An Open-Source Real-Time Motion Correction Plug-In for Single-Photon Calcium Imaging of Head-Mounted Microscopy

A simple MATLAB toolbox for analyzing calcium imaging data in vitro and in vivo

BACKGROUND

Fluorescence imaging of calcium dynamics in neuronal populations is powerful because it offers a way of relating the activity of individual cells to the broader population of nearby cells. The method's growth across neuroscience has particularly been driven by the introduction of sophisticated mathematical techniques related to motion correction, image registration, cell detection, spike estimation, and population characterization. However, for many researchers, making good use of these techniques has been difficult because they have been devised by different workers and impose differing - and sometimes stringent - technical requirements on those who seek to use them.

NEW METHOD

We have built a simple toolbox of analysis routines that encompass the complete workflow for analyzing calcium imaging data. The workflow begins with preprocessing of data, includes motion correction and longitudinal image registration, detects active cells using constrained non-negative matrix factorization, and offers multiple options for estimating spike times and characterizing population activity. The routines can be navigated through a simple graphical user interface. Although written in MATLAB, a standalone version for researchers who do not have access to MATLAB is included.

RESULTS

We have used the toolbox on two very different preparations: spontaneously active brain slices and microendoscopic imaging from deep structures in awake behaving mice. In both cases, the toolbox offered a seamless flow from raw data all the way through to prepared graphs.

CONCLUSION

The field of calcium imaging has benefited from the development of numerous innovative mathematical techniques. Here we offer a simple toolbox that allows ordinary researchers to fully exploit these techniques.

Calcium imaging: a technique to monitor calcium dynamics in biological systems

Calcium ion (Ca2+) is a multifaceted signaling molecule that acts as an important second messenger. During the course of evolution, plants and animals have developed Ca2+ signaling in order to respond against diverse stimuli, to regulate a large number of physiological and developmental pathways. Our understanding of Ca2+ signaling and its components in physiological phenomena ranging from lower to higher organisms, and from single cell to multiple tissues has grown exponentially. The generation of Ca2+ transients or signatures for various stress factor is a well-known mechanism adopted in plant and animal systems. However, the decoding of such remarkable signatures is an uphill task and is always an interesting goal for the scientific community. In the past few decades, studies on the concentration and dynamics of intracellular Ca2+ are significantly increasing and have become a trend in modern biology. The advancement in approaches from Ca2+ binding dyes to in vivo Ca2+ imaging through the use of Ca2+ biosensors to achieve spatio-temporal resolution in micro and milliseconds range, provide us phenomenal opportunities to study live cell Ca2+ imaging or dynamics. Here, we describe the usage, improvement and advancement of Ca2+ based dyes, genetically encoded probes and sensors to achieve extraordinary Ca2+ imaging in plants and animals.

Graphical abstract