register_image_datasource
Register an image alone as a project -- no cell table, no mask.
from plexora import register_image_datasourceregister_image_datasource(
name,
image,
channel_names=None,
copy=False,
data_dir=None,
image_type=None,
pyramidize=None,
image_index=0,
)Writes directly to Plexora's project registry. The project opens
immediately; a mask or a cell table can be attached to it later, by
re-registering the same name with plexora.register_datasource or
plexora.register_anndata_datasource.
When to use
A quick first look at a slide before anything else about it is
known. plexora.create_project(image) does the same job and is
the newer entry point, letting plexora.configure_project fill in
a table or mask afterwards; use register_image_datasource for a
script that only ever has the image.
Parameters
namestrrequiredThe project's name.
imagestr | PathrequiredThe whole-slide image -- OME-TIFF/TIFF, DICOM, or a Zarr store. A web address is read in place.
channel_nameslist[str]default NoneA name for each image
channel, in channel order. Derived from the image's own
metadata (or generic "Channel N" names) when not given.
copybooldefault FalseCopy image into the project's own folder
instead of reading it where it is. Defaults to False.
data_dirstr | Pathdefault NoneThe data root to register the project under. By default the project is registered where new projects go (on your own computer, Documents/Plexora/projects, which the Plexora website opens too) and what registering builds is written to Plexora's configured data directory.
image_typestrdefault None"brightfield" or "fluorescence", to
override how the image is read. Defaults to None, which
decides from the file.
pyramidizebool or strdefault NoneWhat to do with a large
multiplex TIFF that has no reduced-resolution levels. None (the
default) and True write a pyramidized copy once, beside the
original (or in the project's folder when that one is not
writable), and open the copy; the original is never changed. A
16-bit image's copy is <name>.pyramid.approx, about 75% smaller
than an exact copy with every pixel within its noise, unless the setting
compress_pyramids is off; otherwise <name>.pyramid.ome.tiff.
"compressed" or "exact" asks for that kind. False opens the
original as it is.
image_indexintdefault 0Which image of a microscope file that holds several -- a CZI's scenes, an ND2's positions, a LIF's images, an MCD's acquisitions, a VSI's scan areas -- counting from 0 in the order the import dialog lists them. Defaults to 0, the first. Every other format holds one image.
Returns
dictThe project's saved config entry.
Examples
import plexora
plexora.register_image_datasource("quicklook", image="slide.ome.tif")
# The third scene of a slide scan
plexora.register_image_datasource("scene3", image="scan.czi", image_index=2)Related
create_project
Register one project and return its name.
register_datasource
Register an image and a flat cell table as a project, in one call.