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Sparse self-attention aggregation networks for neural sequence slice interpolation
2021
BioData Mining
Preserved Fulltext
Background Microscopic imaging is a crucial technology for visualizing neural and tissue structures. ...
The continuity of biological tissue among serial EM images makes it possible to recover missing tissues utilizing inter-slice interpolation. ...
Lixin Wei and his colleagues (Institute of Automation, CAS) for the Zeiss Supra55 SEM and technical support. ...
doi:10.1186/s13040-021-00236-z
pmid:33522940
fatcat:2rw6v7ondrbsnkhg5dgbb4wum4
Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data using HIT-MAP
2021
Nature Communications
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HIT-MAP will be a valuable resource for the spatial proteomics community for analysing newly generated and retrospective datasets, enabling robust peptide and protein annotation and visualisation in a ...
MALDI-MSI preserves spatial distribution and histology allowing unbiased analysis of complex, heterogeneous tissues. ...
Acknowledgements We would like to thank John Reeves for his valuable advice and suggestions. ...
doi:10.1038/s41467-021-23461-w
pmid:34050164
pmcid:PMC8163805
fatcat:jqhc22hurzg3tkfciw7qsevpkq
Reconstruction of serially acquired slices using physics-based modeling
2003
IEEE Transactions on Information Technology in Biomedicine
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This paper presents an accurate, computationally efficient, fast and fully-automated algorithm for the alignment of 2D serially acquired sections forming a 3D volume. ...
Index Terms-2D serially acquired images, misalignment, image registration, registration error, physics-based deformable modelling. computer vision. ...
Lyroudia, Department of Dentistry, Aristotle University of Thessaloniki, and Ms Anna Digka, dentist and PhD candidate in Endodontology, Department of Dentistry, Aristotle University of Thessaloniki, for ...
doi:10.1109/titb.2003.821335
pmid:15000365
fatcat:5vkfokzfrzasvc4al74ajttuwi
Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions
[article]
2024
arXiv
pre-print
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Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging. ...
fusion, shape-aware, edge-aware, and position-aware units for lesion segmentation. [445] SE Improved U-Net based on Mixed Attention Loss Function model for breast tumor segmentation. [446] SE ResNet34 ...
, matching the HER2 IHC staining that is chemically performed on the same tissue sections. ...
arXiv:2304.06662v4
fatcat:t5nvpybawjhfhiw4h2bekozo74
Synthetic Generation of Three-Dimensional Cancer Cell Models from Histopathological Images
[article]
2021
arXiv
pre-print
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2021 pre-print arXiv:2101.11600v1 fatcat:rb2e6wpllfejrnltupernbeqri
Classical reconstruction algorithms based on image registration of consecutive slides of stained tissues are prone to errors and often not suitable for the training of three-dimensional segmentation algorithms ...
Synthetic generation of three-dimensional cell models from histopathological images aims to enhance understanding of cell mutation, and progression of cancer, necessary for clinical assessment and optimal ...
Cutting-edge cancer segmentation algorithms require a large set of robust three-dimensional data to optimize cancer segmentation ability based on diverse types of tissue. ...
arXiv:2101.11600v2
fatcat:gygol52zfrcr5eojiu4xpzhvae
Contractility Measurements of Human Uterine Smooth Muscle to Aid Drug Development
2018
Journal of Visualized Experiments
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Biopsies are obtained from women undergoing cesarean section delivery with informed consent. ...
Strips develop spontaneous contractions within 2-3 h under set tension and remain stable for many hours (>6 h). ...
For instance, if the application of drug X is for 25 min, use the 25 min preceding the first application of drug X as the control. ...
doi:10.3791/56639
pmid:29443077
pmcid:PMC5841565
fatcat:vms5fl6edjb5lb4tjyfczg2ac4
A new method for three-dimensional immunofluorescence study of the cochlea
2020
Hearing Research
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This technique reduces time and labour required for sectioning of cochleae and can allow visualisation of cellular detail. ...
The technique utilises robust immunofluorescent labelling followed by effective tissue clearing and fast image acquisition using Light Sheet Microscopy. ...
, University of Melbourne for imaging assistance, and Dr Aaron Collins for assistance in preparing figures. ...
doi:10.1016/j.heares.2020.107956
pmid:32464455
fatcat:lorqbsrt5fh5xcxoxzsudzki2u
Simultaneous automatic scoring and co-registration of hormone receptors in tumor areas in whole slide images of breast cancer tissue slides
2016
Cytometry Part A
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Thicker sections are less likely to have common tissue structures across many serial sections, and it will therefore be more difficult to score the exact same tissue region for each marker as parts of ...
As such, we require a robust method of bringing sections from different slides back into a common alignment, such that we can identify the same region of tissue across many sections. ...
doi:10.1002/cyto.a.23035
pmid:28009468
fatcat:zvfo7govjrevfmni5bvpca2mre
A Survey of Methods for 3D Histology Reconstruction
2018
Medical Image Analysis
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This paper reviews almost three decades of methods for 3D reconstruction from serial sections, used in the study of many different types of tissue. ...
However, despite bringing visual awareness, recovering realistic reconstructions is elusive without prior knowledge about the tissue shape. 3D medical imaging made such structural ground truths available ...
Smriti Patodia, from UCL Institute of Neurology (Department of Neuropathology), for her comments on Section 2 and the images used in Figures ...
doi:10.1016/j.media.2018.02.004
pmid:29502034
fatcat:ta5hlvqjpzenxhltfwh6p4mhqq
Characterization of Biological Processes through Automated Image Analysis
2010
Annual Review of Biomedical Engineering
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The text includes a review of image registration and image segmentation methods, as well as algorithms that enable the analysis of cellular architecture, cell morphology, and tissue organization. ...
(12) address the challenge of building large serial-section transmission electron microscopy volumes for the study of neural circuitry. ...
(11) developed for the reconstruction of 3D histopathology volumes from serial sections highlights a number of challenges other researchers have encountered. ...
doi:10.1146/annurev-bioeng-070909-105235
pmid:20482277
fatcat:izhecr6bdzdapmxnnvzhmbpssa
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
[article]
2021
bioRxiv
pre-print
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for whole-cell segmentation. ...
Cell segmentation, the task of uniquely identifying each cell in an image, remains a substantial barrier for tissue imaging, as existing approaches are inaccurate or require a substantial amount of manual ...
Acknowledgments We thank Long Cai, Katy Borner, Matt Thomson, Steve Quake, and Markus Covert for interesting discussions; Sean Bendall, David Glass, and Erin McCaffrey for feedback on the manuscript; Roshan ...
doi:10.1101/2021.03.01.431313
fatcat:xob6ar7uwfh3bpuwowp2lvyp7u
Computer-assisted enhanced volumetric segmentation magnetic resonance imaging data using a mixture of artificial neural networks
2003
Magnetic Resonance Imaging
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An accurate computer-assisted method able to perform regional segmentation on 3D single modality images and measure its volume is designed using a mixture of unsupervised and supervised artificial neural ...
In the first case, a high correlation and parallelism was registered between the volumetric measurements, of the injured and healthy tissue, by the proposed method with respect to the manual measurements ...
Acknowledgments We are grateful to Palmira Villa for her excellent technical assistance, and to the Spanish Agencia Española de Cooperación Internacional (AECI) for financial support for RPA. ...
doi:10.1016/s0730-725x(03)00193-0
pmid:14599541
fatcat:tc6pjt27lbcpblfghxfiwmalpy
Some trends in microscope image processing
2004
Micron
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Acknowledgements I thank the referees for their helpful comments on the first version of the manuscript. ...
The power spectrum, for instance, represents the frequency content of the whole image. ...
One of the recently appearing trends in image segmentation is the awareness that, between these two extremes, i.e. fully interactive and fully automatic segmentation procedures, there is room for semi-automatic ...
doi:10.1016/j.micron.2004.04.006
pmid:15288643
fatcat:i62hiuaw75gtbenwsponfrqh7i
Some trends in microscope image processing
2004
Bioorganic & Medicinal Chemistry
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Acknowledgements I thank the referees for their helpful comments on the first version of the manuscript. ...
The power spectrum, for instance, represents the frequency content of the whole image. ...
One of the recently appearing trends in image segmentation is the awareness that, between these two extremes, i.e. fully interactive and fully automatic segmentation procedures, there is room for semi-automatic ...
doi:10.1016/s0968-4328(04)00095-2
fatcat:y4xfvtgncfglbg4moqpsnwl34u
Multiplexed Immunohistochemistry and Digital Pathology as the Foundation for Next-Generation Pathology in Melanoma: Methodological Comparison and Future Clinical Applications
2021
Frontiers in Oncology
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The state-of-the-art for melanoma treatment has recently witnessed an enormous revolution, evolving from a chemotherapeutic, "one-drug-for-all" approach, to a tailored molecular- and immunological-based ...
Recent advancements in artificial intelligence and single-cell profiling of resected tumor samples are paving the way for this challenging task. ...
A workaround has been to analyze marker expression patterns in serial sections, but this approach does not achieve sufficient detail to get to a robust interpretation. ...
doi:10.3389/fonc.2021.636681
pmid:33854972
pmcid:PMC8040928
fatcat:vqpqkemqp5bpnl6d66k4hmvtkm
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