Contents

• zen_experiment_info

  • class ZenExperiment(object)

zen_experiment_info

Module which contains class ZenExperiment(object) which abstracts the experiment file for a Spinning Disk Zeiss Microscope using Zen Blue or Black software. This allows for reading and editing experiment files.

class ZenExperiment(object)

class microscope_automation.settings.zen_experiment_info.ZenExperiment(experiment_path, experiment_name)

experiment_exists()

Function to check if the experiment name provided in the preference file exists in the Zen software

Input:

none

Output:

a boolean indicating if the experiment exists or not

get_focus_settings()

Function to get all the instances of focus settings in the experiment file

Input:

none

Output:

focus_settings: All instances of focus settings in experiment file

get_objective_position()

Return position of objective used in experiment. Method assumes that only one objective is used in experiment.

Input:

None

Output:

position: integer with position of objective used in experiment

get_tag_value(tag_path)

Function to find the value of a tag in the Zen Experiment file.

Input:

experiment_name: Name of the experiment file

Output:

tag_value: string value of the tag

is_tile_scan()

Test if experiment is tile scan.

Input:

none

Output:

is_tile_scan: True if experiment contains z-stack

is_z_stack()

Test if experiment is z-stack.

Input:

none

Output:

is_z_stack: True if experiment contains z-stack

update_tag_value(tag_path, new_value)

Function to update the value of a tag in the experiment xml file.

Input:

tag_path: Path where the tag is loacted in the xml tree

new_value: The value that needs to be assigned to the tag (string)

Output:

none

update_tile_positions(x_value, y_value, z_value)

In the tile function, correct the hard coded values of the tile region using the values from the automation software

Input:

x_value: float (x - coordinate)

y_value: float (y - coordinate)

z_value: float (z - coordinate)

Output:

none

z_stack_range()

Return range of first z-stack in experiment. Returns 0 if z-stack is not activated.

Input:

none

Output:

z_stack_range: True if experiment contains z-stack