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SarConfoCal
Computes simultaneously both sarcomere shortening and variation of cytoplasmic calcium in confocal microscopy. SarConfoCal is used to analyse scanlines and multi-channel (fluorescence and transmission) from Laser Scanning Confocal Microscopy (LSCM) images of myocytes, then it plots the fluorescence signal and the sarcomere length of each line versus time. It uses the generally untapped information from the transmitted light of the laser, the latter being recorded simultaneously with fluorescent calcium dye signal. Its strength lies in its simplicity of use: myocyte contraction and calcium transient can be simultaneously evaluated with a single laser scanning confocal microscope, whereas such experiments usually require costly and dedicated experimental devices.
CaSiAn / Calcium Signaling Analyzer
Allows users to quantify signal characteristics including individual spike properties and time course statistics. CaSiAn is a program that enables an analysis of large time course data sets and includes a graphical user interface to permit users to control all analysis related parameters and files. It also contains features for: (1) normalization and background removal; (2) peak and nadir detection needed for the definition of interspike intervals (ISIs); or (3) determining a wide range of signal properties.
Toolbox-Romano-et-al
Detects neuronal assemblies into a complete data processing pipeline designed for the comprehensive analysis of fluorescence imaging data. The Toolbox-Romano-et-al is a computational package that consists of (i) modules for video pre-processing, (ii) morphological image segmentation into regions of interest (ROIs) corresponding to single neurons, (iii) extraction of fluorescence signals, (iv) analysis of ROI responses to stimulus and/or behavioral variables, (v) detection of assemblies of ROIs, (vi) exploratory analysis of network dynamics and (vii) the automatic generation of surrogate shuffled datasets to act as controls for statistical purposes.
Scintillate
Offers a platform of pre-processing image tools. Scintillate is an open source software that allows users to evaluate time-series calcium imaging. It was developed with the aim of complementing the existing acquisition and pre-processing systems. The application includes a set of methods for detection and visualization of images. It can estimate the value of the sample being viewed, assess the viability of the preparation in seconds, spare microscope time, lamp hours and reduce distress to the subject.
EllefsenEtAl2014
Automates the determination and the evaluation of local Ca2+ events captured with fast electron-multiplied charge coupled device (EMCCD) cameras. This algorithm provides a method focusing on the analysis of local cellular Ca2+ transients that is able to locate the origin of events and to earmark them to targeted sites both automatically or manually. The tool also produces reports about fluorescence activity and for each site over time as well as statistics about event frequency, amplitude and kinetics.
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