My Pathomation

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====== Accessing the AI image analysis menu ======

===== Requesting an AI image analysis =====

Start by selecting the slide you want to analyse. In the slide menu there is an AI button that opens the menu of available algorithms.

{{ :3.0.0_accessing_the_ai_menu.png?600 |}}

You can select an algorithm compatible with the slide and the intended use.
The menu has a standard naming convention logic to make this clear:
All algorithms are grouped per provider and then further subdivided if they are intended for the full slide WSI or for a Region of interest (ROI)

//Vendor name - Whole slide analysis//

   **AI algorithm name** - //vendor name wsi//

Click on the algorithm you wish to use. For an ROI algorithm you have to either make an area annotation first and select it or opt for a field of view analysis.

{{ :3.0.0_ai_in_roi_start.png?600 |}}

Once you select the AI algorithm of your choice a dialog window opens. You will see (1) the background information regarding the algorithm (2) the cost and balance of your account, if these are correct you can (3) run the analysis.

{{ :3.0.0_starting_an_ai_analysis.png?600 |}}

The algorithm will run in the background and next to the 'tasks' button a red number appears indicating all ongoing tasks. You can continue working while the results are being processed. The 'task' button can be clicked to then reveal status progress bars that show yellow when an analysis is running, green indicates it is ready, red when it failed. To find out more click on the 'i' next to the status bar.

{{ ::3.0.3_tasks_button_2.png?600 |}}

{{ :3.0.0_ai_feedback.png?600 |}}

In case of failure you can see why and contact our helpdesk for support if needed. In case of success you see the algorithm details again with the quantitative results (count, score, %,...) and you can leave feedback for the AI provider.

===== Interpreting AI image analysis results =====

Once a result is in this is indicated in the 'all tasks' bar and progress bars, but most obviously when overlay annotations appear. 

Example of a HER2 biomarker annotation result

{{ :3.0.0_ai_result_1.png?600 |}}

It can be helpful to change the way the annotation result appears, change colours or hide certain categories for easier interpretation. Pull out the right sidebar menu to access the AI result menu. Please note that mousing over a category in the menu triggers a highlight in the viewer screen.

{{ :3.0.0_ai_result_sidebar_menu_open.png?600 |}}

In this example only the weak Stained cells are shown

{{ :3.0.0_ai_result_sidebar_menu_open_deselect.png?600 |}}
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