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pmann [2023/01/16 17:19] angelos [The Pathomation ANNotation interface] |
pmann [2023/01/16 17:22] angelos [The Pathomation ANNotation interface] |
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* Indica Labs .annotations | * Indica Labs .annotations | ||
* Aperio .xml | * Aperio .xml | ||
- | * Images (TIFF, PNG or even whole slide images) | + | * 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 | ||
- | **Note for image overlays** | + | **Notes for image overlays:** |
- | 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. | + | |
+ | * 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 ==== |