Ability to apply BinaryMaskCollection prior to having DecodedIntensityTable?

I am currently working with collaborator data that defines their segmentation mask with a RoiSet.zip file. While I can use this to create a BinaryMaskCollection to filter the final results and assign cell IDs, I would like to be able to use this mask earlier in the pipeline to omit spots that are known to be outside of cells. This would both save computation time while I work on developing our pipeline for seqFISH data and make it simpler to compare intermediate results to those that our collaborator got with their code (since they applied the segmentation mask to the image before running spot detection).

Is there currently a way to do this within starfish?

Hi Cecilia,

There is currently no built-in functionality for doing what you ask (use a BinaryMaskCollection to filter a SpotFindingResults). It is a good idea though. I can also see it being useful for removing false positives in lipofuscin granules if the BinaryMaskCollection is the result of lipofuscin segmentation.