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  • Acquiring Data
  • Currently Implemented Features
  • navigate.model.features.volume_search
  • navigate.model.features.volume_search.VolumeSearch3D
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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

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