PMC:7473770 / 7100-9191 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T37","span":{"begin":322,"end":328},"obj":"Body_part"},{"id":"T38","span":{"begin":1010,"end":1015},"obj":"Body_part"},{"id":"T39","span":{"begin":1029,"end":1035},"obj":"Body_part"},{"id":"T40","span":{"begin":1828,"end":1834},"obj":"Body_part"}],"attributes":[{"id":"A37","pred":"fma_id","subj":"T37","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma9637"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma9637"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T30","span":{"begin":110,"end":115},"obj":"Body_part"},{"id":"T31","span":{"begin":322,"end":328},"obj":"Body_part"},{"id":"T32","span":{"begin":442,"end":447},"obj":"Body_part"},{"id":"T33","span":{"begin":1029,"end":1035},"obj":"Body_part"},{"id":"T34","span":{"begin":1828,"end":1834},"obj":"Body_part"}],"attributes":[{"id":"A30","pred":"uberon_id","subj":"T30","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"},{"id":"A31","pred":"uberon_id","subj":"T31","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A32","pred":"uberon_id","subj":"T32","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"},{"id":"A33","pred":"uberon_id","subj":"T33","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"},{"id":"A34","pred":"uberon_id","subj":"T34","obj":"http://purl.obolibrary.org/obo/UBERON_0000479"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T58","span":{"begin":96,"end":97},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T59","span":{"begin":189,"end":204},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T60","span":{"begin":312,"end":313},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T61","span":{"begin":394,"end":395},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T62","span":{"begin":554,"end":569},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T63","span":{"begin":717,"end":720},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T64","span":{"begin":822,"end":823},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":830,"end":835},"obj":"http://purl.obolibrary.org/obo/UBERON_0007688"},{"id":"T66","span":{"begin":856,"end":857},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T67","span":{"begin":897,"end":898},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T68","span":{"begin":1010,"end":1015},"obj":"http://purl.obolibrary.org/obo/GO_0005623"},{"id":"T69","span":{"begin":1552,"end":1561},"obj":"http://www.ebi.ac.uk/efo/EFO_0000876"},{"id":"T70","span":{"begin":1684,"end":1695},"obj":"http://purl.obolibrary.org/obo/OBI_0000968"},{"id":"T71","span":{"begin":1882,"end":1886},"obj":"http://purl.obolibrary.org/obo/CLO_0001185"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T35","span":{"begin":0,"end":205},"obj":"Sentence"},{"id":"T36","span":{"begin":206,"end":441},"obj":"Sentence"},{"id":"T37","span":{"begin":442,"end":660},"obj":"Sentence"},{"id":"T38","span":{"begin":661,"end":879},"obj":"Sentence"},{"id":"T39","span":{"begin":880,"end":1232},"obj":"Sentence"},{"id":"T40","span":{"begin":1233,"end":1340},"obj":"Sentence"},{"id":"T41","span":{"begin":1341,"end":1422},"obj":"Sentence"},{"id":"T42","span":{"begin":1423,"end":1696},"obj":"Sentence"},{"id":"T43","span":{"begin":1697,"end":1888},"obj":"Sentence"},{"id":"T44","span":{"begin":1889,"end":2091},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}

{"project":"2_test","denotations":[{"id":"32815517-26134789-26997857","span":{"begin":654,"end":658},"obj":"26134789"},{"id":"32815517-29328301-26997858","span":{"begin":1882,"end":1886},"obj":"29328301"},{"id":"32815517-32381790-26997859","span":{"begin":2085,"end":2089},"obj":"32381790"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}

{"project":"MyTest","denotations":[{"id":"32815517-26134789-26997857","span":{"begin":654,"end":658},"obj":"26134789"},{"id":"32815517-29328301-26997858","span":{"begin":1882,"end":1886},"obj":"29328301"},{"id":"32815517-32381790-26997859","span":{"begin":2085,"end":2089},"obj":"32381790"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"116","span":{"begin":277,"end":285},"obj":"Chemical"},{"id":"117","span":{"begin":43,"end":51},"obj":"Disease"}],"attributes":[{"id":"A116","pred":"tao:has_database_id","subj":"116","obj":"MESH:D010232"},{"id":"A117","pred":"tao:has_database_id","subj":"117","obj":"MESH:C000657245"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"The 3D virtual pathohistology approach for Covid-19 presented here was realized by implementing a novel multi-scale phase contrast x-ray tomography concept, with dedicated x-ray optics and instrumentation. Overview and regions-of-interest (ROI) scans were recorded on the same paraffin-embedded sample, covering a maximum tissue cross section of 8 mm by stitching different tomograms, and with a minimum voxel size of 167 nm in certain ROIs. Scale-bridging and dynamic ROI selection in close spatial and temporal proximity was implemented with dedicated instrumentation the GINIX endstation of the beamline P10/PETRA III (DESY, Hamburg) (Salditt et al., 2015). Specifically, we combined two optical geometries, which has only been realized at different synchrotron beamlines before: (i) Parallel beam tomography, covering a large field of view (FOV), with a pixel size of 650 nm. In this setting, a volumetric throughput on the order of 107μm/3s was achieved, while maintaining the ability to segment isolated cells in unstained tissue. (ii) Cone beam geometry for recording of highly magnified holograms, based on advanced x-ray waveguide optics, providing mode filtering, that is, enhanced spatial coherence and smooth wavefronts. Based on the geometrical magnification, the effective pixel size can be adjusted in the range 10 nm–300 nm. The two imaging schemes are shown schematically in Figure 1c and d, respectively. Further, using this particular optics, together with appropriate choices of photon energy and geometric parameters, we can reach extremely small Fresnel numbers F of the deeply holographic regime, well below the typical range exploited at other nano-tomography instruments. This offers the advantage of highest phase sensitivity sufficient to even probe the small electron density variations of unstained tissue, at relatively low dose (Hagemann and Salditt, 2018). To exploit this sensitivity, we use advanced phase retrieval methods including non-linear generalizations of the CTF-method (Cloetens et al., 1999) based on Tikhonov regularization (Lohse et al., 2020)."}