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.
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.
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.
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.
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.
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.