navigate.model.features.volume_search.VolumeSearch3D

class navigate.model.features.volume_search.VolumeSearch3D(model, target_resolution='Nanoscale', target_zoom='N/A', position_id=0, z_step_size=0.1, x_direction='x', y_direction='y', overlap=0.05, analysis_function=None, current_pixel_size=1.0, filter_pixel_number=10)

Bases: object

__init__(model, target_resolution='Nanoscale', target_zoom='N/A', position_id=0, z_step_size=0.1, x_direction='x', y_direction='y', overlap=0.05, analysis_function=None, current_pixel_size=1.0, filter_pixel_number=10)

Initialize VolumeSearch

Parameters:

• model (navigate.model.model.Model) – Navigate Model

• target_resolution (str) – Name of microscope to use for tiled imaging of tissue

• target_zoom (str) – Resolution of microscope (target_resolution) to use for tiled imaging of tissue

• position_id (int) – The index of position in multiposition table

• z_step_size (float) – Target z step size

• overlap (float) – The overlap ratio

• analysis_function (callable) – An analysis function return a labeled object

• current_pixel_size (float) – The current pixel size

• filter_pixel_number (int) – The pixel number to filter a label

Methods

__init__(model[, target_resolution, ...])	Initialize VolumeSearch
cleanup()
data_func(frame_ids)

Attributes

model	Navigate Model
target_resolution	Name of microscope to use for tiled imaging of tissue
target_zoom	Resolution of microscope (target_resolution) to use for tiled imaging
position_id	The index of position
z_step	The Z step size
x_direction	string
y_direction	string
overlap	The overlap ratio
analysis_function	analysis function
current_pixel_size	The current pixel size
filter_pixel_number	The filter pixel number
config_table	Feature configuration

analysis_function

analysis function

Type:

function

config_table

Feature configuration

Type:

dict

current_pixel_size

The current pixel size

Type:

float

filter_pixel_number

The filter pixel number

Type:

int

model

Navigate Model

Type:

navigate.model.model.Model

overlap

The overlap ratio

Type:

float

position_id

The index of position

Type:

int

target_resolution

Name of microscope to use for tiled imaging of tissue

Type:

str

target_zoom

Resolution of microscope (target_resolution) to use for tiled imaging

Type:

str

x_direction

string

y_direction

string

z_step

The Z step size

Type:

float