API#
This page exists to help users navigate the labyrinth of functions and classes that make up Omnipose.
Project structure#
Omnipose is built on Cellpose, and functionally
that means Cellpose actually imports Omnipose to replace many of its
operations with the Omnipose versions with omni=True
. Omnipose was
first packaged into the Cellpose repo before I began making too many
ND-generalizations (full rewrites) for the authors to maintain. Thus was
birthed my cellpose_omni
fork, which I published to PyPi separately
from Omnipose for some time. I later decided that maintaining two
packages for one project was overcomplicated for me and users
(especially for installations from the repo), so the latest version of
cellpose_omni
now lives here. cellpose_omni
still gets installed
as its own subpackage when you install Omnipose. If you have issues
migrating to the new version, make sure to
pip uninstall omnipose cellpose_omni
before re-installing Omnipose.
The install.py
script simply runs pip install -e .{extras}
in
the omnipose
and cellpose
directories.
If you encounter bugs with Omnipose, you can check the main Cellpose repo for related issues and also post them here. I do my best to keep up with with bug fixes and features from the main branch, but it helps me out a lot if users bring them to my attention. If there are any features or pull requests in Cellpose that you want to see in Omnipose ASAP, please let me know.