Three-dimensional tissue volume generation in conventional brightfield microscopy

The purpose of the study is to develop and automate a series of steps for enabling digital 3D tissue volume generation in conventional Brightfield microscopy for histopathology applications. Tissue samples were retrieved from the General Hospital of Athens "Hippocration", Greece. Samples were placed on a microtome that produced consecutive 2 μm sections. Each section was stained using Hematoxylin and Eosin and placed on microscope slides. A histopathologist specified the region of interest (ROI) on each slide. A 2D image was created from each ROI using a LEICA DM2500 microscope with a LEICA DFC 420C camera. Τhe 3D volume was created by stacking consecutive 2D images using a deep learning image interpolation method. The reconstructed 3D tissue volumes were evaluated by an expert histopathologist. Results showed that the 3D volumes might reveal information that is not clearly visible or even undetectable in the conventional 2D Brightfield images. In contrast to other 3D tissue imaging technologies, the proposed method (a) does not depend on the distance of the sample from the objectives producing 3D tissue volumes at any desired magnification, (b) does not require a special instrument, it may be implemented with any conventional Brightfield microscope, and (c) can be used for any given routine application, not only for some specialized clinical studies. The proposed study provides the basis for a feasible, cost-less and time-less upgrade of any standard 2D microscope into a 3D imaging instrument that may enhance the quality of diagnostic assessments in histopathology.

Current Status of Tissue Clearing and the Path Forward in Neuroscience

Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.