Tissue_segmentation - Noise removal

[dtejadam]

Hi,

I’ve attached a summary image of the tissue segmentation for reference.

I encountered an issue during tissue segmentation where not all individual pieces are extracted in alignment with the tissue frame. Specifically, in this example, I identified six tissue pieces—five of which are either noise or belong to other slides.

My goal is to extract only the cells from label 2 (the main tissue), but the cell segmentation also includes the other pieces, which are then counted subsequent analyses.

Is there a way to exclude this noise when doing the Tissue_segmentation or should I filter it later based on the coordinates when working with the AnnData file?

Thank you!