The design and engineering of organic fluorescent Ca2+ indicators approximately 30 years ago opened the door for imaging cellular Ca2+ signals with a high degree of temporal and spatial resolution. Over this time, Ca2+ imaging has revolutionized our approaches for tissue-level spatiotemporal analysis of functional organization and has matured into a powerful tool for in situ imaging of cellular activity in the living animal. In vivo Ca2+ imaging with temporal resolution at the millisecond range and spatial resolution at micrometer range has been achieved through novel designs of Ca2+ sensors, development of modern microscopes and powerful imaging techniques such as two-photon microscopy.
Finds and investigates Ca2+ sparks in x-y image stacks in an automatic manner. xySpark can study the amplitude, width, frequency, duration, and mass of a spark. It can identify cells within confocal fluorescence images, compensation for slow changes in background fluorescence during data collection. This tool utilizes the mean cell fluorescence to determine the correction factor. It was applied to cardiac myocytes.
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.
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.
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.
Developed for automatic detection and classification of Local Ca Releases (LCRs). Complex lcr detector is able to differentiate high amplitude and low amplitude neighboring release events. In short, it can detect peaks of a wide range of amplitudes. This tool tracks the LCR complex spatiotemporal evolution, including births, deaths, separations and collisions.
Provides an analysis environment for data exploration and region of interest (ROI) creation at arbitrary spatial scales. SamuROI is built to exploit image series of intensity changes of fluorescent indicators over time. This software allows data browsing and deep analysis by incorporating a graphical user interface with command-line interactions by using Jupyter Notebooks.
Automates Local Ca2+ Release (LCR) analysis in two dimensional movies of Ca2+ signals in sinoatrial node cells (SANC). SANC Analyser can be applied to any kind of a spontaneously contracting cell. It can be helpful in studies of physiology and biophysics of Ca2+ signaling in other cell types, including neurons and muscle cells of non-cardiac origin, in which Ca2+ signals are typically challenging to detect due to motion artifacts.
Identifies and analyses time-dependent increases in intensity of a fluorescent indicator recorded by high-speed 2D cameras. XYT Event Detector was created to recognize Local Calcium Releases (LCR) in cardiac pacemaker cells. It uses stacks of images of calcium (Ca) signals measured in living cells. The tool can detect and eliminate global signal shifts and transients and focus only local signals.
Corrects piecewise rigid motion of calcium imaging data. NoRMCorre is based on template alignment and operates by estimating a non-uniform yet smooth motion field. It splits the field of view (FOV) into overlapping patches. This tool can account for non-uniform artifacts along all axes, aiming to capture non-rigid brain movement as well. It is useful to measure the crispness of a registered images.
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.
Automates calcium (Ca) spark analysis in confocal line-scan images. SparkMaster is based on the standard algorithm of Ca spark analysis. It was tested by analyzing images obtained in different cellular preparation such as intact and permeabilized ventricular cardiomyocytes, permeabilized mammalian skeletal muscle, and intact smooth muscle cells. The tool is able to perform a detailed kinetic analysis in a wide range of cellular preparations and experimental conditions.
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.
Aims to embed photon counting into most existing multi-photon imaging systems. PySight is a program dedicated to perform planar and volumetric imaging. It can calculate the difference between photon arrival times and the respective synchronization signals from the laser beam steering element. It integrates features for solving distinct laminar dynamics simultaneously sampled by the variofocal lens, rather than merely extending the effective depth of field using Bessel beams.
Segments cells in large scale wide-field calcium imaging datasets. ACSAT automatically determines global and local threshold values based on pixel intensity levels within a time-collapsed image of a recorded image sequence. It provides a thresholding method that uses global and local schemes to address variations in fluorescence intensity levels of GCaMP even within the same image field.
Finds cells in calcium imaging movies. HNNCcorr fragments cells one at a time by identifying distinct sets of pixels that are nearly identical in correlation space. It employs a combinatorial optimization problem known as head and neck cancer (HNC). This tool can be applied to calcium imaging movies collected with light-field microscopy as well as for the detection of subcellular components.
Automates the discovery of the location and gating behavior of ion channels. CellSpecks can detect subtle events where manual identification is tedious if not impossible. It can read and process video stacks and individual images. This tool illustrates various steps and results of the algorithm, allowing the experimenter to confirm the effectiveness of the algorithm for their particular dataset. It is useful for molecules studied through fluorescence microscopy.
Provides a computational toolbox for large scale calcium imaging analysis. CaImAn implements a set of methods required in the calcium imaging movies analysis pipeline. It also utilizes algorithms for motion correction, movie manipulation and source and spike extraction. These features include handling of very large datasets, source extraction and denoising, deconvolution and spike extraction.
Retrieves cells from calcium imaging data with multiple coupled active contours. ABLE can approximates the local region around a single cell with two sub-regions, the cell interior and exterior. It enables the segmentation of irregular shapes such as cell bodies attached to dendritic branches. This tool integrates minimal assumptions about the objects to be detected. It can be applied to a variety of data types with minimal adjustment.
Assists users to manage a wide range of imaging conditions and qualities. MIN1PIPE is a program that includes features to automatically remove background while preserving signals, correct movements with no assumptions of the types of movements, and to deliver separated neuronal region of interests (ROIs). Moreover, this tool is developed for single-photon based miniscope imaging. Individual modules can also be independently combined with other processing algorithms.
Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of applications such as cell/nuclei counting, cell/nuclei tracking, 3D neuron detection and analysis, machine learning cell classification, particle tracking, wound healing and calcium oscillation tracking. Aivia also comes with editing tools to help get even better results.