OpenHiCAMM: High-Content Screening Software for Complex Microscope Imaging Workflows

摘要

class="head no_bottom_margin" id="sec1title">IntroductionLarge-scale genome sequencing has rapidly facilitated the investigation and analysis of gene and protein functions and interactions. Efforts to interpret sequence data and to understand how they are used to control cellular, tissue, or organ system development have quickly revealed the limitations in our molecular understanding of multicellular organisms. Spatial gene expression is important for understanding the events that are necessary for the development of metazoans, and large-scale studies are underway for a number of species (e.g., , , , ). Indeed, even the existence of uniform cells or tissues has been questioned, and their variance has been masked by single measurements ().High-content screening (HCS) is routinely used in cell culture imaging, pharmaceutical drug discovery, genome-wide RNA interference (RNAi), and CRISPR (). Commercial equipment is readily available () and able to scan multi-well plates and slides. Commercial automated microscopes are integrated packages of robotics, microscope, and software, limiting possible customizations, especially for well-suited existing microscope systems. Imaging is done in a single pass, requiring a compromise between resolution and field depth. For single cell samples, this means a tradeoff between resolution and cell density. Transient transfections may not have sufficient cell transfection density for high-resolution imaging. For larger samples, such as histological sections, organoids, or whole-mount samples of model organisms or tissues, specimens need to be tiled at low resolution or placed at a predefined position.We describe new software for high-throughput imaging, specifically designed to automate image acquisition that requires multi-step workflows contingent on image analysis and multiple imaging modalities. The software, OpenHiCAMM (Open Hi Content Acquisition for μManager) controls optical microscopes and interfaces with an automated slide loader to perform fully automated HCS.