{"id":["SWHID:swh:1:dir:3f0e4eed83a1fc303963218b5dc3d407c7ec8f7e"],"title":["TissueTag: Jupyter Image Annotator"],"description":["TissueTag consists of two major components:\n1) Jupyter-based image annotation tool:Utilising the Bokeh Python library (http://www.bokeh.pydata.org) empowered by Datashader (https://datashader.org/index.html) and holoviews (https://holoviews.org/index.html) for pyramidal image rendering.\nThis tool offers a streamlined annotation solution with subpixel resolution for quick interactive annotation of various image types (e.g., brightfield, fluorescence). TissueTag produces labelled images (e.g., cortex, medulla) and logs all tissue labels,\nand annotation resolution and colours for reproducibility.\n\n2) Mapping annotations to data: This component facilitates the migration of annotations to spots/cells based on overlap with annotated structures.\nIt also logs the minimum Euclidean distance of each spot/cell to the discrete annotations,\noffering continuous annotation. This contains spatial neighbourhood information,\nadding to the x-y coordinates of a given spot or cell,\nand is foundational for calculating a morphological axis (OrganAxis, see tutorials).\n\nNote: A labeled image is an integer array where each pixel value (0,1,2,…) corresponds to an annotated structure.\n\nAnnotator: Enables interactive annotation of predefined anatomical objects via convex shape filling while toggeling between reference and annotation image.\n\nWe envision this tool as a foundational starting point as its simplicity and transparent nature allows for many potential enhancements, additions and spinoffs.\nSo contributions and suggestions are highly appreciated!\n\nCurated online tutorial for OrganAxis (https://organ-axis-tutorial.readthedocs.io)."],"authors":{"ORCID:0000-0002-7034-0524":{"id":["ORCID:0000-0002-7034-0524"],"family_name":["Yayon"],"personal_name":["Nadav"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]},"ROR:02catss52":{"organization_name":["European Bioinformatics Institute"]}}},"ORCID:0000-0002-8070-0378":{"id":["ORCID:0000-0002-8070-0378"],"family_name":["Amsalem"],"personal_name":["Oren"],"affiliations":{"ROR:04drvxt59":{"organization_name":["Beth Israel Deaconess Medical Center"]}}},"ORCID:0000-0002-8327-8096":{"id":["ORCID:0000-0002-8327-8096"],"family_name":["Yang"],"personal_name":["Andrian"],"affiliations":{"ROR:05nz0zp31":{"organization_name":["Wellcome/MRC Cambridge Stem Cell Institute"]},"ROR:02catss52":{"organization_name":["European Bioinformatics Institute"]}}},"ORCID:0000-0002-2586-9576":{"id":["ORCID:0000-0002-2586-9576"],"family_name":["Polański"],"personal_name":["Krzysztof"],"affiliations":{"ROR:05cy4wa09":{"organization_name":["Wellcome Sanger Institute"]}}}}}