The geomcell step of the pipeline writes out the boundaries of the
segmented cells by reading from the component tiff.
To run geomcell on a single slide, run:
geomcellsample \\<Dpath>\<Dname> <SlideID>
To run geomcell on a whole cohort of slides, run:
geomcellcohort \\<Dpath>\<Dname>
(See here for definitions
of the terms in <angle brackets>.)
To see more command line arguments, run geomcellsample --help or geomcellcohort --help.
The outputs will be in \\<Dpath>\<Dname>\<SlideID>\geom. A csv file will
be created for each HPF containing information about the cells in that HPF.
geomcell does significant cleanup of the cells:
- in the membrane layers, sometimes the membrane is broken. In the primary
region of the HPF (defined by mx1, my1, mx2, my2),
geomcelltries to connect the broken pieces. Outside the primary region, no repairs are done, and the cell will likely be discarded by one of the subsequent cleanup steps. - Membranes are filled in.
- Narrow tails coming off of a cell, with a width of one pixel, are discarded. If a narrow bridge connects two components, that bridge is also discarded.
- If there are disconnected components (including ones that are now disconnected after discarding a bridge), only the larger one is kept.
- If the cell's area is less than (3 microns)^2, it is discarded.