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Add masking of bright background objects #57

Merged
merged 4 commits into from
May 22, 2023
Merged

Add masking of bright background objects #57

merged 4 commits into from
May 22, 2023

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elaubsch
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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 the decoding_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 inputs spots_image, segmentation_image, and background_image. It also checks the values of threshold and mask_threshold.

Test cases have been added to cover these two new functions.

@elaubsch elaubsch added the enhancement New feature or request label May 22, 2023
@elaubsch elaubsch merged commit 6f5ef83 into master May 22, 2023
@elaubsch elaubsch deleted the mly/mask branch May 22, 2023 23:10
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