pmann
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pmann [2022/10/13 10:44] yves |
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 | ||
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| + | **Notes for image overlays:** | ||
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| + | * 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 ==== | ||
pmann.1665647068.txt.gz ยท Last modified: 2022/10/13 10:44 by yves
