bactoscoop.omni¶

Classes and public operations¶

class bactoscoop.omni.Omnipose(imgs, paths)¶

Omnipose.

Parameters:

imgs – Input imgs consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
paths – Input paths consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.

Returns:

None (no explicit return statement).

Assigned state: self.imgs, self.files, self.use_GPU, self.masks, self.flows, self.selected_imgs, self.selected_files, self.model.

Omnipose.load_models(model_name)¶

Load the desired omnipose model.

Parameters:: model_name – Omnipose model identifier; default collection model is bact_phase_omni.
Returns:: None (no explicit return statement).

Assigned state: self.model.

Original docstring (legacy wording may differ from the current signature)

Load the desired omnipose model.

Omnipose.process(n=(0,), mask_thresh=1, minsize=300)¶

Segment the raw images and get their masks.

Parameters:

n – Selected image positions; wrapper accepts None for all. Indices must be nonempty, unique valid integers.
mask_thresh – Threshold passed as Omnipose mask_threshold.
minsize – Minimum accepted segmentation-mask size in pixels.

Returns:

None (no explicit return statement).

Assigned state: self.masks, self.flows, self.selected_imgs, self.selected_files.

Explicitly raised exceptions: ValueError. Errors from called functions can also propagate or be recorded.

Original docstring (legacy wording may differ from the current signature)

Segment the raw images and get their masks.

Omnipose.save_masks()¶

Save the segmentation masks.

Explicitly raised exceptions: RuntimeError, ValueError. Errors from called functions can also propagate or be recorded.

Original docstring (legacy wording may differ from the current signature)

Save the segmentation masks.

Omnipose.compiled_process(n, mask_thresh, minsize)¶

Sequentially process and save the masks in one method.

Parameters:

n – Selected image positions; wrapper accepts None for all. Indices must be nonempty, unique valid integers.
mask_thresh – Threshold passed as Omnipose mask_threshold.
minsize – Minimum accepted segmentation-mask size in pixels.

Returns:

None (no explicit return statement).

Original docstring (legacy wording may differ from the current signature)

Sequentially process and save the masks in one method.