The annowarp step of the pipeline writes out the pathologist annotations,
which were drawn on the qptiff image, in im3 coordinates. It does this
by aligning tiles of the whole slide image, created in the zoom step,
to the qptiff and creating a warp map.
To run annowarp on a single slide, run:
annowarpsample \\<Dpath>\<Dname> <SlideID> --zoomroot \\<Zpath>
To run stitchmask on a whole cohort of slides, run:
annowarpcohort \\<Dpath>\<Dname> --zoomroot \\<Zpath>
(See here for definitions
of the terms in <angle brackets>.)
To see more command line arguments, run the scripts with --help.
The outputs are in the \\<Dpath>\<Dname>\<SlideID>\dbload folder.
They include:
<SlideID>_annotations.csv- metadata about the annotations<SlideID>_annowarp.csv- alignment results for each tile of the wsi and qptiff<SlideID>_annowarp-stitch.csv- the result of the stitching<SlideID>_vertices.csv- the vertices of each of the annotations, including the original and warped coordinates<SlideID>_regions.csv- the polygons of each of the annotations