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

Abstract

ScintillateAn open-source graphical viewer for time-series calcium imaging evaluation and preprocessing Dublon, I. A N; Nilsson, Markus; Balkenius, A.; Anderson, P.; Larsson, M. C. Methods, 273, 120-127. DOI: 10.1016/j.jneumeth.2016 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights.• Users may download and print one copy of any publication from the public portal for the purpose of private study or research.• You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal Final version of authors manuscript for archival at institutional repository Abstract BackgroundCalcium 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 calciumreporter 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 methodThe 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. ResultsWe imaged transgenic flies expressing Calcium-sensitive reporter proteins within projection neurons and moth mushroom bodies stained with a Ca 2+ sensitive bath-applied dye. Instantaneous pre-stimulation background subtraction allowed us to appraise strong genetically encoded neuronal Ca 2+ responses in flies and weaker, less apparent, responses within moth mushroom bodies. Comparison with existing methodsAt 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. ConclusionsWe provide a multi-platform open-source system to evaluate time-series images.Abbreviations: ΔF, change of intensity between frames; ICA, independent component analysis

Mesoscale brain explorer, a flexible python-based image analysis and visualization tool

“…Vobi One is, to our knowledge, the only software toolbox with significant architectural and functional similarity to MBE. Two further recently published toolboxes, FluoroSNNAPP and Scintillate, 46 , 47 are related but are aimed at different end-users. FluoroSNNAPP is a MATLAB package for the automated quantification of single-cell dynamics and network activity 46 .…”

“…Scintillate is a MATLAB package that offers real-time ΔF/F0 while image acquisition is on-going, providing the user with signal change information and the means to further refine subsequent acquisitions 47 . Once signal change has been pinpointed, the user may change objectives, center the image over that specific area, or alter camera settings 47 . Scintillate is thus intended for use during data collection, while MBE is designed for data analysis after collection and is very appropriate for on the go analysis during an experiment by inexperienced users.…”