The deepzoom step of the pipeline runs on the output of zoom and creates
image tiles at various zoom levels, each one more zoomed out than the previous
one. These image tiles will be used to create the viewable images in cellview.
To run deepzoom on a single slide, run:
deepzoomsample \\<Dpath>\<Dname> <SlideID> --deepzoomroot \\<DZpath>
To run deepzoom on a whole cohort of slides, run:
deepzoomcohort \\<Dpath>\<Dname> --deepzoomroot \\<DZpath>
(See here for definitions
of the terms in <angle brackets>.)
To see more command line arguments, run deepzoomsample --help or deepzoomcohort --help.
The outputs will be in \\<DZpath>\<SlideID>\. zoomlist.csv contains
a list of all the images, where each image is 256x256 pixels and contains
a tile of the zoomed image. Z0 is the most zoomed out and Z9 is the
most zoomed in.