multiScope module

class multiScope.multiScopeModel

Bases: object

The main model class of the multi-scale microscope. Here all hardware components are initialized, started/controlled.

__init__()

Initialize the multiScopeModel.

acquire_stack_highres(current_startposition, current_laserline, filepath, modality)

Starts a custody thread to run a high-resolution stack acquisition (SPIM or ASLM). Also updates the buffer used.

Parameters:

  • current_startposition – start position for the stack acquisition

  • current_laserline – which wavelength is acquired.

  • filepath – filepath to save acquired low-resolution image stack.

  • modality – ASLM or SPIM?

acquire_stack_lowres(current_startposition, current_laserline, filepath)

Starts a custody thread to run a low-resolution stack acquisition. Also updates the buffer used.

Parameters:

  • current_startposition – start position for the stack acquisition

  • current_laserline – which wavelength is acquired.

  • filepath – filepath to save acquired low-resolution image stack.

calculate_ASLMparameters(desired_exposuretime)

Calculate and set the parameters for an ASLM acquisition.

Parameters:

desired_exposuretime – the exposure time that is desired for the whole acquisition

changeHRtoLR()

Change the microscope from a high-resolution to a low-resolution acquisition configuration (flip mirror)

changeLRtoHR()

Change the microscope from a low-resolution to a high-resolution acquisition configuration (flip mirror)

check_movementboundaries(array)

Define here the movement boundaries of your stage system.

Parameters:

array – [axialPosition, lateralPosition, updownPosition, anglePosition], a list of position the stages moves to.

Returns:

an array which has no out of range positions

close()

Close all opened channels, tasks, camera, NI board, stages and display.

move_to_position(positionlist)

Move to specified position according to positionlist

Parameters:

positionlist – list of positions in format, e.g. [44280000, -2000000000, -2587870000]

prepare_acquisition(current_startposition, laser)

Prepare acquisition by moving filter wheel and stage system to the correct position, and updating buffer sizes.

Parameters:

  • current_startposition – position to move the stage to for starting a stack.

  • laser – wavelength to image.

preview_highres_ASLM()

Starts a custody thread to run a high-resolution ASLM preview.

preview_highres_static()

Starts a custody thread to run a high-resolution SPIM preview.

preview_lowres()

Starts a custody thread to run a low-resolution preview.

save_currentpositionToFile(filepath, current_startposition)

Saves current position to file/append it, called by stack_acquisition_master.

Parameters:

  • filepath – filepath to save current position.

  • current_startposition – position to save to file.

set_laserpower(powersettings)

Update the laser intensity by setting the corresponding NI board voltage sent to the laser.

Parameters:

powersettings – np.array with 4 entries for 4 lasers

smooth_sawtooth(array, window_len=101)

Smooth an array with a defined window length.

Parameters:

  • array – Array to smooth

  • window_len – Window length over which to average values.

Returns:

smoothened array.

stack_acquisition_master(current_folder, current_position, whichlaser, resolutionmode)

Start stack acquisitions of different channels and resolution modes, including setting laser powers, saving of start position to file, generation of filepaths, and decides which stack acquisition method to call.

Parameters:

  • current_folder – folder to save the acquired data

  • current_position – start position for the stack streaming

  • whichlaser – which channels to image

  • resolutionmode – which scale, options: low, highASLM, highSPIM

update_bufferSize()

This handles the size of the buffers during acquisitions. For example, if there is a change in plane number or ROI, updates the buffers accordingly.