navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn

class navigate.model.features.remove_empty_tiles.DetectTissueInStackAndReturn(model, planes=1, percentage=0.75, detect_func=None, threshold=150)

Bases: DetectTissueInStack

__init__(model, planes=1, percentage=0.75, detect_func=None, threshold=150)

Initialize the DetectTissueInStackAndReturn class.

Parameters:

modelobject

The model object representing the microscope.

planesint, optional

The number of Z planes to capture in the stack. Default is 1.

percentagefloat, optional

The minimum fraction of tissue-positive frames required for the stack to be considered as having tissue. Default is 0.75 (75%).

detect_funcfunction, optional

The custom tissue detection function to use. If not specified, the default detect_tissue3 function will be used. The function must accept (image_data, threshold) and return whether the frame contains tissue.

thresholdfloat, optional

The intensity threshold passed to detect_func. Default is 150.

Methods

__init__(model[, planes, percentage, ...])	Initialize the DetectTissueInStackAndReturn class.
end_func_data()	Data processing function to end the data phase.
end_func_signal()	Signal processing function to end the signal phase.
in_func_data(frame_ids)	Data processing function to analyze image frames for tissue presence.
in_func_signal()	Signal processing function to move the microscope stage.
pre_func_data()	Initialization function for data processing.
pre_func_signal()	Initialization function for signal processing.
signal_response_func()	Return the result if there is an tissue

Attributes

end_func_data()

Data processing function to end the data phase.

This method is called to determine whether the data phase should end. It checks

if the specified number of frames have been received.

Returns:

bool

True if the data phase should end, False otherwise.

end_func_signal()

Signal processing function to end the signal phase.

This method is called to determine whether the signal phase should end. It checks if the specified number of Z planes have been scanned.

Returns:

bool

True if the signal phase should end, False otherwise.

in_func_data(frame_ids)

Data processing function to analyze image frames for tissue presence.

This method is called during the data processing phase to analyze image frames for tissue presence. It checks if any of the received frames contain sufficient tissue.

Parameters:

frame_idslist

A list of frame IDs to analyze.

Returns:

bool

True if tissue is detected, False otherwise.

in_func_signal()

Signal processing function to move the microscope stage.

This method is called during the signal processing phase to move the microscope

stage to the specified Z and F positions. It increments the Z and F positions for each scan.

pre_func_data()

Initialization function for data processing.

This method is called at the beginning of the data processing phase and initializes variables for tracking received frames and tissue detection.

Returns:

None

pre_func_signal()

Initialization function for signal processing.

This method is called at the beginning of the signal processing phase and initializes the necessary parameters for moving the microscope stage.

signal_response_func()

Return the result if there is an tissue

detect_func

The tissue detection function used to analyze image frames.

Type:

function

model

The model object representing the microscope.

Type:

navigate.model.Model

percentage

The minimum percentage of images having tissue in a stack.

Type:

float

planes

The number of Z planes to capture in the stack.

Type:

int

threshold

The intensity threshold for tissue detection.

Type:

float