pmann
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pmann [2022/03/30 12:02] antreas |
pmann [2023/01/16 17:22] (current) angelos [The Pathomation ANNotation interface] |
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| * Indica Labs .annotations | * Indica Labs .annotations | ||
| * Aperio .xml | * Aperio .xml | ||
| + | * Images (TIFF, PNG or even other whole slide images) | ||
| To associate external files with a slide you have to use the API call [[https://docs.pathomation.com/pma.core.api/#/Api/Slide_SetExternalAnnotationFiles|SetExternalAnnotationFiles]]. This takes an array of tuples containing the //Name// and //Path// for each associated 3rd party annotations file. For //Name// you can use any text to differentiate from other annotations an the //Path// needs to be a //virtual path// to the file containing the annotations. | To associate external files with a slide you have to use the API call [[https://docs.pathomation.com/pma.core.api/#/Api/Slide_SetExternalAnnotationFiles|SetExternalAnnotationFiles]]. This takes an array of tuples containing the //Name// and //Path// for each associated 3rd party annotations file. For //Name// you can use any text to differentiate from other annotations an the //Path// needs to be a //virtual path// to the file containing the annotations. | ||
| You can get the previously set external annotations files for a slide via the [[https://docs.pathomation.com/pma.core.api/#/Api/Slide_GetExternalAnnotationFiles|GetExternalAnnotationFiles]] API call, which returns the array of //Name/Path// tuples for each file associated with any slide | You can get the previously set external annotations files for a slide via the [[https://docs.pathomation.com/pma.core.api/#/Api/Slide_GetExternalAnnotationFiles|GetExternalAnnotationFiles]] API call, which returns the array of //Name/Path// tuples for each file associated with any slide | ||
| + | |||
| + | **Notes for image overlays:** | ||
| + | |||
| + | * Image overlays should have transparency otherwise they will completely hide the whole slide image. Image formats that support alpha channel are PNG and certain TIFF configurations. | ||
| + | * When using an image as an annotation layer, PMA.core assumes that the aspect ratio of the overlay and the whole slide image are exactly the same. | ||
| ==== Example ==== | ==== Example ==== | ||
| + | |||
| Lets suppose we have a slide called //Slide.mrxs// that we want to attach 2 separate annotation files from 3rd party sources, and the two files are in the virtual directory called //Slides// | Lets suppose we have a slide called //Slide.mrxs// that we want to attach 2 separate annotation files from 3rd party sources, and the two files are in the virtual directory called //Slides// | ||
| * Slide1.mld | * Slide1.mld | ||
| * Slide1.xml | * Slide1.xml | ||
| + | |||
| The first file contains some cell counting information and the second file contains some regions of interest so we want to name them based on that to distinguish more easily, and keep in mind that the name of a external file is presented to the user on all viewer products of the Pathomation platform. | The first file contains some cell counting information and the second file contains some regions of interest so we want to name them based on that to distinguish more easily, and keep in mind that the name of a external file is presented to the user on all viewer products of the Pathomation platform. | ||
| So we call the [[https://docs.pathomation.com/pma.core.api/#/Api/Slide_SetExternalAnnotationFiles|SetExternalAnnotationFiles]] API with query string parameters | So we call the [[https://docs.pathomation.com/pma.core.api/#/Api/Slide_SetExternalAnnotationFiles|SetExternalAnnotationFiles]] API with query string parameters | ||
| - | ?pathOrUid=Slides/Slide1.mrxs&sessionId={sessionId} | + | ''?pathOrUid=Slides/Slide1.mrxs&sessionId={sessionId}'' |
| and with the following json data on the body | and with the following json data on the body | ||
| [ | [ | ||
pmann.1648630976.txt.gz ยท Last modified: 2022/03/30 12:02 by antreas
