PMC:7473770 / 11754-13079 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7473770","sourcedb":"PMC","sourceid":"7473770","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7473770","text":"Next, we present representative slices through the reconstruction volumes of all samples for all acquisition scales. Figure 3 presents the stitched reconstruction volumes, recorded under conditions of local tomography, see Table 3. Conventional HE-stained histology images of all samples are shown in Appendix 1—figure 1. Since these volumes are computed from stitching up to 20 individual tomograms, the question arises to which extend the image quality is limited by potential artifacts of local tomography, that is, errors due to the fact that part of the sample is outside the reconstruction volume. For this reason, 1 mm punches were taken after the stitched overview and rescanned in the parallel beam configuration, without local tomography conditions, since they fitted within the FOV. The results are presented in Figure 4, and validate the previous stitching results. The 1 mm punches then also provided an appropriate size for the cone-beam recordings, which are shown in Figure 5. Importantly, in each scan the previous level guided the choice for the next FOV and informed about the larger environment. In the following, we briefly discuss the samples one-by-one, with regard to all acquisition scales. A comparison of morphological features between conventional and virtual histology is shown in the Appendix 1.","tracks":[{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T48","span":{"begin":301,"end":309},"obj":"Body_part"},{"id":"T49","span":{"begin":1314,"end":1322},"obj":"Body_part"}],"attributes":[{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma14542"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma14542"},{"subj":"T48","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T49","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T43","span":{"begin":109,"end":115},"obj":"Body_part"},{"id":"T44","span":{"begin":1208,"end":1214},"obj":"Body_part"},{"id":"T45","span":{"begin":1232,"end":1254},"obj":"Body_part"}],"attributes":[{"id":"A43","pred":"uberon_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"},{"id":"A44","pred":"uberon_id","subj":"T44","obj":"http://purl.obolibrary.org/obo/UBERON_0002542"},{"id":"A45","pred":"uberon_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/UBERON_0034768"},{"subj":"T43","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T44","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T45","pred":"source","obj":"LitCovid-PD-UBERON"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T94","span":{"begin":1216,"end":1217},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T94","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T65","span":{"begin":0,"end":116},"obj":"Sentence"},{"id":"T66","span":{"begin":117,"end":231},"obj":"Sentence"},{"id":"T67","span":{"begin":232,"end":603},"obj":"Sentence"},{"id":"T68","span":{"begin":604,"end":793},"obj":"Sentence"},{"id":"T69","span":{"begin":794,"end":877},"obj":"Sentence"},{"id":"T70","span":{"begin":878,"end":992},"obj":"Sentence"},{"id":"T71","span":{"begin":993,"end":1115},"obj":"Sentence"},{"id":"T72","span":{"begin":1116,"end":1215},"obj":"Sentence"},{"id":"T73","span":{"begin":1216,"end":1325},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T65","pred":"source","obj":"LitCovid-sentences"},{"subj":"T66","pred":"source","obj":"LitCovid-sentences"},{"subj":"T67","pred":"source","obj":"LitCovid-sentences"},{"subj":"T68","pred":"source","obj":"LitCovid-sentences"},{"subj":"T69","pred":"source","obj":"LitCovid-sentences"},{"subj":"T70","pred":"source","obj":"LitCovid-sentences"},{"subj":"T71","pred":"source","obj":"LitCovid-sentences"},{"subj":"T72","pred":"source","obj":"LitCovid-sentences"},{"subj":"T73","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"147","span":{"begin":245,"end":247},"obj":"Chemical"}],"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_"}],"attributes":[{"subj":"147","pred":"source","obj":"LitCovid-PubTator"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-FMA-UBERON","color":"#93ecbf","default":true},{"id":"LitCovid-PD-UBERON","color":"#eca593"},{"id":"LitCovid-PD-CLO","color":"#939aec"},{"id":"LitCovid-sentences","color":"#b5ec93"},{"id":"LitCovid-PubTator","color":"#ec93cf"}]}]}}