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Scintillate: An open-source graphical viewer for time-series calcium imaging evaluation and pre-processing

Dublon, Ian and Nilsson, Markus and Balkenius, Anna and Anderson, Peter and Larsson, Mattias (2016). Scintillate: An open-source graphical viewer for time-series calcium imaging evaluation and pre-processing. Journal of neuroscience methods. 273, 120-127
[Journal article]

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Official URL: http://dx.doi.org/10.1016/j.jneumeth.2016.08.010

Abstract

Background
Calcium imaging is based on the detection of minute signal changes in an image time-series encompassing pre- and post-stimuli. Depending on the function of the elicited response, change may be pronounced, as in the case of a genetically encoded calcium-reporter protein, or subtle, as is the case in a bath-applied dye system. Large datasets are thus often acquired and appraised only during post-processing where specific Regions of Interest (ROIs) are examined.

New method 
The scintillate software provides a platform allowing for near instantaneous viewing of time-sequenced tiffs within a discrete GUI environment. Whole sequences may be evaluated. In its simplest form scintillate provides change in florescence (ΔF) across the entiretiffimage matrix. Evaluating image intensity level differences across the whole image allows the user to rapidly establish the value of the preparation, withouta prioriROI-selection. Additionally, an implementation of Independent Component Analysis (ICA) provides additional rapid insights into areas of signal change.
 
Results 
We imaged transgenic flies expressing Calcium-sensitive reporter proteins within projection neurons and moth mushroom bodies stained with a Ca2+sensitive bath-applied dye. Instantaneous pre-stimulation background subtraction allowed us to appraise strong genetically encoded neuronal Ca2+responses in flies and weaker, less apparent, responses within moth mushroom bodies. Comparison with existing methods At the time of acquisition, whole matrix ΔF analysis alongside ICA is ordinarily not performed. We found it invaluable, minimising time spent with unresponsive samples, and assisting in optimisation of subsequent acquisitions.
 
Conclusions 
We provide a multi-platform open-source system to evaluate time-series images. Abbreviations ΔF,change of intensity between frames; ICA,independent component analysis

Authors/Creators:Dublon, Ian and Nilsson, Markus and Balkenius, Anna and Anderson, Peter and Larsson, Mattias
Title:Scintillate: An open-source graphical viewer for time-series calcium imaging evaluation and pre-processing
Series/Journal:Journal of neuroscience methods (BIB9033457)
Year of publishing :2016
Volume:273
Page range:120-127
Number of Pages:8
Publisher:Elsevier
ISSN:0165-0270
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Accepted version
Full Text Status:Restricted
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Other Biological Topics
(A) Swedish standard research categories 2011 > 3 Medical and Health Sciences > 301 Basic Medicine > Neurosciences
Agrovoc terms:image processing, fluorescence, microscopy
Keywords:optical imaging, Fluorescence, Pre-processing, Calcium imaging, ICA, GUI
URN:NBN:urn:nbn:se:slu:epsilon-e-3750
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-3750
Additional ID:
Type of IDID
DOI10.1016/j.jneumeth.2016.08.010
ID Code:13774
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Protection Biology
Deposited By: SLUpub Connector
Deposited On:01 Nov 2016 07:36
Metadata Last Modified:01 Nov 2016 07:36

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