IMART software for correction of motion artifacts in images collected in intravital microscopy

Abstract

Intravital microscopy is a uniquely powerful tool, providing the ability to characterize cell and organ physiology in the natural context of the intact, living animal. With the recent development of high-resolution microscopy techniques such as confocal and multiphoton microscopy, intravital microscopy can now characterize structures at subcellular resolution and capture events at sub-second temporal resolution. However, realizing the potential for high resolution requires remarkable stability in the tissue. Whereas the rigid structure of the skull facilitates high-resolution imaging of the brain, organs of the viscera are free to move with respiration and heartbeat, requiring additional apparatus for immobilization. In our experience, these methods are variably effective, so that many studies are compromised by residual motion artifacts. Here we demonstrate the use of IMART, a software tool for removing motion artifacts from intravital microscopy images collected in time series or in three dimensions.

Intravital microscopy of the lung: minimizing invasiveness

“…The geometric transformation required to correct these deformations is often non-rigid and non-linear. Therefore, it cannot be expressed under a matrix form and requires a sophisticated processing that can be achieved by deformation of an iteratively deformed grid of control points [63].…”

“…In particular, a strategy based on the use of a uniform grid of control points to reduce distortion-induced dissimilarities between sequential images in IVM has been developed and fruitfully used for lung IVM [28,63,65,66]. The underlying premise is that two consecutive frames of either a z-stack or a time-series would be very similar without motion artifacts [63].…”

A simple approach for measuring FRET in fluorescent biosensors using two-photon microscopy

“…Additionally, gating the image collection to respiration can minimize the motion artifacts in tissues such as the lung 25,26 . Finally, motion-induced distortions can be eliminated from the collected images using various methods of digital image analysis [27][28][29][30][31] .…”

Four Dimensional Image Registration for Intravital Microscopy

“…This technique initially starts with a rigid registration step and then uses localized non-rigid registration. The four spectral channels are transformed to grayscale images using the spectral channel weights described in [20,21]. First, rigid registration is used to reduce global motion artifacts between images.…”

“…We use the non-rigid method described in our previous work [20,21] because this method can effectively eliminate 3D non-rigid motion artifacts between focal slices. This technique initially starts with a rigid registration step and then uses localized non-rigid registration.…”