Martin Rueckl, Stephen C. Lenzi, Laura Moreno-Velasquez, Daniel Parthier, Dietmar Schmitz, Sten Ruediger, Friedrich W. Johenning
Abstract
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 Ca(2+)-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 Ca(2+) imaging datasets, particularly when these have been acquired at different spatial scales.
This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 14 July 2017.
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Altmetric has tracked 23,577,761 research outputs across all sources so far. This one has received more attention than most of these and is in the 74th percentile.
So far Altmetric has tracked 775 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 8.1. This one has gotten more attention than average, scoring higher than 63% of its peers.
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We're also able to compare this research output to 16 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 68% of its contemporaries.
