Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update segmentation.py #72

Merged
merged 3 commits into from
Apr 9, 2024
Merged

Update segmentation.py #72

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
82a8475
Update segmentation.py
a-jacobo Feb 7, 2024
d3fd41c
added default model_type if not provided to cellpose
JoOkuma Feb 7, 2024
075a089
Merge branch 'public/main' into CellPose_Custom_Models
JoOkuma Apr 5, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions ultrack/imgproc/segmentation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -214,7 +214,10 @@ def inverted_edt(
class Cellpose:
def __init__(self, **kwargs) -> None:
"""See cellpose.models.Cellpose documentation for details."""
from cellpose.models import Cellpose as _Cellpose
from cellpose.models import CellposeModel as _Cellpose

if "pretrained_model" not in kwargs and "model_type" not in kwargs:
kwargs["model_type"] = "cyto"

self.model = _Cellpose(**kwargs)

Expand All @@ -223,5 +226,5 @@ def __call__(self, image: ArrayLike, **kwargs) -> np.ndarray:
Predicts image labels.
See cellpose.models.Cellpose.eval documentation for details.
"""
labels, _, _, _ = self.model.eval(image, **kwargs)
labels, _, _ = self.model.eval(image, **kwargs)
return labels
Loading