working_with_annotations
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working_with_annotations [2022/03/08 16:03] antreas [Exporting and format conversion] |
working_with_annotations [2022/03/25 18:47] (current) yves [Working with annotations] |
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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 two main types of annotations **PMA.core annotations** and **3rd party annotations** and also some native annotations for the //3dHistech MRXS// and //Hamamatsu NDPI// formats. | + | ^ Annotation type ^ Origin ^ Format ^ Read/Write ^ |
| + | | Pathomation | PMA.studio; SDK | WKT | Read/write | | ||
| + | | 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 | | ||
| - | PMA.core uses it's own internal format with the following structure: | + | ==== Internal storage ==== |
| - | * Geometry: based on WKT(Well-known text). Supports the following shapes //Polygon, Linestring, Point and Multipoint// | + | PMA.core uses its own internal format with the following structure: |
| - | * Color: the outline color in html format | + | * 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 [[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// | ||
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| ==== 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. | ||
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| (//PMA.core annotations, Native annotations , Visiopharm , Indica Labs , Aperio//) to each of the 3rd party formats(Visiopharm Indica Labs Aperio). This call also supports two more very useful formats for use outside of PMA.core i.e. the CSV and WKT(Well-Known text) formats. PMA.core will try to convert each format as flawlessly as possible but some shapes are not compatible to shapes in other formats. If the source and destination formats are the same PMA.core will not perform any conversion, it will output the original file. | (//PMA.core annotations, Native annotations , Visiopharm , Indica Labs , Aperio//) to each of the 3rd party formats(Visiopharm Indica Labs Aperio). This call also supports two more very useful formats for use outside of PMA.core i.e. the CSV and WKT(Well-Known text) formats. PMA.core will try to convert each format as flawlessly as possible but some shapes are not compatible to shapes in other formats. If the source and destination formats are the same PMA.core will not perform any conversion, it will output the original file. | ||
| + | ==== More background ==== | ||
| + | |||
| + | Did you know that PMA.core is actually a great tool to integrate different annotations originating for different sources? For more background, have a look at the [[pmann|Pathomation ANNotation subset of functionality]] in the API. | ||
| + | We have [[https://realdata.pathomation.com/annotations-et-al/|a blog article on annotations and how to handle them]], not just within PMA.core, but throughout [[https://www.pathomation.com/platform|the entire Pathomation software platform]]. | ||
working_with_annotations.1646744610.txt.gz · Last modified: 2022/03/08 16:03 by antreas
