working_with_annotations
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working_with_annotations [2022/03/25 18:42] yves |
working_with_annotations [2022/09/10 14:48] (current) yves |
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| ===== Working with annotations ===== | ===== Working with annotations ===== | ||
| - | |||
| - | ==== Annotation types ==== | ||
| PMA.core supports three types of annotations PMA.core annotations, native annotations, and 3rd party annotations. | PMA.core supports three types of annotations PMA.core annotations, native annotations, and 3rd party annotations. | ||
| ^ Annotation type ^ Origin ^ Format ^ Read/Write ^ | ^ Annotation type ^ Origin ^ Format ^ Read/Write ^ | ||
| - | | Pathomation | PMA.studio; SDK | WKT | Read/write | | + | | Pathomation | PMA.studio; SDK | [[https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry|WKT]] | Read/write | |
| - | | Native | Vendor-specific viewer; Pannotamic viewer; ImageScope | Embedded in the vendor file format | Read-only | | + | | Native | Vendor-specific viewer; Pannoramic viewer; ImageScope | Embedded in the vendor file format | Read-only | |
| | Third-party | Indica Labs HALO; Definiens; Visiopharm | .Annotation XML; .XML; .MLD (binary) | Read-only | | | Third-party | Indica Labs HALO; Definiens; Visiopharm | .Annotation XML; .XML; .MLD (binary) | Read-only | | ||
| + | ==== Internal storage ==== | ||
| PMA.core uses its own internal format with the following structure: | PMA.core uses its own internal format with the following structure: | ||
| - | * Geometry: based on WKT(Well-known text). Supports the following shapes //Polygon, Linestring, Point and Multipoint// | + | * Geometry: based on WKT ([[https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry|Well-known text]]). Supports the following shapes //Polygon, Linestring, Point and Multipoint// |
| - | * Color: the outline color in html format | + | * Color: the outline color in [[https://www.w3schools.com/html/html_colors.asp|html format]] |
| * Fill Color: the fill color(if any), only valid for closed shapes like polygon | * Fill Color: the fill color(if any), only valid for closed shapes like polygon | ||
| * Classification: A text specifying the classification of an annotation like tumor, necrosis etc. | * Classification: A text specifying the classification of an annotation like tumor, necrosis etc. | ||
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| * Indica Labs //.annotations// | * Indica Labs //.annotations// | ||
| * Aperio //.xml// | * Aperio //.xml// | ||
| + | |||
| + | |||
| ==== Creating and saving ==== | ==== Creating and saving ==== | ||
| - | == PMA.core annotations == | + | |
| + | === PMA.core annotations === | ||
| For reading the PMA.core annotations for a slide you can use the API call [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.GetAnnotations|GetAnnotations]], that returns all PMA.core annotation in json format. | For reading the PMA.core annotations for a slide you can use the API call [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.GetAnnotations|GetAnnotations]], that returns all PMA.core annotation in json format. | ||
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| All other PMA.core annotations functionality is provided via the [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.SaveAnnotations|SaveAnnotations]] API call. This call can create new, update and delete many annotations in one API call. PMA.core also provides the functionality to get the length and/or the surface area for already saved annotations via the [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.GetAnnotationDistance|GetAnnotationDistance]] and [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.GetAnnotationSurfaceArea|GetAnnotationSurfaceArea]] API calls. | All other PMA.core annotations functionality is provided via the [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.SaveAnnotations|SaveAnnotations]] API call. This call can create new, update and delete many annotations in one API call. PMA.core also provides the functionality to get the length and/or the surface area for already saved annotations via the [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.GetAnnotationDistance|GetAnnotationDistance]] and [[https://docs.pathomation.com/pma.core.api/#/Api/PMA.Services.Api.HistoScope.GetAnnotationSurfaceArea|GetAnnotationSurfaceArea]] API calls. | ||
| - | == 3rd Party annotations == | + | === 3rd Party annotations === |
| PMA.core can leverage the use of 3rd party annotations via the External Files interface and the associated API calls. | PMA.core can leverage the use of 3rd party annotations via the External Files interface and the associated API calls. | ||
working_with_annotations.1648222971.txt.gz · Last modified: 2022/03/25 18:42 by yves
