NasimJ
commented
2 years ago If we want the subsamples to have overlap and only from the field numbers 1,2,3,4 then we could do this with 4 config files, otherwise, we would need more, because the fields in the config file is the field number, not the number of fields.
For the subsample to not have overlap (or have partial overlap), we could subsample 4 fields from 9 fields by choosing fields 2, 4, 6, and 8. To subsample 3 fields from 9 fields, we could choose fields 3, 5, and 7, and so on.
I think for this purpose we would want our subsamples to have overlap (to have the same cell numbers and to be the exact subsample of the category above it), but I think this is something to consider.
We may also want to consider the site location discussion from slack; there will be differences in the cell numbers if site 1 located in a corner vs the center of a well.
bethac07
We have a qualitative difference between conditions that have higher FOV counts (20X, typically) those with lower FOV counts (10X, typically, though not exclusively). This matches previous work
A couple of complicating factors here though -
1) 4 fields of 10X vs 9 fields of 20X may have equal numbers of cells, even with lower numbers of fields. We've always speculated that more fields is better data because more cells, but maybe it isn't - maybe it's more chances to get a really good segmentation, or some other thing we haven't thought of. Our previous experiments were all tested at the same magnification, with cell count and FOV count essentially perfectly correlated, so we have no data addressing this directly. 2) It may truly be that other magnifications really are worse than our standard 20X, but right now we can't tell because we know that FOV count MAY be a contributing factor.
To address these, I think we need to do 2 things -