Description of feature
Baysor scale param corresponds to the cell radius and not the diameter
Using --scale 30 on Xenium data with an expected cell radius of 30 µm (60 µm diameter) results in under-segmentation across many tissue types. This needs to change with a standard table where users can select the scale factor based on the cells they are looking at.
If the scale factor is too large (eg. current value - 30) this results in undersegmented cells due to cell merging
if the scale factor is low this would result in over-segmented cells.
We need to come up with a reference table in the README
Description of feature
Baysor scale param corresponds to the
cell radiusandnot the diameterUsing
--scale 30on Xenium data with an expected cell radius of30 µm(60 µm diameter) results in under-segmentation across many tissue types. This needs to change with a standard table where users can select the scale factor based on the cells they are looking at.If the scale factor is too large (eg. current value - 30) this results in undersegmented cells due to cell merging
if the scale factor is low this would result in over-segmented cells.
We need to come up with a reference table in the README