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Add conversion support for index images to ImgLib2 and legacy ImageJ ROIs #283

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merged 13 commits into from
Jan 9, 2024
Merged

Add conversion support for index images to ImgLib2 and legacy ImageJ ROIs #283

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79b4b84
Add index image converts to convert module
elevans Aug 21, 2023
41345b1
Add try/except for RoiManager call
elevans Aug 22, 2023
e4ee4a5
Add test for index image to ImgLib2 ROI
elevans Aug 22, 2023
f64ee63
Add Cellpose/StarDist use case
elevans Aug 28, 2023
f06dbb0
Improve section using matplotlib
elevans Oct 3, 2023
05c6be7
Add type hint for _get_contours() method
elevans Oct 3, 2023
e96f855
Use imglib2 instead of numpy to generate contours
elevans Oct 4, 2023
58cae9d
Use %pip install magic on use case notebook
elevans Oct 11, 2023
59e9987
Use combo !mamba and !pip shell commands
elevans Jan 3, 2024
e3710d8
Add Cellpose/StarDist notebook to RTD use cases
elevans Jan 3, 2024
efd8b51
Add note to adjust brightness/contrast
elevans Jan 8, 2024
eaa7e97
Use the WritablePolygon2D interface for ROIs
elevans Jan 8, 2024
f205852
Auto adjust the output cyto channel
elevans Jan 8, 2024
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4 changes: 4 additions & 0 deletions src/imagej/_java.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,6 +130,10 @@ def Img(self):
def ImgView(self):
return "net.imglib2.img.ImgView"

@JavaClasses.java_import
def DefaultWritablePolygon2D(self):
return "net.imglib2.roi.geom.real.DefaultWritablePolygon2D"

@JavaClasses.java_import
def ImgLabeling(self):
return "net.imglib2.roi.labeling.ImgLabeling"
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5 changes: 4 additions & 1 deletion src/imagej/convert.py
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Expand Up @@ -510,12 +510,15 @@ def index_img_to_roi_manager(
print("The RoiManager is unavailable in headless mode.")


def _get_contours(ij: "jc.ImageJ", index_img: np.ndarray) -> List:
def _get_contours(
ij: "jc.ImageJ", index_img: np.ndarray
) -> List["jc.DefaultWritablePolygon2D"]:
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"""
Compute contours from an index image.

:param ij: The ImageJ2 gateway (see imagej.init)
:param index_img: An ImgLib2 or NumPy index image
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:return: A list of imglib2 2D poylgon ROIs
"""
contours = []
labels = np.unique(index_img)
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