image_AICS

The image_AICS module contains a class ImageAICS which stores and displays image data. This class is used throughout the project to interact with images taken by the microscope’s camera.

class ImageAICS

class microscope_automation.util.image_AICS.ImageAICS(data=None, meta=None)[source]

store and display image data

add_data(data)[source]

add image data

Input:

data: numpy array with image data

Output:

none

add_meta(meta)[source]

Add meta data. Use keys as defined in OME-XML.

Input:

meta: dictionary with meta data

Output:

none

create_file_name(template)[source]

Create file name based on meta data and template.

Input:

template: string with filename with path for saved image in original format or tuple with path to directory and template for file name

Output:

filePath: file name and path for image

get_data()[source]

retrieve image data as numpy array.

Input:

none

Output:

data: numpy array with image data

get_meta(key=None)[source]

Retrieve meta data. Use keys as defined in OME-XML.

Input:

none

Output:

meta: dictionary with meta data

parse_file_template(template)[source]

Create file name based on meta data and template.

Input:

template: string with filename

Output:

fileName: file name for image

save_as_tiff(path, bits=16)[source]

Save data portion of image as .tif file.

Input:

path: file path with extension .tif as string

bits: bit depth of image. Default: 16

Output:

none

show(title='ImageAICS', channel=0, z=0, t=0)[source]

display image data

Input:

title: string with title for window. Default=’ImageAICS’

channel: channel for display. Default = 0

z: z slice. Default = 0

t: time point. Default = 0

Output:

none