microscope_automation.connectors package

Submodules

microscope_automation.connectors.connect_slidebook module

Communication layer for 3i Slidebook This layer sends http commands to a command and data servers. Slidebook calls a MatLab library that pulls the commands from the server queue

Date Created: January 26, 2020

class microscope_automation.connectors.connect_slidebook.ConnectMicroscope(cmd_url='http://127.0.0.1:5000', data_url='http://127.0.0.1:5100', microscope='3iW1-0', dummy=False)

Bases: object

clear_experiments()

Clear experiments queue

count_experiments()

Return number of experiments inqueue

create_experiment_path(experiment, experiment_folder)

Creates complete path to capture settings. Raises exception if experiment does not exist.

Input:

experiment: string with name of capture settings (with or w/o extension .exp.prefs)

experiment_folder: folder for capture settings

Output:

experiment_path: path to experiment

delete_experiment(experiment_id)

Delete experiment by id

execute_experiment(capture_settings, locations, objective='')

Execute experiments with parameters defined in experiment on multiple positions.

Input:

capture_settings: string with name of experiment as defined within Microscope software

objective: objective used to acquire image. If none keep objective.

locations: list with (x,y,z) stage locations

Output:

success: True when experiment was successfully posted on command server

get_about_command_service()

Retrieve information about command service

get_about_data_service()

Retrieve information about data service

get_experiment(experiment_id)

Return experiment by id

get_experiment_dict()

Retrieve dictionary with all experiments on queue

get_focus_pos()

Return current position of focus drive.

Input:

none

Output:

zPos: position of focus drive in micrometer

get_focus_settings(experiment_path=None, experiment_name=None)

Get focus settings. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

none

get_microscope_name()

Returns name of the microscope from hardware that is controlled by this class

Input:

none

Output:

Microscope: name of Microscope

get_next_experiment()

Return next (oldest) experiments in queue

get_objective_position_from_experiment_file(experiment_path=None, experiment_name=None)

Function to get the position of the objective used in the experiment Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

none

get_stage_pos(repetitions=5, wait=1)

Return most recent position of Microscope stage.

Input:

repetitions: number of times to try to get a response

wait: wait time per repetition in sec

Output:

xPos, yPos, zPos: x and y position of stage in micrometer

is_tile_scan(experiment_path=None, experiment_name=None)

Function to check if the experiment is a tile scan. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

none

is_z_stack(experiment_path=None, experiment_name=None)

Function to check if the experiment contains z-stack acquisition. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

none

live_mode_start(experiment)

Start live mode. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment: name of experiment

Output:

none

live_mode_stop(experiment)

Stop live mode. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment: name of experiment

Output:

none

load_image(image, get_meta_data=False)

Load most recent image from data service and return it a class ImageAICS

Input:

image: image object of class ImageAICS.

get_meta: if true, retrieve meta data from file. Default is False

Output:

image: image with data and meta data as ImageAICS class

move_focus_to(zPos)

Move focus to new position. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

zPos, yPos: new focus position in micrometers.

Output:

zFocus: new position of focus drive

move_focus_to_load()

Move focus to load position if defined.

Input:

zPos, yPos: new focus position in micrometers.

Output:

zFocus: new position of focus drive

move_focus_to_work()

Move focus to work position if defined.

Input:

zPos, yPos: new focus position in micrometers.

Output:

zFocus: new position of focus drive

move_stage_to(xPos, yPos, zPos, capture_settings=None, test=False)

Move stage to new position.

Input:

xPos, yPos, zPos: new stage and objective position in micrometers.

capture_settings: capture settings in Slidebook Capture dialog to move stage

test: not used but included for consistency with ZEN Blue API

Output:

xPos, yPos, zPos: new stage and objective position in micrometers

not_implemented(method_name)

Raise exception if method is not implemented.

Input:

method_name: method that calls this method

Output:

none

post_experiment(experiment)

Post experiment as last entry on queue and return updated experiment

remove_all()

Remove all images from queue at data service.

Input:

none

Output:

none

save_image(fileName)

Save last acquired ImageAICS in original file format using microscope software

Raises HardwareCommandNotDefinedError

Input:

file: file name and path for ImageAICS save

Output:

none

set_focus_load_position()

Retrieve current position and set as load position.

Input:

none

Output:

zLoad: current focus position in mum

set_focus_work_position()

Retrieve current position and set as work position.

Input:

none

Output:

z_work: current focus position in mum

snap_image(capture_settings, objective='')

Snap image with parameters defined in experiment at current location. Raise exception if request was not successful

Input:

capture_settings: string with name of capture_settings as defined within Microscope software

objective: objective used to acquire image. If none keep objective.

Return:

response: Return dictionary with response from commands microservice

stop()

Stop Microscope immediately

trigger_pump(seconds, port='COM1', baudrate=19200)

Trigger pump

Input:

seconds: the number of seconds pump is activated

port: com port, default = ‘COM1’

baudrate: baudrate for connection, can be set on pump, typically = 19200

Output:

none

update_tile_positions(experiment_path, experiment_name, x_value, y_value, z_value)

Function to define the position of the tile. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

x_value: float (x - coordinate)

y_value: float (y - coordinate)

z_value: float (z - coordinate)

Output:

none

validate_experiment(experiment_path=None, experiment_name=None)

Function to check if the experiment is defined in the Slidebook software

Input:

experiment_path: path of the experiment file - does not matter for Zen Black

experiment_name: name of the experiment

Output:

valid_experiment: bool describing if the experiment is valid

z_down_relative(delta)

Move focus relative to current position away from sample. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

delta: absolute distance in mum

Output:

z: new position of focus drive

z_relative_move(delta)

Move focus relative to current position. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

delta: distance in mum

Output:

z: new position of focus drive

z_stack_range(experiment_path=None, experiment_name=None)

Function to get the range of first z-stack in experiment. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

none

z_up_relative(delta)

Move focus relative to current position towards sample. Included for parity between Microscope connections.

Raises HardwareCommandNotDefinedError.

Input:

delta: absolute distance in mum

Output:

z: new position of focus drive

microscope_automation.connectors.connect_slidebook.show_image(image, meta_data)

Show image

microscope_automation.connectors.connect_zen_black module

microscope_automation.connectors.connect_zen_blue module

Communication layer for Zen Blue API Date Created: June 09, 2016

class microscope_automation.connectors.connect_zen_blue.ConnectMicroscope(connect_dll=True)

Bases: object

Simulation: Connect to Carl Zeiss ZEN blue Python API.

To be able to use ZEN services in a COM environment, the ZEN functionality must be registered as follows as administrator (right click when opening command prompt to run as administrator) (you might have to update versions):

pushd “C:WindowsMicrosoft.NETFramework64v4.0.30319” SET dll-1=”C:Program FilesCarl ZeissZEN 2ZEN 2 (blue edition)Zeiss.Micro.Scripting.dll” regasm /u /codebase /tlb %dll-1% regasm /codebase /tlb %dll-1%

SET dll-2=”C:Program FilesCarl ZeissZEN 2ZEN 2 (blue edition)Zeiss.Micro.LM.Scripting.dll” regasm /u /codebase /tlb %dll-2% regasm /codebase /tlb %dll-2% popd

close_experiment(experiment=None)

Closes experiment and forces reload.

Input:

experiment: string with name of experiment defined within Microscope software

Output:

none

create_experiment_path(experiment, experiment_folder)

Creates complete path to experiment. Raises exception if experiment does not exist

Input:

experiment: string with name of experiment (with or w/o extension .czexp)

experiment_folder: folder for capture settings

Output:

experiment_path: path to experiment

execute_experiment(experiment=None, pos_list=None)

Execute experiments with parameters defined in experiment. Image object is stored in self.image. Takes all images that are part of experiment (e.g. all slices).

Input:

experiment: string with name of experiment defined within Microscope software. If None use actual experiment.

pos_list: if experiment has tiles enabled execute experiment at positions [(x1, y1, z1), (x2 …]. Supports only one block experiments.

Output:

none

find_autofocus(experiment)

Focus with ZEN software autofocus.

Input:

experiment: string with name for experiment defined in ZEN

Output:

zPos: position of focus drive after autofocus

find_surface()

Find cover slip using Definite Focus 2.

Input:

none

Output:

z: position of focus drive after find surface

get_all_objectives(n_positions)

Retrieve name and magnification of all objectives. Warning! The objectives will move.

Input:

n_positions: number of objective positions

Output:

objectives_dict: dictionary of all objectives mounted at microscope in form {‘magnification’: {‘Position’: position, ‘Name’: name}

get_autofocus_ready()

Check if auto focus position for DF2 was stored and recall_focus should work.

Raises AutofocusNotSetError if not ready. Raises AutofocusObjectiveChangedError if there is an issue with objective_name

Input:

none

Output:

ready: True if DF2 was initialized and recall_focus should work.

get_experiment_folder()

Return path to user specific experiment file.

Input:

none

Output:

experiment_path: path to experiment file

get_focus_pos()

Return current position of focus drive.

Input:

none

Output:

zPos: position of focus drive in micrometer

get_focus_settings(experiment_path, experiment_name)

Function to get the focus settings used in the experiment

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

focus_settings: All instances of focus settings in experiment file

get_last_known_focus_position()

Retrieves focus position used for recovery if autofocus fails. Will raise AutofocusNotSetError exception if not defined

Input:

focusPostion: position in um to be used for autofocus recovery

Output:

none.

get_microscope_name()

Returns name of the microscope from hardware that is controlled by this class.

Input:

none

Output:

Microscope: name of Microscope

get_objective_magnification()

Get magnification of actual objective.

Input:

none

Output:

magnification: magnification of actual objective, objective in imaging position

get_objective_name()

Get name of actual objective.

Input:

none

Output:

name: name of actual objective, objective in imaging position

get_objective_position()

Get position of actual objective.

Input:

none

Output:

position: position of actual objective, objective in imaging position

get_objective_position_from_experiment_file(experiment_path, experiment_name)

Function to get the position of the objective used in the experiment

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

position: the integer position of the objective

get_stage_pos()

Return current position of Microscope stage.

Input:

none

Output:

xPos, yPos: x and y position of stage in micrometer

is_tile_scan(experiment_path=None, experiment_name=None)

Function to check if the experiment is a tile scan

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

tile_scan_bool: bool describing if the experiment contains a tile scan

is_z_stack(experiment_path=None, experiment_name=None)

Function to check if the experiment is a z-stack experiment

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

z_stack_experiment: bool describing if the experiment acquires a z stack

live_mode_start(experiment=None)

Start live mode of ZEN software.

Input:

experiment: name of ZEN experiment (default = None)

Output:

imgLive: image of type ZenImage

live_mode_stop(experiment=None)

Stop live mode of ZEN software.

Input:

experiment: name of ZEN experiment (default = None)

Output:

none

load_image(image, get_meta=False)

Load image using aicsimage and return it a class ImageAICS

Input:

image: image object of class ImageAICS. Holds meta data at this moment, no image data.

get_meta: if true, retrieve meta data from file. Default is False

Output:

image: image with data and meta data as ImageAICS class

move_focus_to(zPos)

Move focus to new position.

Input:

zPos, yPos: new focus position in micrometers.

move_focus_to_load()

Move focus to load position if defined.

Input:

zPos, yPos: new focus position in micrometers.

move_focus_to_work()

Move focus to work position if defined.

Input:

zPos, yPos: new focus position in micrometers.

Output:

none

move_stage_to(xPos, yPos, zPos=None, experiment=None, test=False)

Move stage to new position.

Input:

xPos, yPos: new stage position in micrometers.

zPos, experiment: not used but included for consistency with Slidebook API

test: if True return travel path and do not move stage

Output:

xPos, yPos: x and y position of stage in micrometer after stage movement (if test = False)

x_path, y_path: projected travel path (if test = True)

recall_focus(pre_set_focus=True)

Find stored focus position as offset from coverslip. Stored focus position is lost when switching objective, even when returning to original objective.

Input:

pre_set_focus: Move focus to previous auto-focus position. This makes definite focus more robust

Output:

z: position of focus drive after recall focus

recover_focus()

Try to recover from autofocus failure.

Input:

none

Output:

none

remove_all()

Remove all images from display within ZEN software.

Input:

none

Output:

none

run_macro(macro_name, macro_param=None, trials=3)

Function to run a given Zen Blue Macro

Input:

macro_name: name of the macro

macro_param: parameters to pass into the macro

trials: maximum number of attempts to run the macro. Gives user the option to fix any errors that arise.

Output:

none

save_image(fileName)

Save last acquired ImageAICS in original file format using microscope software.

Input:

file: file name and path for ImageAICS save

set_autofocus_not_ready()

Set flag that auto focus position for DF2 is not ready and recall_focus will not work.

Input:

none

Output:

none

set_autofocus_ready()

Set flag that auto focus position for DF2 was stored and recall_focus should work.

Input:

none

Output:

none

set_experiment(experiment=None, pos_list=None)

Sets the experiment with ZEN API

Input:

experiment: string with name of experiment defined within Microscope software. If None use actual experiment.

pos_list: if experiment has tiles enabled execute experiment at positions [(x1, y1, z1), (x2 …]. Supports only one block experiments.

Output:

exp_class: the instance of the experiment returned by ZEN API

set_focus_load_position()

retrieve current position and set as load position.

Input:

none

Output:

zLoad: current focus position in mum

set_focus_work_position()

retrieve current position and set as work position.

Input:

none

Output:

z_work: current focus position in mum

set_last_known_focus_position(focusPostion)

Stores focus position used for recovery if autofocus fails.

Input:

focusPostion: position in um to be used for autofocus recovery

Output:

none.

show_image()

Display last acquired image in ZEN software.

Input:

none

Output:

none

snap_image(experiment=None)

Snap image with parameters defined in experiment. Image object is stored in self.image. Acquires single image from experiment (e.g. single slice of stack).

Input:

experiment: string with name of experiment as defined within Microscope software. If None use active experiment.

Output:

none

stop()

Stop Microscope immediately

store_focus()

Store actual focus position as offset from coverslip. Stored focus position is lost when switching objective, even when returning to original objective.

Input:

none

Output:

z: position of focus drive after store focus

switch_objective(targetPosition, load=True)

Switches objective.

Input:

targetPosition: Position of new objective on objective switcher

load: if True, move objective to load position before switching. Default: True

Output:

objectiveName: name of new objective

trigger_pump(seconds, port='COM1', baudrate=19200)

Trigger pump

Input:

seconds: the number of seconds pump is activated

port: com port, default = ‘COM1’

baudrate: baudrate for connection, can be set on pump, typically = 19200

Output:

none

update_tile_positions(experiment_path, experiment_name, x_value, y_value, z_value)

Function to define the position of the tile

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

x_value: float (x - coordinate)

y_value: float (y - coordinate)

z_value: float (z - coordinate)

Output:

none

validate_experiment(experiment_path=None, experiment_name=None)

Function to check if the experiment is defined in the Zen blue software

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

valid_experiment: bool describing if the experiment is valid

wait_for_experiment(experiment)

Wait until experimentis active experiment.

Input:

experiment: string with name of experiment defined within Microscope software.

Output:

none

wait_for_objective(target_objective)

Wait until objective is in place.

Input:

target_objective: string with name of objective.

Output:

None

z_down_relative(delta)

Move focus relative to current position away from sample.

Input:

delta: absolute distance in mum

Output:

z: new position of focus drive

z_relative_move(delta)

Move focus relative to current position.

Input:

delta: distance in mum

Output:

z: new position of focus drive

z_stack_range(experiment_path=None, experiment_name=None)

Function to get the range of first z-stack in experiment.

Input:

experiment_path: path of the experiment file

experiment_name: name of the experiment

Output:

zstack_range: range of the z-stack

z_up_relative(delta)

Move focus relative to current position towards sample.

Input:

delta: absolute distance in mum

Output:

z: new position of focus drive

microscope_automation.connectors.connect_zen_blue.test_connect_zen_blue(test=['test_definite_focus', 'execute_experiment', 'snap_image', 'get_all_objectives', 'trigger_pump', 'test_focus', 'save_image', 'test_stage'])

Test suite to test module with Zeiss SD hardware or test hardware.

Input:

test: list with tests to perform

Output:

success: True when test was passed

microscope_automation.connectors.connect_zen_blue.test_definite_focus(microscope, interactive=False)

Test DefiniteFocus 2 with ZEN Blue on spinning disk.

Input:

microscope: instance of class ConnectMicroscope interactive: if true allow input from microscope

Output:

success: True when test was passed

microscope_automation.connectors.connect_zen_blue_dummy module

Dummy function for ZEN blue conection Created on Sep 23, 2016

@author: winfriedw

class microscope_automation.connectors.connect_zen_blue_dummy.Acquisition(microscope_status)

Bases: object

Simulate image acquisition

AcquireImage_3(expClass)

Execute(experiment)

FindAutoFocus()

Use the autofocus of the current experiment to find the sample.

Input:

none

Output:

none

FindAutoFocus_2(experiment)

Use the autofocus of the current experiment to find the sample.

Input:

experiment: String name of experiment in ZEN blue software

Output:

none

FindSurface()

Finds the surface using definite focus.

Input:

none

Output:

none

RecallFocus()

Finds the surface + offset.

Input:

none

Output

none

StartLive()

StartLive_2(experiment)

StopLive()

StopLive_2(expClass)

StoreFocus()

Initializes the definite focus on the current position.

Input:

none

Output:

none

class microscope_automation.connectors.connect_zen_blue_dummy.Application(microscope_status)

Bases: object

Pause(message)

RunMacro(macro_name)

RunMacro_2(macro_name, macro_params)

class microscope_automation.connectors.connect_zen_blue_dummy.Devices(microscope_status)

Bases: object

Simulated device objects

class microscope_automation.connectors.connect_zen_blue_dummy.Documents

Bases: object

Add(image)

RemoveAll(remove)

class microscope_automation.connectors.connect_zen_blue_dummy.Experiments(microscope_status)

Bases: object

ActiveExperiment()

Contains(expClass)

GetByName(experiment)

class microscope_automation.connectors.connect_zen_blue_dummy.Focus(microscope_status)

Bases: object

property ActualPosition

Get the current z position for focus drive

Apply()

Applies the target parameter values.

Input:

none

Output:

none

MoveTo(z)

Moves to the specified focus position.

Input:

z: Focus position in um

Output:

none

class microscope_automation.connectors.connect_zen_blue_dummy.GetActiveObject(name)

Bases: object

Simulation for connection to ZEN blue software.

class microscope_automation.connectors.connect_zen_blue_dummy.Image

Bases: object

Save_2(fileName)

class microscope_automation.connectors.connect_zen_blue_dummy.MicroscopeStatus

Bases: object

Create instance of this class to keeps track of microscope status.

Input:

none

Output:

none

property objective_name

Get name for actual objective

property objective_position

Get position for objective in objective changer

property xPos

Get absolute x position for stage

property yPos

Get absolute y position for stage

property zPos

Get absolute z position for focus drive

class microscope_automation.connectors.connect_zen_blue_dummy.ObjectiveChanger(microscope_status)

Bases: object

property ActualPosition

Get name of actual objective position in ojbective turret

property ActualPositionName

Get name of actual objectve

Apply()

GetMagnificationByPosition(position)

GetNameByPosition(position)

class microscope_automation.connectors.connect_zen_blue_dummy.Stage(microscope_status)

Bases: object

property ActualPositionX

Get actual x position for stage

property ActualPositionY

Get actual y position for stage

Apply()

Module contents

Connectors package for Microscope Automation.