Preprocessing and Registration of Miniscope-Based Calcium Imaging of the Rodent Brain

Abstract

<p><strong>Abstract.</strong> Microscopic imaging is central to the brain and cognition studies in animals and often requires advanced image processing. In vivo recordings on awake behaving animals require stabilization of the images as the tissue in the images undergoes non-rigid deformations due to animal movement, pulse beat and breathing of the animal. Here we propose an approach to compensation for the tissue motion in calcium imaging data acquired with miniaturized wearable microscopes (miniscopes) from live rodent brains. Our approach includes preprocessing of the images in which we compensate for non-uniform illumination, remove calcium transients and instrument-specific noise. For image registration we use the multiscale mutual information based non-rigid algorithm with B-spline transformation model. We present the preliminary results of such motion compensation approach applied to the real miniscope image stacks.</p>