Comparative analysis of tissue reconstruction algorithms for 3D histology

Abstract

MotivationDigital pathology enables new approaches that expand beyond storage, visualization or analysis of histological samples in digital format. One novel opportunity is 3D histology, where a three-dimensional reconstruction of the sample is formed computationally based on serial tissue sections. This allows examining tissue architecture in 3D, for example, for diagnostic purposes. Importantly, 3D histology enables joint mapping of cellular morphology with spatially resolved omics data in the true 3D context of the tissue at microscopic resolution. Several algorithms have been proposed for the reconstruction task, but a quantitative comparison of their accuracy is lacking.ResultsWe developed a benchmarking framework to evaluate the accuracy of several free and commercial 3D reconstruction methods using two whole slide image datasets. The results provide a solid basis for further development and application of 3D histology algorithms and indicate that methods capable of compensating for local tissue deformation are superior to simpler approaches.Availability and implementationCode: https://github.com/BioimageInformaticsTampere/RegBenchmark. Whole slide image datasets: http://urn.fi/urn: nbn: fi: csc-kata20170705131652639702.Supplementary information Supplementary data are available at Bioinformatics online.

3D-Printed Whole Prostate Models with Tumor Hotspots Using Dual-Extruder Printer

“…However, since tumor annotations were available for data reconstructed with SIFT keypoints, improving the reconstruction step was left out of the scope of this article. Quantitative error estimation of the SIFT keypoint based 3D reconstruction is presented by Kartasalo et al [9]. Without native 3D imaging like µCT, quantitative error estimation between 3D models and actual organ is non-trivial and out of the scope of this article.…”

“…Commonly, sections are hematoxylin-eosin (HE)-stained and imaged with light microscopy, producing a sequential stack of WSIs. 3D reconstruction techniques are then used to align image stacks for 3D representations [9].…”

Society of Toxicologic Pathology Digital Pathology and Image Analysis Special Interest Group Article*: Opinion on the Application of Artificial Intelligence and Machine Learning to Digital Toxicologic Pathology

“…For example, feature-based algorithms could be implemented to register serial sections, thus decreasing the need for manual input. 147 There have been numerous image-registration algorithms employed for 3D histology 148 including one used by an imaging system that scans each section as it is being cut 149 and other private companies also offer AI solutions for keeping images in register to supplement their image analysis software 116,138 and to aid in the creation of 3D images.…”

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“…Such techniques were still being used when Sydney Brenner in the early 1970's first applied computers to solve the onerous challenge of preparing and robustly examining serial section reconstructions [10,11]. Modern advances in computing power, software engineering, imaging technology and visualization tools have more recently permitted switch to a variety of 3D reconstruction methodologies that have revolutionized the fields of molecular-, cellular-, tissue-, and organ biology [12][13][14][15][16][17][18][19][20][21][22][23][24]. Presently, at least at mathematically, even four-dimensional (4D) conceptualization of objects is possible [23,[25][26][27].…”

“…Modern advances in computing power, software engineering, imaging technology and visualization tools have more recently permitted switch to a variety of 3D reconstruction methodologies that have revolutionized the fields of molecular-, cellular-, tissue-, and organ biology [12][13][14][15][16][17][18][19][20][21][22][23][24]. Presently, at least at mathematically, even four-dimensional (4D) conceptualization of objects is possible [23,[25][26][27]. As proposed by Alan Turing [28] in his pioneering work, in biology, function emanates from accretion of various infinitesimal physical and biochemical events that happen between and among the individual structural components at different levels of organization, from molecular-, cellular-to organ-system levels.…”