Closed pakiessling closed 3 months ago
Hi, thanks for trying proseg!
--perimeter-bound
argument is not on a super interpretable scale, but controls the allowable ratio of "effective" surface area to volume. You can try to make that a little higher if the morphology looks off.--initial-voxel-size
. By default proseg starts with 4x4 micron voxels and and increases resolution until it's sampling 1x1 voxels. The resolution increases are controlled by the --schedule
parameter. With the default sampling schedule the voxel size with be the initial voxel size divided by 4. The voxel size on the z-axis is just the z-span of the data divided by the number of voxel layers.--voxel-layers 1
). Ty!
Hi, I am trying Proseg with my own datasets and I have a few questions regarding the choice of parameters.
1) I am working with muscle tissue and cells are commonly 5 times as long as they are wide. What does this mean in terms of setting the perimeter-bound argument? What does 1.3 mean? 2) I am taking the membrane based segmentation of the Merscope as prior. Should I instead segment DAPI or does this not matter much? 3) Should ncomponents simply be the number of major cell types I expect? 4) How do I choose the voxel lengths? Should the xy-voxel be bigger in my case as I have very big cells? 5) How to properly deal with the z-axis? Our tissue slices are only 5 µm thick and the z coordinates reported by the Merscope tend to be unreliable. How do I choose z-voxels or should I maybe completely ignore it?
Thank you so much!