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importing_annotations_to_training_sessions [2024/07/17 16:16] (current)
chris created
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 +===== Importing Annotations to Training Sessions =====
 +
 +Annotations are a valuable source of information for whole slide images.\\
 +Not only can human-made annotations draw Users attention to specific parts of an image without needing someone to directly show it, but annotations are also frequently how AI analyses are exported and displayed.
 +
 +Thankfully, Pathotrainer is extremely adaptable when it comes to displaying your Annotations or making new ones. 
 +
 +=== Existing Annotations ===
 +
 +If an image in a Case Collection has existing annotations,​ these will be detected and the option to toggle them on and off will appear automatically in the top right of the viewport in a training session.
 +
 +It doesn'​t matter if they are Third-Party (e.g. Halo, Visiopharm…) or made in Pathomation software, all detected annotations for that image in that folder will appear.\\
 +You can also adjust the opacity of annotations using the slider bar underneath the name.\\
 +Native annotations made using a Pathomation product e.g. PMA.studio, Pathotrainer will be listed as ‘NativeAnnotations’:​
 +
 +{{ :​annotation1.png?​800 |}}
 +
 +Third Party annotations will recognized and toggleable by ‘brand name’ e.g. Aperio:
 +
 +{{ :​annotation2.png?​800 |}}
 +
 +Some types of annotations such as Visiopharm have multiple ‘classes’ of annotations which can be individually toggled on or off:
 + 
 +{{ :​annotation3.png?​800 |}}
 +
 +===What If I Don’t Already Have Annotations?​===
 +If you don’t already have annotations,​ you can make in your preferred Pathomation software such as PIMSLS, or in Pathotrainer directly.\\
 +In Pathotrainer,​ when you are Creating a Case Collection or Editing an existing one, you can click on the image or the Annotations button for an image in a case to modify annotations:​
 + 
 +{{ :​annotation4.png?​800 |}}
 +
 +Clicking either will take you to the image configuration menu.
 +Here you will find a few tools:
 +  - The image bar along the top which allows you to navigate between different images in a case
 +  - The annotation toolbar which you can use to make your own annotations
 +  - The image viewport where you can inspect and edit the image selected in (1) 
 +  - The existing annotations menu box where you can toggle on/off the visibility of existing annotations using the checkbox and adjust their opacity using the slider bar – please note this does NOT affect how they will appear in a training session to an end user – they will be able to toggle on/off the annotations and adjust the opacity themselves.
 +
 +{{ :​annotation5.png?​800 |}}
 +
 +When you are done editing your custom annotations,​ be sure to hit save.
 +
 +{{ :​annotation6.png?​800 |}}
 +
 +===My Image Has Annotations But I Want To Hide Them For A Training Session===
 +
 +Not a problem - in this case, we recommend duplicating the image to another folder using PMA.core / your storage management software of choice. Then using the duplicate in the case collection / training session. ​
 +Make sure you do not copy any third party annotation files with the image file.
  
importing_annotations_to_training_sessions.txt · Last modified: 2024/07/17 16:16 by chris