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Automated Landmarking

Automated Landmarking Options

 

We start by creating a new empty population set for our landmarks.

Here we gate for CD3+ T cells: CD3 high, CD4 low, CD8 low, & other non-T cell markers low like CD68 for example.

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Visualize Automated Landmarks

After generating automated landmarks the population set will be filled. Only a few cells per image will be classified as landmarks - they can be seen when turning off the channels.

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Review Automated Landmarks

We need to verify the automated landmarks by reviewing them.

From the menu: Populations -> Review Population Set
Make sure ‘Automated Landmarks’ is also selected as the output set (we are editing the labels of this population set without writing label changes to an additional population set.)

Since we have associated channels to cell types in our CellTypeTable used for the automated landmarking we can use the Auto Channel Select option, so the corresponding channels will be visible when we get to the landmark cell (e.g. FOXP3, CD4, and CD3 will be turned on when a Treg landmark is being reviewed). Randomizing the order here is not desirable as we want to review each cell type in order (e.g. all the CD8T cells then all the B cells). Randomizing the order is useful when reviewing

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