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.
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.
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.
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.
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.
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.