Questions about tissue regions

[zijianni]

Questions about tissue regions

[zijianni]

Hi Changfeng,

Thanks for your interests in using SpotClean! You've raised a good point that there could be unwanted tissue spots due to tissue folds. You can consider removing these spots after applying SpotClean since the tissue folds also naturally contribute to spot swapping across the slide. Including them during SpotClean should lead to more accurate estimation.

In my perspective, tissue folds should still be classified as tissue rather than background. You can further annotate them to be e.g. unwanted tissue spots and use it to further filter the spots.

[cf98]

Hi Changfeng,

Thanks for your interests in using SpotClean! You've raised a good point that there could be unwanted tissue spots due to tissue folds. You can consider removing these spots after applying SpotClean since the tissue folds also naturally contribute to spot swapping across the slide. Including them during SpotClean should lead to more accurate estimation.

In my perspective, tissue folds should still be classified as tissue rather than background. You can further annotate them to be e.g. unwanted tissue spots and use it to further filter the spots.

Thank you!