Navigating the Light-Sheet Image Analysis Software Landscape: Concepts for Driving Cohesion From Data Acquisition to Analysis

From the combined perspective of biologists, microscope instrumentation developers, imaging core facility scientists, and high performance computing experts, we discuss the challenges faced when selecting imaging and analysis tools in the field of light-sheet microscopy. Our goal is to provide a contextual framework of basic computing concepts that cell and developmental biologists can refer to when mapping the peculiarities of different light-sheet data to specific existing computing environments and image analysis pipelines. We provide our perspective on efficient processes for tool selection and review current hardware and software commonly used in light-sheet image analysis, as well as discuss what ideal tools for the future may look like.

Automated summary

This article discusses the challenges of selecting imaging and analysis tools in light-sheet microscopy from the perspective of biologists, microscope developers, imaging scientists, and computing experts. It aims to provide a contextual framework for basic computing concepts that can help cell and developmental biologists map different light-sheet data to existing computing environments and image analysis pipelines, while also reviewing current hardware and software commonly used in this field. The article also delves into potential future developments in tool selection for light-sheet image analysis.