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.
Modules#
Omnipose