The zoom step of the pipeline creates a single, stitched image for the whole slide based on the output of the align step. From each HPF, its primary region as defined by (mx1, my1, mx2, my2) is taken from the component tiff and inserted into the large image. The image is also normalized for average brightness in the tissue regions.
To run zoom on a single slide, run:
zoomsample \\<Dpath>\<Dname> <SlideID>
To run zoom on a whole cohort of slides, run:
zoomcohort \\<Dpath>\<Dname>
(See here for definitions
of the terms in <angle brackets>.)
To see more command line arguments, run zoomsample --help or zoomcohort --help.
The outputs will be in \\<Dpath>\<Dname>\<SlideID>\wsi\, which will contain one file
for each unmixed layer. The files are named <SlideID>-Z9-L<layer>-wsi.png,
where Z9 refers to the fact that this is the most zoomed in version of the image.
The zoomed out versions will be created in the deepzoom step.