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

Abstract

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.

Volumetric imaging of human mesenchymal stem cells (hMSCs) for non-destructive quantification of 3D cell culture growth

“…The stripe artifacts, which arise from scattering and/or absorption of the illumination beam by small objects such as air bubbles, debris, or un-melted agarose particles, in LSM images can be removed via a number of hardware and image-processing methods, such as digital scanned lightsheet microscopy (DSLM) with pivot scanning or median digital filtering [ 87 ]. Future image analysis pipelines could include corrections for uneven illumination, striping artifacts, or photobleaching [ 88 ]. Photobleaching, a chemical alteration of fluorophores that render them unable to fluoresce, is not a concern in esLSM as it does not involve an energy transition; however, extra care has to be taken in esLSM to utilize the full dynamic range of the detector without saturation, even with very low incident laser power.…”

Tissue clearing and its applications in human tissues: A review

“…[ 90 ] Furthermore, all JPEG 2000 encoding and decoding steps are difficult to parallelize, challenging for effective use of modern multicore computer hardware. Conversely, HDF5, another popular compression format for image files, [ 91 ] provides lossless data compression and storage data in blocks for fast access to arbitrary regions of interest. The hierarchical data format 5 (HDF5) interface does not parallelize writes and requires a high‐performance computer.…”

A Hitchhiker's guide through the bio‐image analysis software universe

“…Similarly, in the microscope hardware and control oriented context, a list of useful software was published [7]. Also for lightsheet microscopy, there is a specific list of software for acquisition and analysis available [8]. There are a large number of software tools and applications that have been specifically developed for the cryo‐electron microscopy (cryoEM); a comprehensive list of software for the cryoEM community can be found from wikibooks [9].…”