neuralib.segmentation.cellpose.core.AbstractCellPoseOption

class neuralib.segmentation.cellpose.core.AbstractCellPoseOption

Bases: AbstractSegmentationOption

__init__()

Methods

__init__()
eval()	eval the model in single file or batch files, and save the results
foreach_normalize_image()	Normalize the image in batch mode
foreach_raw_image()	Load image from a directory and convert to grayscale
ij_roi_output(filepath)	Get imageJ/Fiji .roi output save path
launch_cellpose_gui()	AttributeError: 'MainW' object has no attribute 'load_3D'.
launch_napari()	napari viewer
main([args, parse_only, system_exit])	parsing the commandline input args and call run().
new_parser(**kwargs)	create an ArgumentParser.
normalize_image()	Normalize the image
raw_image()	Load image from file and convert to grayscale
run()	called after main()
seg_output(filepath)	Get segmented output save path

Attributes

DESCRIPTION	parser description.
EPILOG	parser epilog.
EX_GROUP_SOURCE
USAGE	parser usage.
batch_mode	Flag batch mode
cellpose_view	launch cellpose gui for the analyzed result
chan_nuclear	nuclear channel
chan_seg	channel for segmentation default:{'none': -1, 'gray': 0, 'red': 1, 'green': 2, 'blue': 3}
diameter	diameter for each neuron (number of each pixel)
directory	images directory for batch processing
directory_suffix	suffix in batch mode
file	image file path
file_mode	Flag file mode
force_re_eval	force re-evaluate the result
model	which pretrained model
napari_view	view in napari
no_normalize	NOT DO Percentile-based image normalization for eval
save_ij_roi	if save also the imageJ/Fiji compatible .roi file

DESCRIPTION: str = 'ABC for GUI Cellpose'

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

model: Literal['cyto', 'cyto2', 'cyto3']

which pretrained model

chan_seg: int

channel for segmentation default:{‘none’: -1, ‘gray’: 0, ‘red’: 1, ‘green’: 2, ‘blue’: 3}

chan_nuclear: int

nuclear channel

diameter: int

diameter for each neuron (number of each pixel)

cellpose_view: bool

launch cellpose gui for the analyzed result

seg_output(filepath)

Get segmented output save path

Parameters:

filepath (Path) – filepath for image

Returns:

segmented output save path

Return type:

Path

launch_napari()

napari viewer

launch_cellpose_gui()

AttributeError: ‘MainW’ object has no attribute ‘load_3D’. Cellpose version 3.0.10.

TODO open issue in cellpose -> move load_3D instance attribute to line above io._load_image() in MainW.__init__()