deepinterpolation	Lecoq et al. 2021
82	BEAR	2021	Cell extraction	• Neural network approximation of PCA for cell extraction. • https://github.com/NICALab/BEAR	Han et al. 2021
83	CaPTure	2021	Cell extraction	• ROI segmentation and activity extraction. • https://github.com/LieberInstitute/CaPTure	Tippani et al. 2021
84	CASCADE	2021	Trace analysis	• Spike inference based on dual ephys/calcium imaging recordings. • https://github.com/HelmchenLabSoftware/Cascade	Rupprecht et al. 2021
85	VolPy	2021	Analysis pipeline	• Voltage imaging analysis pipeline integrated into CaImAn. • https://github.com/flatironinstitute/CaImAn	Cai et al. 2021
86	DeepCAD	2021	Denoising	• Deep neural network based denoising. • https://github.com/cabooster/DeepCAD-RT	Li et al. 2021
87	SpecSeg	2021	Cell 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	2021	Cell 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	2021	Motion correction	• Affine transformation of subfields followed by stitching subfields together. • https://github.com/ryhattori/PatchWarp	Hattori and Komiyama 2021
90	MVG-CNN	2021	Region 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	2021	Motion correction	• Variational optical flow for non-uniform motion correction • https://github.com/phflot/flow_registration	Flotho et al. 2022
92	SUNS	2021	Cell segmentation	• Cell segmentation using shallow U-Nets. • https://github.com/YijunBao/Shallow-UNet-Neuron-Segmentation_SUNS	Bao et al. 2021
93	Carignan	2021	Cell extraction	• Online cell extraction and triggering based on OnACID and CaImAn. • https://github.com/tzklab/carignan	Taniguchi et al. 2021
94	MullenClassifier	2021	Cell sorting	• Feature extraction from cell images and tracs followed by supervised learning classifier.	Mullen et al. 2021
95	timeUnet	2021	Denoising	• Deep learning for denoising with temporal information added in. • https://github.com/BoHuangLab/Transfer-Learning-Denoising/	Wang et al. 2021
96	EMC²	2021	Motion 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	2022	Cell extraction	• Dictionary-based learning of activity traces followed by graph-based segmentation. • https://github.com/adamshch/GraFT-analysis	Charles et al. 2022
98	CaPTure	2022	Analysis pipeline	• Binary/watershed segmentation followed by ROI-based mean traces. • https://github.com/LieberInstitute/CaPTure	Tippani et al. 2022
99	SpecSeg	2022	Cell segmentation	• Cross spectral power-based segmentation of neurons and neurites. • https://github.com/Leveltlab/SpectralSegmentation	de Kraker et al. 2022
100	CITE-On	2022	Cell extraction	• Online cell detection and trace extraction using CNNs. • https://gitlab.iit.it/fellin-public/cite-on	Sità et al. 2022
101	DL-assisted 2P fiberscope	2022	Denoising	• Denoising 2P fiberscope data using deep neural network (conditional generative adversarial network). • https://figshare.com/articles/dataset/Data/19193792	Guan et al. 2022
102	4SM	2022	Cell extraction	• Generative adversarial network for image segmentation. • https://github.com/SharifAmit/4SM	Kamran et al. 2022
103	DeepCAD-RT	2022	Denoising	• Improved version of DeepCAD for real time performance. • https://github.com/cabooster/DeepCAD-RT/	Li et al. 2023a
104	SEUDO	2022	Trace analysis	• Mixture of Gaussians + maximum likelihood; post-hoc activity trace correction. • https://github.com/adamshch/SEUDO	Gauthier et al. 2022
105	AxialMotionCorrect	2022	Motion correction	• Axial motion correction via multi-plane scanning plus maximum likelihood optimization. • https://gitlab.com/anflores/axial_motion_correction	Flores-Valle and Seelig 2022
106	FIFER	2022	Motion 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
107	NWB	2022	Data handling	• Neurodata Without Borders (NWB) to standardize ephys and imaging data across tools. • https://github.com/NeurodataWithoutBorders	Rübel et al. 2022
108	DeCalciOn	2023	Online analysis pipeline	• Integrate hardware and software to online decode calcium signals. • https://github.com/zhe-ch/ACTEV	Chen et al. 2023
109	jGCaMP8	2023	Calcium indicator	• Improved calcium indicators with increased sensitivity and reduced background.	Zhang et al. 2023a
110	NeuroSeg-II	2023	Cell segmentation	• 2P cell segmentation using region-based convolutional neural network with modifications. • https://github.com/XZH-James/NeuroSeg2	Xu et al. 2023
111	CaliAli	2023	Cross-session alignment	• Cross-session alignment using vasculature information. • https://github.com/CaliAli-PV/CaliAli	Vergara et al. 2023
112	DeepWonder	2023	Cell extraction	• Deep-learning-based cell finding for widefield datasets. • https://github.com/yuanlong-o/Deep_widefield_cal_inferece	Zhang et al. 2023b
113	ASTRA	2023	Cell segmentation	• Deep neural network for astrocyte segmentation. • https://gitlab.iit.it/fellin-public/astra	Bonato et al. 2023
114	SRDTrans	2023	Denoise	• Spatial redundancy for training followed by spatiotemporal transformer architecture to reduce CNN bias/issues. • https://github.com/cabooster/SRDTrans	Li et al. 2023b
115	REALS	2023	Motion 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
116	LD-MCM	2023	Motion 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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Footnotes

-biafra

bahanonu [at] alum.mit.edu

spatiotemporal domain of neuroscience methods
29 may 2019 | neuroscience

An updated spatiotemporal domain of neuroscience methods graphic, inspired by from Sejnow[...]ski, 2014. More changes will be added in time.

humanity's dirge
14 june 2021 | filugori

A short dirge that introduces one of the themes of Filugori, my planned book on man's conquest of space.[...]

guild wars 2 chef excel guide
08 september 2012 | guild wars 2

The chef's ingredients are scattered throughout the Guild Wars 2 map, but the profession is a cheap way to get 10 levels quickly. Because I[...] am OCD and would rather not read text when I can browse a spreadsheet, compiled information from a couple of sources that is more easily searchable.

bio42: notes
12 may 2013 | teaching

While teaching bio42 (cell biology and animal physiology) I created weekly notes to help students in my section study and focus on the impo[...]rtant materials presented in the class. I built off of the latex boilerplate that I have been improving over time to create weekly notes. This highlights why I love LaTeX so much, especially for larger projects that are heavily linked—it allows easy annotation, indexing, creation of new document styles, and other related processes rapidly and consistently. Plus, separating content and style is always a plus and images stay uncoupled from a propriety source (e.g. Word files).

I really love the resulting notes and student feedback was quite positive. I thought sharing them might be useful for others in the future. The source latex files and raw images can be sent upon request (I'm considering making a Github repository in the future). I'll briefly talk about the document below and certain decisions that were made to get it to its current state.

Biafra Ahanonu, PhD

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29 may 2019 | neuroscience

humanity's dirge
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bio42: notes
12 may 2013 | teaching