neuralib.stardist.run_2d.StarDist2DOptions

class neuralib.stardist.run_2d.StarDist2DOptions

Bases: AbstractSegmentationOptions

__init__()

Methods

__init__()
eval(**kwargs)	eval the model in single file or batch files in directory, and save the results
foreach_process_image([to_gray])	Iterates over image files in the specified directory, processes each image, and yields the file path along with the processed image.
ij_roi_output(filepath)	Get imageJ/Fiji .roi output save path
launch_napari([with_widget])	Launch napari viewer for stardist results
main([args, parse_only, system_exit])	parsing the commandline input args and call run().
new_parser(**kwargs)	create an ArgumentParser.
process_image([to_gray])	Process the image for segmentation.
run()	called after main().
seg_output(filepath)	Get segmented output save path

Attributes

DESCRIPTION	parser description.
EPILOG	parser epilog.
EX_GROUP_SOURCE
GROUP_IO
USAGE	parser usage.
batch_mode	flag batch mode
directory	directory for batch imaging processing
directory_suffix	suffix in the directory for batch mode (default: '.tif')
file	image file path
file_mode	flag file mode
invalid_existed_result	force re-evaluate the result (default: False)
model	stardist pretrained model (default: '2D_versatile_fluo')
napari_view	view result by napari GUI, only available in single file mode (default: False)
no_normalize	not do percentile-based image normalization (default: False)
prob_thresh	Consider only object candidates from pixels with predicted object probability above this threshold.
save_ij_roi	if save also the imageJ/Fiji compatible .roi file (default: False)
with_norm	flag normalize image

DESCRIPTION: str | None = 'Run the Stardist model for segmentation'

parser description. Could be override as a method if its content is dynamic-generated.

model: Literal['2D_versatile_fluo', '2D_versatile_he', '2D_paper_dsb2018', '2D_demo']

stardist pretrained model (default: ‘2D_versatile_fluo’)

prob_thresh: float | None

Consider only object candidates from pixels with predicted object probability above this threshold. Seealso: stardist.models.base._predict_instances_generator: prob_thresh (default: None)

run()

called after main(). Used for runs the main execution logic of the object

seg_output(filepath)

Get segmented output save path

Parameters:

filepath (Path) – filepath for image

Returns:

segmented output save path

Return type:

Path

eval(**kwargs)

eval the model in single file or batch files in directory, and save the results

Return type:

None

launch_napari(with_widget=False, **kwargs)

Launch napari viewer for stardist results

Parameters:

with_widget (bool) – If True, launch also with the starDist widget (required package stardist-napari)