Add masking of bright background objects #57
Merged
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This PR adds a function,
_mask_spots
, to the Polaris application, which creates a mask for bright fluorescent objects in the background image of a FISH sample. It then marks all detected spots inside this mask as 'masked', so they can be exclude from downstream analysis. This information is added to thedecoding_result
and appears as an additional column in the main Polaris output.Because of the increasing complexity of the Polaris prediction inputs, a function ,
_validate_prediction_input
was added to Polaris. This method checks the shapes of the inputsspots_image
,segmentation_image
, andbackground_image
. It also checks the values ofthreshold
andmask_threshold
.Test cases have been added to cover these two new functions.