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Falk M, Ynnerman A, Treanor D, Lundstrom C. Interactive Visualization of 3D Histopathology in Native Resolution. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2018; 25:1008-1017. [PMID: 30130214 DOI: 10.1109/tvcg.2018.2864816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We present a visualization application that enables effective interactive visual analysis of large-scale 3D histopathology, that is, high-resolution 3D microscopy data of human tissue. Clinical work flows and research based on pathology have, until now, largely been dominated by 2D imaging. As we will show in the paper, studying volumetric histology data will open up novel and useful opportunities for both research and clinical practice. Our starting point is the current lack of appropriate visualization tools in histopathology, which has been a limiting factor in the uptake of digital pathology. Visualization of 3D histology data does pose difficult challenges in several aspects. The full-color datasets are dense and large in scale, on the order of 100,000 × 100,000× 100 voxels. This entails serious demands on both rendering performance and user experience design. Despite this, our developed application supports interactive study of 3D histology datasets at native resolution. Our application is based on tailoring and tuning of existing methods, system integration work, as well as a careful study of domain specific demands emanating from a close participatory design process with domain experts as team members. Results from a user evaluation employing the tool demonstrate a strong agreement among the 14 participating pathologists that 3D histopathology will be a valuable and enabling tool for their work.
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Zhang B, Zhou Z, Tao Y, Lin H. A novel robust color gradient estimator for photographic volume visualization. J Vis (Tokyo) 2018. [DOI: 10.1007/s12650-018-0477-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Wuttisarnwattana P, Gargesha M, Hof WV, Cooke KR, Wilson DL. Automatic Stem Cell Detection in Microscopic Whole Mouse Cryo-Imaging. IEEE TRANSACTIONS ON MEDICAL IMAGING 2016; 35:819-29. [PMID: 26552080 PMCID: PMC4873963 DOI: 10.1109/tmi.2015.2497285] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
With its single cell sensitivity over volumes as large as or larger than a mouse, cryo-imaging enables imaging of stem cell biodistribution, homing, engraftment, and molecular mechanisms. We developed and evaluated a highly automated software tool to detect fluorescently labeled stem cells within very large ( ∼ 200 GB) cryo-imaging datasets. Cell detection steps are: preprocess, remove immaterial regions, spatially filter to create features, identify candidate pixels, classify pixels using bagging decision trees, segment cell patches, and perform 3D labeling. There are options for analysis and visualization. To train the classifier, we created synthetic images by placing realistic digital cell models onto cryo-images of control mice devoid of cells. Very good cell detection results were (precision=98.49%, recall=99.97%) for synthetic cryo-images, (precision=97.81%, recall=97.71%) for manually evaluated, actual cryo-images, and false positives in control mice. An α-multiplier applied to features allows one to correct for experimental variations in cell brightness due to labeling. On dim cells (37% of standard brightness), with correction, we improved recall (49.26%→ 99.36%) without a significant drop in precision (99.99%→ 99.75%) . With tail vein injection, multipotent adult progenitor cells in a graft-versus-host-disease model in the first days post injection were predominantly found in lung, liver, spleen, and bone marrow. Distribution was not simply related to blood flow. The lung contained clusters of cells while other tissues contained single cells. Our methods provided stem cell distribution anywhere in mouse with single cell sensitivity. Methods should provide a rational means of evaluating dosing, delivery methods, cell enhancements, and mechanisms for therapeutic cells.
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Affiliation(s)
- Patiwet Wuttisarnwattana
- Department of Computer Engineering, Chiang Mai University, Chiang Mai, Thailand, and Biomedical Engineering Center, Chiang Mai University, Chiang Mai, Thailand
| | | | - Wouter van’t Hof
- Cell Processing Facility, Cleveland Cord Blood Center, Cleveland, OH, USA
| | - Kenneth R. Cooke
- Department of Pediatric Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - David L. Wilson
- D.L. Wilson is with Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, USA, Department of Radiology, University Hospitals of Cleveland, Cleveland, OH, USA and BioInVision, Inc., Mayfield Village, OH, USA
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Intuitive transfer function design for photographic volumes. J Vis (Tokyo) 2014. [DOI: 10.1007/s12650-014-0267-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Detection and quantification of fluorescent cell clusters in cryo-imaging. Int J Biomed Imaging 2012; 2012:698413. [PMID: 22481905 PMCID: PMC3317210 DOI: 10.1155/2012/698413] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 12/16/2011] [Indexed: 01/27/2023] Open
Abstract
We developed and evaluated an algorithm for enumerating fluorescently labeled cells (e.g., stem and cancer cells) in mouse-sized, microscopic-resolution, cryo-image volumes. Fluorescent cell clusters were detected, segmented, and then fit with a model which incorporated a priori information about cell size, shape, and intensity. The robust algorithm performed well in phantom and tissue imaging tests, including accurate (<2% error) counting of cells in mouse. Preliminary experiments demonstrate that cryo-imaging and software can uniquely analyze delivery, homing to an organ and tissue distribution of stem cell therapeutics.
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Powell KA, Wilson D. 3-dimensional imaging modalities for phenotyping genetically engineered mice. Vet Pathol 2011; 49:106-15. [PMID: 22146851 DOI: 10.1177/0300985811429814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A variety of 3-dimensional (3D) digital imaging modalities are available for whole-body assessment of genetically engineered mice: magnetic resonance microscopy (MRM), X-ray microcomputed tomography (microCT), optical projection tomography (OPT), episcopic and cryoimaging, and ultrasound biomicroscopy (UBM). Embryo and adult mouse phenotyping can be accomplished at microscopy or near microscopy spatial resolutions using these modalities. MRM and microCT are particularly well-suited for evaluating structural information at the organ level, whereas episcopic and OPT imaging provide structural and functional information from molecular fluorescence imaging at the cellular level. UBM can be used to monitor embryonic development longitudinally in utero. Specimens are not significantly altered during preparation, and structures can be viewed in their native orientations. Technologies for rapid automated data acquisition and high-throughput phenotyping have been developed and continually improve as this exciting field evolves.
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Affiliation(s)
- K A Powell
- Small Animal Imaging Shared Resource, The James Comprehensive Cancer Center Department of Biomedical Informatics, Ohio State University, Columbus, Ohio, USA.
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Konikoff CE, Karr TL, McCutchan M, Newfeld SJ, Kumar S. Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Dev Dyn 2011; 241:150-60. [PMID: 21960044 DOI: 10.1002/dvdy.22749] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Overlaps in spatial patterns of gene expression are frequently an initial clue to genetic interactions during embryonic development. However, manual inspection of images requires considerable time and resources impeding the discovery of important interactions because tens of thousands of images exist. The FlyExpress discovery platform was developed to facilitate data-driven comparative analysis of expression pattern images from Drosophila embryos. RESULTS An image-based search of the BDGP and Fly-FISH datasets conducted in FlyExpress yields fewer but more precise results than text-based searching when the specific goal is to find genes with overlapping expression patterns. We also provide an example of a FlyExpress contribution to scientific discovery: an analysis of gene expression patterns for multigene family members revealed that spatial divergence is far more frequent than temporal divergence, especially after the maternal to zygotic transition. This discovery provides a new clue to molecular mechanisms whereby duplicated genes acquire novel functions. CONCLUSIONS The application of FlyExpress to understanding the process by which new genes acquire novel functions is just one of a myriad of ways in which it can contribute to our understanding of developmental and evolutionary biology. This resource has many other potential applications, limited only by the investigator's imagination.
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Affiliation(s)
- Charlotte E Konikoff
- School of Life Sciences and Center for Evolutionary Medicine and Informatics in the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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Krishnamurthi G, Wang CY, Steyer G, Wilson DL. Removal of subsurface fluorescence in cryo-imaging using deconvolution. OPTICS EXPRESS 2010; 18:22324-38. [PMID: 20941133 PMCID: PMC3408948 DOI: 10.1364/oe.18.022324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We compared image restoration methods [Richardson-Lucy (RL), Wiener, and Next-image] with measured "scatter" point-spread-functions, for removing subsurface fluorescence from section-and-image cryo-image volumes. All methods removed haze, delineated single cells from clusters, and improved visualization, but RL best represented structures. Contrast-to-noise and contrast-to-background improvement from RL and Wiener were comparable and 35% better than Next-image. Concerning detection of labeled cells, ROC analyses showed RL ≈Wiener > Next-image >> no processing. Next-image was faster than other methods and less prone to image processing artifacts. RL is recommended for the best restoration of the shape and size of fluorescent structures.
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Affiliation(s)
- Ganapathy Krishnamurthi
- 10900 Euclid Avenue, Wickenden Bldg, School of Biomedical Engineering, Cleveland OH 44106,
USA
| | - Charlie Y. Wang
- 10900 Euclid Avenue, Wickenden Bldg, School of Biomedical Engineering, Cleveland OH 44106,
USA
- Department of Radiology, Case Western Reserve University and Case Medical Center, Cleveland OH 44106,
USA
| | - Grant Steyer
- 10900 Euclid Avenue, Wickenden Bldg, School of Biomedical Engineering, Cleveland OH 44106,
USA
| | - David L. Wilson
- 10900 Euclid Avenue, Wickenden Bldg, School of Biomedical Engineering, Cleveland OH 44106,
USA
- Department of Radiology, Case Western Reserve University and Case Medical Center, Cleveland OH 44106,
USA
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Roy D, Gargesha M, Steyer GJ, Hakimi P, Hanson RW, Wilson DL. Multi-scale characterization of the PEPCK-C mouse through 3D cryo-imaging. Int J Biomed Imaging 2010; 2010:105984. [PMID: 20467563 PMCID: PMC2868186 DOI: 10.1155/2010/105984] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 02/24/2010] [Indexed: 12/13/2022] Open
Abstract
We have developed, for the Case 3D Cryo-imaging system, a specialized, multiscale visualization scheme which provides color-rich volume rendering and multiplanar reformatting enabling one to visualize an entire mouse and zoom in to organ, tissue, and microscopic scales. With this system, we have anatomically characterized, in 3D, from whole animal to tissue level, a transgenic mouse and compared it with its control. The transgenic mouse overexpresses the cytosolic form of phosphoenolpyruvate carboxykinase (PEPCK-C) in its skeletal muscle and is capable of greatly enhanced physical endurance and has a longer life-span and reproductive life as compared to control animals. We semiautomatically analyzed selected organs such as kidney, heart, adrenal gland, spleen, and ovaries and found comparatively enlarged heart, much less visceral, subcutaneous, and pericardial adipose tissue, and higher tibia-to-femur ratio in the transgenic animal. Microscopically, individual skeletal muscle fibers, fine mesenteric blood vessels, and intestinal villi, among others, were clearly seen.
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Affiliation(s)
- Debashish Roy
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106, USA
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