Making microscopy count: quantitative light microscopy of dynamic processes in living plants

Abstract

Summary Cell theory has officially reached 350 years of age as the first use of the word ‘cell’ in a biological context can be traced to a description of plant material by Robert Hooke in his historic publication ‘Micrographia: or some physiological definitions of minute bodies’. The 2015 Royal Microscopical Society Botanical Microscopy meeting was a celebration of the streams of investigation initiated by Hooke to understand at the subcellular scale how plant cell function and form arises. Much of the work presented, and Honorary Fellowships awarded, reflected the advanced application of bioimaging informatics to extract quantitative data from micrographs that reveal dynamic molecular processes driving cell growth and physiology. The field has progressed from collecting many pixels in multiple modes to associating these measurements with objects or features that are meaningful biologically. The additional complexity involves object identification that draws on a different type of expertise from computer science and statistics that is often impenetrable to biologists. There are many useful tools and approaches being developed, but we now need more interdisciplinary exchange to use them effectively. In this review we show how this quiet revolution has provided tools available to any personal computer user. We also discuss the oft‐neglected issue of quantifying algorithm robustness and the exciting possibilities offered through the integration of physiological information generated by biosensors with object detection and tracking.

Single-Cell Approaches for Understanding Morphogenesis Using Computational Morphodynamics

“…On the other hand, such diversity also brings about the fragmentation of the community regarding tools of choice and, more importantly, file and data formats. Advances in the state-of-the-art allow us to observe biological phenomena at different scales and complexities from single molecule to whole organs [58,59]. It is of paramount importance to agree on file and data standards within the community that maximise transferability of both raw image and processed data, such that we can increase power, accuracy and efficiency of quantification protocols.…”

Introduction 10th International Botanical Microscopy Meeting Special Issue

“…Over the years, they have earned a reputation as being one of the most useful and interesting venues for researchers involved in the microscopical study of plant cells and tissues. As noted by Fricker et al (2016), we botanists have a proud history that goes back 350 years to some of the earliest microscopical investigations ever made. In 1665, Robert Hooke, upon observing small compartments in cork tissue, coined the term "cell", which is recognized as the basic building block of all living organisms.…”

“…An important goal for all microscopical studies is to provide quantitation of the structures and events being observed. Fricker et al (2016) address this directly and provide an overview of computational approaches for gleaning quantitative data from our many micrographs. Many different programs and associated analytical tools are noted and brief summaries of how they can help are provided.…”

“…As noted by Fricker et al . (), we botanists have a proud history that goes back 350 years to some of the earliest microscopical investigations ever made. In 1665, Robert Hooke, upon observing small compartments in cork tissue, coined the term “cell”, which is recognized as the basic building block of all living organisms.…”