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

Dublon, I. A N; Nilsson, Markus LU ; Balkenius, A.; Anderson, P. and Larsson, M. C. (2016) In Journal of Neuroscience Methods 273. p.120-127
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... (More)

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 entire tiff image matrix. Evaluating image intensity level differences across the whole image allows the user to rapidly establish the value of the preparation, without a priori ROI-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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Calcium imaging, Fluorescence, GUI, ICA, optical imaging, Pre-processing
in
Journal of Neuroscience Methods
volume
273
pages
8 pages
publisher
Elsevier
external identifiers
  • Scopus:84985041094
ISSN
0165-0270
DOI
10.1016/j.jneumeth.2016.08.010
language
English
LU publication?
yes
id
c2a4c531-bad3-4f91-9d6f-87760ca0228f
date added to LUP
2016-10-13 10:04:45
date last changed
2016-10-14 03:00:02
@misc{c2a4c531-bad3-4f91-9d6f-87760ca0228f,
  abstract     = {<p>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 entire tiff image matrix. Evaluating image intensity level differences across the whole image allows the user to rapidly establish the value of the preparation, without a priori ROI-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 Ca<sup>2+</sup> sensitive bath-applied dye. Instantaneous pre-stimulation background subtraction allowed us to appraise strong genetically encoded neuronal Ca<sup>2+</sup> 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.</p>},
  author       = {Dublon, I. A N and Nilsson, Markus and Balkenius, A. and Anderson, P. and Larsson, M. C.},
  issn         = {0165-0270},
  keyword      = {Calcium imaging,Fluorescence,GUI,ICA,optical imaging,Pre-processing},
  language     = {eng},
  month        = {11},
  pages        = {120--127},
  publisher    = {ARRAY(0xaf58ae8)},
  series       = {Journal of Neuroscience Methods},
  title        = {Scintillate : An open-source graphical viewer for time-series calcium imaging evaluation and pre-processing},
  url          = {http://dx.doi.org/10.1016/j.jneumeth.2016.08.010},
  volume       = {273},
  year         = {2016},
}