dc.contributor.author
Rueckl, Martin
dc.contributor.author
Lenzi, Stephen C.
dc.contributor.author
Moreno-Velasquez, Laura
dc.contributor.author
Parthier, Daniel
dc.contributor.author
Schmitz, Dietmar
dc.contributor.author
Ruediger, Sten
dc.contributor.author
Johenning, Friedrich W.
dc.date.accessioned
2018-06-08T11:00:43Z
dc.date.available
2017-09-18T12:27:14.880Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/21463
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-24755
dc.description.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 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.
en
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
calcium imaging
dc.subject
analysis software
dc.subject
Python programming
dc.subject
Open Source Software
dc.subject.ddc
600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit
dc.title
SamuROI, a Python-Based Software Tool for Visualization and Analysis of
Dynamic Time Series Imaging at Multiple Spatial Scales
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
Front. Neuroinform. - 11 (2017), Artikel Nr. 44
dcterms.bibliographicCitation.doi
10.3389/fninf.2017.00044
dcterms.bibliographicCitation.url
http://doi.org/10.3389/fninf.2017.00044
refubium.affiliation
Charité - Universitätsmedizin Berlin
de
refubium.mycore.fudocsId
FUDOCS_document_000000027987
refubium.note.author
Der Artikel wurde in einer reinen Open-Access-Zeitschrift publiziert.
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000008763
dcterms.accessRights.openaire
open access