ArticleBioinformatics (Oxford, England)2018
Comparative analysis of tissue reconstruction algorithms for 3D histology.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Advancing three-dimensional tendon imaging using laboratory X-ray phase contrast techniques and refined sample preparation.Scientific reports · 2026Article
- Three-dimensional reconstruction of gigapixel whole-mount histopathology specimens with RAPID.Scientific reports · 2026Article
- SparStVR - exploring sparse 3D histology data in virtual reality.Communications engineering · 2026Article
- Reproducibility of digital pathology features extracted from deep learning and foundational AI models on sequential tissue slides.Scientific reports · 2025Article
- From traditional to deep learning approaches in whole slide image registration: A methodological review.Journal of pathology informatics · 2025Review
- 3D visualization of uterus and ovary: tissue clearing techniques and biomedical applications.Frontiers in bioengineering and biotechnology · 2025Review
- Tissue clearing and imaging approaches for in toto analysis of the reproductive system†.Biology of reproduction · 2024Review
- Three-dimensional histology reveals dissociable human hippocampal long-axis gradients of Alzheimer's pathology.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Spatial landmark detection and tissue registration with deep learning.Nature methods · 2024Article
- 3D visualization and printing: An "Anatomical Engineering" trend revealing underlying morphology via innovation and reconstruction towards future of veterinary anatomy.Anatomical science international · 2024Review
- Three-dimensional histology reveals dissociable human hippocampal long axis gradients of Alzheimer's pathology.bioRxiv : the preprint server for biology · 2023Article
- Decoding the tumor microenvironment with spatial technologies.Nature immunology · 2023Review
- Comparison of consecutive and restained sections for image registration in histopathology.Journal of medical imaging (Bellingham, Wash.) · 2023Article
- A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.Scientific data · 2023Article
- Virtual alignment of pathology image series for multi-gigapixel whole slide images.Nature communications · 2023Article
- Article
- CODA: quantitative 3D reconstruction of large tissues at cellular resolution.Nature methods · 2022Article
- Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment.Heliyon · 2022Article
- Tutorial: methods for three-dimensional visualization of archival tissue material.Nature protocols · 2021Review
- Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration.BMC cancer · 2021Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Digital 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. Results: We 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 implementation: Code: 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.