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Schoppe O, Pan C, Coronel J, Mai H, Rong Z, Todorov MI, Müskes A, Navarro F, Li H, Ertürk A, Menze BH. Deep learning-enabled multi-organ segmentation in whole-body mouse scans. Nat Commun 2020; 11:5626. [PMID: 33159057 PMCID: PMC7648799 DOI: 10.1038/s41467-020-19449-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/12/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-body imaging of mice is a key source of information for research. Organ segmentation is a prerequisite for quantitative analysis but is a tedious and error-prone task if done manually. Here, we present a deep learning solution called AIMOS that automatically segments major organs (brain, lungs, heart, liver, kidneys, spleen, bladder, stomach, intestine) and the skeleton in less than a second, orders of magnitude faster than prior algorithms. AIMOS matches or exceeds the segmentation quality of state-of-the-art approaches and of human experts. We exemplify direct applicability for biomedical research for localizing cancer metastases. Furthermore, we show that expert annotations are subject to human error and bias. As a consequence, we show that at least two independently created annotations are needed to assess model performance. Importantly, AIMOS addresses the issue of human bias by identifying the regions where humans are most likely to disagree, and thereby localizes and quantifies this uncertainty for improved downstream analysis. In summary, AIMOS is a powerful open-source tool to increase scalability, reduce bias, and foster reproducibility in many areas of biomedical research.
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Affiliation(s)
- Oliver Schoppe
- Department of Informatics, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany.
| | - Chenchen Pan
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Javier Coronel
- Department of Informatics, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Hongcheng Mai
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Zhouyi Rong
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Mihail Ivilinov Todorov
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
- Graduate School of Systemic Neurosciences (GSN), Munich, Germany
| | - Annemarie Müskes
- Berlin-Brandenburg Center for Regenerative Therapies, Charité, Universitätsmedizin Berlin, Berlin, Germany
| | - Fernando Navarro
- Department of Informatics, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Hongwei Li
- Department of Informatics, Technical University of Munich, Munich, Germany
| | - Ali Ertürk
- Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Zentrum München, Neuherberg, Germany.
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany.
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Bjoern H Menze
- Department of Informatics, Technical University of Munich, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.
- Institute for Advanced Study, Department of Informatics, Technical University of Munich, Munich, Germany.
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
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Li Y, Ruan YY, Stanley EL, Skelton J, Hulcr J. Plasticity of mycangia in Xylosandrus ambrosia beetles. Insect Sci 2019; 26:732-742. [PMID: 29571219 DOI: 10.1111/1744-7917.12590] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 02/27/2018] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Insects that depend on microbial mutualists evolved a variety of organs to transport the microsymbionts while dispersing. The ontogeny and variability of such organs is rarely studied, and the microsymbiont's effects on the animal tissue development remain unknown in most cases. Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae or Platypodinae) and their mutualistic fungi are an ideal system to study the animal-fungus interactions. While the interspecific diversity of their fungus transport organ-mycangia-is well-known, their developmental plasticity has been poorly described. To determine the ontogeny of the mycangium and the influence of the symbiotic fungus on the tissue development, we dissected by hand or scanned with micro-CT the mycangia in various developmental stages in five Xylosandrus ambrosia beetle species that possess a large, mesonotal mycangium: Xylosandrus amputatus, Xylosandrus compactus, Xylosandrus crassiusculus, Xylosandrus discolor, and Xylosandrus germanus. We processed 181 beetle samples from the United States and China. All five species displayed three stages of the mycangium development: (1) young teneral adults had an empty, deflated and cryptic mycangium without fungal mass; (2) in fully mature adults during dispersal, the pro-mesonotal membrane was inflated, and most individuals developed a mycangium mostly filled with the symbiont, though size and symmetry varied; and (3) after successful establishment of their new galleries, most females discharged the bulk of the fungal inoculum and deflated the mycangium. Experimental aposymbiotic individuals demonstrated that the pronotal membrane invaginated independently of the presence of the fungus, but the fungus was required for inflation. Mycangia are more dynamic than previously thought, and their morphological changes correspond to the phases of the symbiosis. Importantly, studies of the fungal symbionts or plant pathogen transmission in ambrosia beetles need to consider which developmental stage to sample. We provide illustrations of the different stages, including microphotography of dissections and micro-CT scans.
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Affiliation(s)
- You Li
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, USA
| | - Yong-Ying Ruan
- School of Applied Chemistry and Biological Technology, Postdoctoral Innovation Practice Base, Shenzhen Polytechnic, Shenzhen, Guangdong, China
| | - Edward L Stanley
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - James Skelton
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, USA
| | - Jiri Hulcr
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, USA
- Entomology and Nematology Department, University of Florida, Gainesville, Florida, USA
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Akselrod-Ballin A, Dafni H, Addadi Y, Biton I, Avni R, Brenner Y, Neeman M. Multimodal Correlative Preclinical Whole Body Imaging and Segmentation. Sci Rep 2016; 6:27940. [PMID: 27325178 PMCID: PMC4914843 DOI: 10.1038/srep27940] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/27/2016] [Indexed: 01/10/2023] Open
Abstract
Segmentation of anatomical structures and particularly abdominal organs is a fundamental problem for quantitative image analysis in preclinical research. This paper presents a novel approach for whole body segmentation of small animals in a multimodal setting of MR, CT and optical imaging. The algorithm integrates multiple imaging sequences into a machine learning framework, which generates supervoxels by an efficient hierarchical agglomerative strategy and utilizes multiple SVM-kNN classifiers each constrained by a heatmap prior region to compose the segmentation. We demonstrate results showing segmentation of mice images into several structures including the heart, lungs, liver, kidneys, stomach, vena cava, bladder, tumor, and skeleton structures. Experimental validation on a large set of mice and organs, indicated that our system outperforms alternative state of the art approaches. The system proposed can be generalized to various tissues and imaging modalities to produce automatic atlas-free segmentation, thereby enabling a wide range of applications in preclinical studies of small animal imaging.
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Affiliation(s)
| | - Hagit Dafni
- Department of Veterinary Resources Weizmann Institute, Rehovot 76100 Israel
| | - Yoseph Addadi
- Department of Biological Services Weizmann Institute, Rehovot 76100 Israel
| | - Inbal Biton
- Department of Veterinary Resources Weizmann Institute, Rehovot 76100 Israel
| | - Reut Avni
- Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel
| | - Yafit Brenner
- Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel
| | - Michal Neeman
- Department of Biological Regulation Weizmann Institute, Rehovot 76100 Israel
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Jung JY, Naleway SE, Yaraghi NA, Herrera S, Sherman VR, Bushong EA, Ellisman MH, Kisailus D, McKittrick J. Structural analysis of the tongue and hyoid apparatus in a woodpecker. Acta Biomater 2016; 37:1-13. [PMID: 27000554 PMCID: PMC5063634 DOI: 10.1016/j.actbio.2016.03.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/21/2016] [Accepted: 03/17/2016] [Indexed: 11/21/2022]
Abstract
UNLABELLED Woodpeckers avoid brain injury while they peck at trees up to 20Hz with speeds up to 7m/s, undergoing decelerations up to 1200g. Along with the head, beak and neck, the hyoid apparatus (tongue bone and associated soft tissues) is subjected to these high impact forces. The shape of the hyoid apparatus is unusual in woodpeckers and its structure and mechanical properties have not been reported in detail. High-resolution X-ray micro-computed tomography and scanning electron microscopy with energy dispersive X-ray spectroscopy were performed and correlated with nanoindentation mapping. The hyoid apparatus has four distinct bone sections, with three joints between these sections. Nanoindentation results on cross-sectional regions of each bone reveal a previously unreported structure consisting of a stiff core and outer, more compliant shell with moduli of up to 27.4GPa and 8.5GPa, respectively. The bending resistance is low at the posterior section of the hyoid bones, indicating that this region has a high degree of flexibility to absorb impact. These new structural findings can be applied to further studies on the energy dissipation of the woodpecker during its drumming behavior, and may have implications for the design of engineered impact-absorbing structures. STATEMENT OF SIGNIFICANCE Woodpeckers avoid brain injury while they peck at trees, which results in extreme impact conditions. One common adaptation in woodpeckers is the unusual shape of the elongated tongue, also called the hyoid apparatus. The relationship between the structure and mechanical properties of the bony part of the hyoid apparatus has not been previously reported. A three dimensional model of the bony tongue was developed, and the hardness and stiffness were evaluated. A new type of bone structure, which is opposite of typical skeletal bone structure was found. The combined microstructural and mechanical property analysis indicate possible energy absorption routes for the hyoid apparatus and are applicable to the design of engineered structures.
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Affiliation(s)
- Jae-Young Jung
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Steven E Naleway
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nicholas A Yaraghi
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Steven Herrera
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Vincent R Sherman
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research and Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Kisailus
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA 92521, USA
| | - Joanna McKittrick
- Materials Science and Engineering Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093, USA
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Song Z, Xu X, Dong J, Xing L, Zhang M, Liu X, Zhang Y, Li S, Berggren P. Acoustic property reconstruction of a pygmy sperm whale (Kogia breviceps) forehead based on computed tomography imaging. J Acoust Soc Am 2015; 138:3129-3137. [PMID: 26627786 DOI: 10.1121/1.4935135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Computed tomography (CT) imaging and sound experimental measurements were used to reconstruct the acoustic properties (density, velocity, and impedance) of the forehead tissues of a deceased pygmy sperm whale (Kogia breviceps). The forehead was segmented along the body axis and sectioned into cross section slices, which were further cut into sample pieces for measurements. Hounsfield units (HUs) of the corresponding measured pieces were obtained from CT scans, and regression analyses were conducted to investigate the linear relationships between the tissues' HUs and velocity, and HUs and density. The distributions of the acoustic properties of the head at axial, coronal, and sagittal cross sections were reconstructed, revealing that the nasal passage system was asymmetric and the cornucopia-shaped spermaceti organ was in the right nasal passage, surrounded by tissues and airsacs. A distinct dense theca was discovered in the posterior-dorsal area of the melon, which was characterized by low velocity in the inner core and high velocity in the outer region. Statistical analyses revealed significant differences in density, velocity, and acoustic impedance between all four structures, melon, spermaceti organ, muscle, and connective tissue (p < 0.001). The obtained acoustic properties of the forehead tissues provide important information for understanding the species' bioacoustic characteristics.
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Affiliation(s)
- Zhongchang Song
- Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, People's Republic of China
| | - Xiao Xu
- Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics, Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, People's Republic of China
| | - Jianchen Dong
- Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics, Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, People's Republic of China
| | - Luru Xing
- Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics, Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, People's Republic of China
| | - Meng Zhang
- Radiology Department, People's Hospital of Sanya, Sanya 572000, People's Republic of China
| | - Xuecheng Liu
- College of Ocean and Earth Sciences, Xiamen University, Xiping Building, Xiangan South Road, Xiangan District, Xiamen 361005, People's Republic of China
| | - Yu Zhang
- Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen 361005, People's Republic of China
| | - Songhai Li
- Sanya Key Laboratory of Marine Mammal and Marine Bioacoustics, Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, People's Republic of China
| | - Per Berggren
- Dove Marine Laboratory, School of Marine Science and Technology, Newcastle University, Cullercoats, North Shields NE30 4PZ, United Kingdom
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Allison PG, Chandler MQ, Rodriguez RI, Williams BA, Moser RD, Weiss CA, Poda AR, Lafferty BJ, Kennedy AJ, Seiter JM, Hodo WD, Cook RF. Mechanical properties and structure of the biological multilayered material system, Atractosteus spatula scales. Acta Biomater 2013; 9:5289-96. [PMID: 23149253 DOI: 10.1016/j.actbio.2012.11.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 10/22/2012] [Accepted: 11/02/2012] [Indexed: 11/29/2022]
Abstract
During recent decades, research on biological systems such as abalone shell and fish armor has revealed that these biological systems employ carefully arranged hierarchical multilayered structures to achieve properties of high strength, high ductility and light weight. Knowledge of such structures may enable pathways to design bio-inspired materials for various applications. This study was conducted to investigate the spatial distribution of structure, chemical composition and mechanical properties in mineralized fish scales of the species Atractosteus spatula. Microindentation tests were conducted, and cracking patterns and damage sites in the scales were examined to investigate the underlying protective mechanisms of fish scales under impact and penetration loads. A difference in nanomechanical properties was observed, with a thinner, stiffer and harder outer layer (indentation modulus ∼69 GPa and hardness ∼3.3 GPa) on a more compliant and thicker inner layer (indentation modulus ∼14.3 GPa and hardness ∼0.5 GPa). High-resolution scanning electron microscopy imaging of a fracture surface revealed that the outer layer contained oriented nanorods embedded in a matrix, and that the nanostructure of the inner layer contained fiber-like structures organized in a complex layered pattern. Damage patterns formed during microindentation show complex deformation mechanisms. Images of cracks identify growth through the outer layer, then deflection along the interface before growing and arresting in the inner layer. High-magnification images of the crack tip in the inner layer show void-linking and fiber-bridging exhibiting inelastic behavior. The observed difference in mechanical properties and unique nanostructures of different layers may have contributed to the resistance of fish scales to failure by impact and penetration loading.
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Affiliation(s)
- P G Allison
- Geotechnical and Structures Laboratory, US Army Engineer Research and Development Center, 3909 Halls Ferry Rd., Vicksburg, MS 39180, USA.
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Abstract
The endoskeletal structure of the Sea Urchin, Centrostephanus rodgersii, has numerous long spines whose known functions include locomotion, sensing, and protection against predators. These spines have a remarkable internal microstructure and are made of single-crystal calcite. A finite-element model of the spine’s unique porous structure, based on micro-computed tomography (microCT) and incorporating anisotropic material properties, was developed to study its response to mechanical loading. Simulations show that high stress concentrations occur at certain points in the spine’s architecture; brittle cracking would likely initiate in these regions. These analyses demonstrate that the organization of single-crystal calcite in the unique, intricate morphology of the sea urchin spine results in a strong, stiff and lightweight structure that enhances its strength despite the brittleness of its constituent material.
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Affiliation(s)
- Naomi Tsafnat
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Sydney, New South Wales, Australia.
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Abstract
Thirty red-eared slider terrapins (Trachemys scripta elegans) were examined by ultrasound to establish the normal ultrasonographic appearance of their coelomic structures. They were not sedated, and owing to their small size they were examined through the inguinal window of the carapace. High resolution transducers (7.5 and 11 MHz) enhanced the ultrasonographic imaging of the bowel, urinary bladder, liver, gall bladder, heart, kidney and gonads, but the pancreas, adrenal glands, thyroid glands and spleen could not be visualised.
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Affiliation(s)
- J Martorell
- Department of Animal Medicine and Surgery, Autonomous University of Barcelona, 08193 Bellaterra, Barcelona, Spain
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Abstract
The deposition of four crystal types at the growth surface of the septa of several color morphs of the coral Galaxea fascicularis was investigated over a 24-h period. Results suggest that nanocrystals, on denticles at the apices of exsert septa, may be the surface manifestation of centers of calcification. These crystals were also found on the septa of the axial corallite of Acropora formosa. The deposition of nanocrystals appears to be independent of diurnal rhythms. Internally and proximal to the septal apices, distinct clusters of polycrystalline fibers originate from centers of calcification and form fanlike fascicles. Upon these fascicles, acicular crystals grow and extend to form the visible fasciculi at the skeletal surface. Deposition of aragonitic fusiform crystals in both G. fascicularis and A. formosa occurs without diurnal rhythm. Nucleation of fusiform crystals appears to be independent of centers of calcification and may occur by secondary nucleation. Formation of semi-solid masses by fusiform crystals suggests that the crystals may play a structural role in septal extension. Lamellar crystals, which have not been reported as a component of scleractinian coral skeletons before, possess distinct layers of polyhedral plates, although these layers also do not appear to be associated with daily growth increments. The relationship of lamellar crystals to other components of the scleractinian coral skeleton and their involvement in skeletal growth is unknown.
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Affiliation(s)
- Peta L Clode
- Department of Zoology, La Trobe University, Melbourne, Victoria 3086, Australia
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