SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales
The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibi...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2017-06-01
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| Series: | Frontiers in Neuroinformatics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fninf.2017.00044/full |
| _version_ | 1818258429350772736 |
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| author | Martin Rueckl Stephen C. Lenzi Stephen C. Lenzi Laura Moreno-Velasquez Laura Moreno-Velasquez Daniel Parthier Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Sten Ruediger Friedrich W. Johenning Friedrich W. Johenning Friedrich W. Johenning |
| author_facet | Martin Rueckl Stephen C. Lenzi Stephen C. Lenzi Laura Moreno-Velasquez Laura Moreno-Velasquez Daniel Parthier Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Sten Ruediger Friedrich W. Johenning Friedrich W. Johenning Friedrich W. Johenning |
| author_sort | Martin Rueckl |
| collection | DOAJ |
| description | The measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales. |
| first_indexed | 2024-12-12T17:59:24Z |
| format | Article |
| id | doaj.art-b50d215b1897427e98d12e2f0b293be9 |
| institution | Directory Open Access Journal |
| issn | 1662-5196 |
| language | English |
| last_indexed | 2024-12-12T17:59:24Z |
| publishDate | 2017-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroinformatics |
| spelling | doaj.art-b50d215b1897427e98d12e2f0b293be92022-12-22T00:16:38ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962017-06-011110.3389/fninf.2017.00044271620SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial ScalesMartin Rueckl0Stephen C. Lenzi1Stephen C. Lenzi2Laura Moreno-Velasquez3Laura Moreno-Velasquez4Daniel Parthier5Dietmar Schmitz6Dietmar Schmitz7Dietmar Schmitz8Dietmar Schmitz9Dietmar Schmitz10Sten Ruediger11Friedrich W. Johenning12Friedrich W. Johenning13Friedrich W. Johenning14Institute of Physics, Humboldt Universität BerlinBerlin, GermanyInstitute of Physics, Humboldt Universität BerlinBerlin, GermanyNeuroscience Research Center, Charité Universitätsmedizin BerlinBerlin, GermanyNeuroscience Research Center, Charité Universitätsmedizin BerlinBerlin, GermanyBerlin Institute of Health (BIH)Berlin, GermanyNeuroscience Research Center, Charité Universitätsmedizin BerlinBerlin, GermanyNeuroscience Research Center, Charité Universitätsmedizin BerlinBerlin, GermanyEinstein Center for NeuroscienceBerlin, GermanyBernstein Center for Computational NeuroscienceBerlin, GermanyCluster of Excellence ‘Neurocure’Berlin, GermanyDZNE-German Center for Neurodegenerative DiseaseBerlin, GermanyInstitute of Physics, Humboldt Universität BerlinBerlin, GermanyNeuroscience Research Center, Charité Universitätsmedizin BerlinBerlin, GermanyBerlin Institute of Health (BIH)Berlin, GermanyEinstein Center for NeuroscienceBerlin, GermanyThe measurement of activity in vivo and in vitro has shifted from electrical to optical methods. While the indicators for imaging activity have improved significantly over the last decade, tools for analysing optical data have not kept pace. Most available analysis tools are limited in their flexibility and applicability to datasets obtained at different spatial scales. Here, we present SamuROI (Structured analysis of multiple user-defined ROIs), an open source Python-based analysis environment for imaging data. SamuROI simplifies exploratory analysis and visualization of image series of fluorescence changes in complex structures over time and is readily applicable at different spatial scales. In this paper, we show the utility of SamuROI in Ca2+-imaging based applications at three spatial scales: the micro-scale (i.e., sub-cellular compartments including cell bodies, dendrites and spines); the meso-scale, (i.e., whole cell and population imaging with single-cell resolution); and the macro-scale (i.e., imaging of changes in bulk fluorescence in large brain areas, without cellular resolution). The software described here provides a graphical user interface for intuitive data exploration and region of interest (ROI) management that can be used interactively within Jupyter Notebook: a publicly available interactive Python platform that allows simple integration of our software with existing tools for automated ROI generation and post-processing, as well as custom analysis pipelines. SamuROI software, source code and installation instructions are publicly available on GitHub and documentation is available online. SamuROI reduces the energy barrier for manual exploration and semi-automated analysis of spatially complex Ca2+ imaging datasets, particularly when these have been acquired at different spatial scales.http://journal.frontiersin.org/article/10.3389/fninf.2017.00044/fullcalcium imaginganalysis softwarePython programmingOpen Source Softwaremicroscopyfluorescence |
| spellingShingle | Martin Rueckl Stephen C. Lenzi Stephen C. Lenzi Laura Moreno-Velasquez Laura Moreno-Velasquez Daniel Parthier Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Dietmar Schmitz Sten Ruediger Friedrich W. Johenning Friedrich W. Johenning Friedrich W. Johenning SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales Frontiers in Neuroinformatics calcium imaging analysis software Python programming Open Source Software microscopy fluorescence |
| title | SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales |
| title_full | SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales |
| title_fullStr | SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales |
| title_full_unstemmed | SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales |
| title_short | SamuROI, a Python-Based Software Tool for Visualization and Analysis of Dynamic Time Series Imaging at Multiple Spatial Scales |
| title_sort | samuroi a python based software tool for visualization and analysis of dynamic time series imaging at multiple spatial scales |
| topic | calcium imaging analysis software Python programming Open Source Software microscopy fluorescence |
| url | http://journal.frontiersin.org/article/10.3389/fninf.2017.00044/full |
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