MosaicPlanner: Hardware Agnostic Array Tomography Acquisition Software

Abstract

Array tomography (AT) is a technique for acquiring high resolution highly multiplexed imagery from series of ultra-thin sections arranged as an array on a rigid substrate. Specialized microscope control has been required to utilize AT as an imaging technique, which is often time consuming, and yields small volume data sets. Here we present MosaicPlanner, an open source software platform for light level AT, that streamlines the acquisition process and utilizes the general microscope control API provided by Micro-Manager, allowing AT data to be acquired on a wide variety of microscope hardware. This report provides a description of the MosaicPlanner software design, and platform improvements that were implemented to increase the acquisition speed of high volume, multiplexed AT datasets.