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?