Index

_

__init__() (acquisition_array_class.acquisition_arrays method) (automated_microscopy.drift_correction.drift_correction method) (automated_microscopy.image_deposit.images_InMemory_class method) (automated_microscopy.template_matching.automated_templateMatching method) (auxiliary_code.concurrency_tools.CustodyThread method) (auxiliary_code.concurrency_tools.ObjectInSubprocess method) (auxiliary_code.concurrency_tools.ResultThread method) (auxiliary_code.write_parameters.write_Params method) (gui.advancedsettings_window.AdvancedSettings_Tab method) (gui.main_window.MultiScope_MainGui method) (gui.run_window.Run_Tab method) (gui.smart_window.SmartMicroscopySettings_Tab method) (gui.stages_window.Stages_Tab method) (gui.Welcome_window.Welcome_Tab method) (multiScale_main.MultiScale_Microscope_Controller method) (multiScope.multiScopeModel method) (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthentic_cam_object method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) (src.filter_wheel.ludlcontrol.LudlFilterwheel method) (src.filter_wheel.Synthetic_Filterwheel.Synthetic_Filterwheel method) (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) (src.slit.slit_cmd.slit_ximc_control method) (src.stages.rotation_stage_cmd.SR2812_rotationstage method) (src.stages.synthetic_rotation_stage.Synthetic_rotationstage method) (src.stages.synthetic_translation_stage.Synthetic_translationstage method) (src.stages.translation_stage_cmd.SLC_translationstage method)

A

abort_stack() (multiScale_main.MultiScale_Microscope_Controller method) abort_timelapse() (multiScale_main.MultiScale_Microscope_Controller method) acquire_stack() (multiScale_main.MultiScale_Microscope_Controller method) acquire_stack_highres() (multiScope.multiScopeModel method) acquire_stack_lowres() (multiScope.multiScopeModel method) acquire_stack_task() (multiScale_main.MultiScale_Microscope_Controller method) acquire_timelapse() (multiScale_main.MultiScale_Microscope_Controller method) acquire_timelapse_task() (multiScale_main.MultiScale_Microscope_Controller method) acquisition_array_class module acquisition_arrays (class in acquisition_array_class) addhighresPos() (gui.stages_window.Stages_Tab method) addlowresPos() (gui.stages_window.Stages_Tab method) addNewImage() (automated_microscopy.image_deposit.images_InMemory_class method) adjustableslit_max (auxiliary_code.constants.Stage_parameters attribute) adjustmentfactor (auxiliary_code.constants.NI_board_parameters attribute) AdvancedSettings_Tab (class in gui.advancedsettings_window) Analog_Out (class in src.ni_board.ni_synthetic) (class in src.ni_board.vni) ao_nchannels (auxiliary_code.constants.NI_board_parameters attribute) ao_type (auxiliary_code.constants.NI_board_parameters attribute) ao_type_constant (auxiliary_code.constants.NI_board_parameters attribute)

ASLM_parameters (class in auxiliary_code.constants) assert_lib_compatibility() (src.stages.translation_stage_cmd.SLC_translationstage method) automated_microscopy module automated_microscopy.drift_correction module automated_microscopy.image_deposit module automated_microscopy.template_matching module automated_templateMatching (class in automated_microscopy.template_matching) auxiliary_code module auxiliary_code.concurrency_tools module auxiliary_code.constants module auxiliary_code.napari_in_subprocess module auxiliary_code.write_parameters module avail_filters (auxiliary_code.constants.FilterWheel_parameters attribute)

C

calculate_ASLMparameters() (multiScope.multiScopeModel method) calculate_axialdrift() (automated_microscopy.drift_correction.drift_correction method) calculate_Lateral_drift() (automated_microscopy.drift_correction.drift_correction method) calculate_pixelcoord_from_physicalcoordinates() (automated_microscopy.drift_correction.drift_correction method) Camera_parameters (class in auxiliary_code.constants) change_angle() (gui.stages_window.Stages_Tab method) change_currentposition() (gui.stages_window.Stages_Tab method) change_voltage() (gui.advancedsettings_window.AdvancedSettings_Tab method) changefilter() (multiScale_main.MultiScale_Microscope_Controller method) changeHRtoLR() (multiScope.multiScopeModel method) changeLRtoHR() (multiScope.multiScopeModel method) changeROI() (multiScale_main.MultiScale_Microscope_Controller method) check_error() (in module src.ni_board.vni) check_movementboundaries() (multiScope.multiScopeModel method)

close() (multiScale_main.MultiScale_Microscope_Controller method) (multiScope.multiScopeModel method) (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthentic_cam_object method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) (src.filter_wheel.ludlcontrol.LudlFilterwheel method) (src.filter_wheel.Synthetic_Filterwheel.Synthetic_Filterwheel method) (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) (src.stages.rotation_stage_cmd.SR2812_rotationstage method) (src.stages.synthetic_rotation_stage.Synthetic_rotationstage method) (src.stages.synthetic_translation_stage.Synthetic_translationstage method) (src.stages.translation_stage_cmd.SLC_translationstage method) comport (auxiliary_code.constants.FilterWheel_parameters attribute) CustodyThread (class in auxiliary_code.concurrency_tools)

D

deletehighresPos() (gui.stages_window.Stages_Tab method) deletelowresPos() (gui.stages_window.Stages_Tab method) deleteme() (gui.Welcome_window.Welcome_Tab method) disable_keyboard_movement() (multiScale_main.MultiScale_Microscope_Controller method)

disktosave (auxiliary_code.constants.microscope_configuration attribute) display() (in module auxiliary_code.napari_in_subprocess) display_tree() (gui.stages_window.Stages_Tab method) drift_correction (class in automated_microscopy.drift_correction)

E

enable_keyboard_movement() (multiScale_main.MultiScale_Microscope_Controller method) end_preview() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method)

ExitIfError() (src.stages.rotation_stage_cmd.SR2812_rotationstage method)

F

filterwheel (auxiliary_code.constants.microscope_configuration attribute) FilterWheel_parameters (class in auxiliary_code.constants) find_closestLowResTile() (automated_microscopy.drift_correction.drift_correction method) find_corresponsingHighResTiles() (automated_microscopy.drift_correction.drift_correction method)

findReference() (src.stages.synthetic_translation_stage.Synthetic_translationstage method) (src.stages.translation_stage_cmd.SLC_translationstage method) finish() (src.camera.Synthetic_camera.Synthentic_cam_object method) flip_mirror_line (auxiliary_code.constants.NI_board_parameters attribute)

G

get_highresASLM_preview_array() (acquisition_array_class.acquisition_arrays method) get_highResASLM_StackAq_array() (acquisition_array_class.acquisition_arrays method) get_highresSPIM_preview_array() (acquisition_array_class.acquisition_arrays method) get_highResSPIM_StackAq_array() (acquisition_array_class.acquisition_arrays method) get_imageroi() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) get_lowres_preview_array() (acquisition_array_class.acquisition_arrays method) get_lowRes_StackAq_array() (acquisition_array_class.acquisition_arrays method) get_result() (auxiliary_code.concurrency_tools.ResultThread method) getAngle() (src.stages.rotation_stage_cmd.SR2812_rotationstage method) (src.stages.synthetic_rotation_stage.Synthetic_rotationstage method) getwelcome_parameters() (gui.Welcome_window.Welcome_Tab method) gui module

gui.advancedsettings_window module gui.main_window module gui.run_window module gui.smart_window module gui.stages_window module gui.Welcome_window module

H

highres_camera (auxiliary_code.constants.microscope_configuration attribute) (auxiliary_code.constants.NI_board_parameters attribute) highres_line_digitization_time (auxiliary_code.constants.Camera_parameters attribute)

home_stage() (src.slit.slit_cmd.slit_ximc_control method) HR_height_pixel (auxiliary_code.constants.Camera_parameters attribute) HR_width_pixel (auxiliary_code.constants.Camera_parameters attribute)

I

Image_parameters (class in auxiliary_code.constants) image_retrieval() (automated_microscopy.image_deposit.images_InMemory_class method) images_InMemory_class (class in automated_microscopy.image_deposit)

indicate_driftcorrectionCompleted() (automated_microscopy.drift_correction.drift_correction method) init_previewbuffer() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method)

K

key_pressed() (multiScale_main.MultiScale_Microscope_Controller method)

L

laser488 (auxiliary_code.constants.NI_board_parameters attribute) laser552 (auxiliary_code.constants.NI_board_parameters attribute) laser594 (auxiliary_code.constants.NI_board_parameters attribute) laser640 (auxiliary_code.constants.NI_board_parameters attribute) led (auxiliary_code.constants.NI_board_parameters attribute) LED_line (auxiliary_code.constants.NI_board_parameters attribute) line_selection (auxiliary_code.constants.NI_board_parameters attribute) loadhighresPosList() (gui.stages_window.Stages_Tab method)

loadlowresPosList() (gui.stages_window.Stages_Tab method) low_to_highres_calibration_height (auxiliary_code.constants.Camera_parameters attribute) low_to_highres_calibration_width (auxiliary_code.constants.Camera_parameters attribute) lowres_camera (auxiliary_code.constants.microscope_configuration attribute) (auxiliary_code.constants.NI_board_parameters attribute) lowres_line_digitization_time (auxiliary_code.constants.Camera_parameters attribute) LR_height_pixel (auxiliary_code.constants.Camera_parameters attribute) LR_width_pixel (auxiliary_code.constants.Camera_parameters attribute) LudlFilterwheel (class in src.filter_wheel.ludlcontrol)

M

makeMosaic() (gui.stages_window.Stages_Tab method) ManualMove() (src.stages.rotation_stage_cmd.SR2812_rotationstage method) max_mSPIM_constant (auxiliary_code.constants.NI_board_parameters attribute) maxVol_constant (auxiliary_code.constants.NI_board_parameters attribute) microscope_configuration (class in auxiliary_code.constants) minVol_constant (auxiliary_code.constants.NI_board_parameters attribute) module acquisition_array_class automated_microscopy automated_microscopy.drift_correction automated_microscopy.image_deposit automated_microscopy.template_matching auxiliary_code auxiliary_code.concurrency_tools auxiliary_code.constants auxiliary_code.napari_in_subprocess auxiliary_code.write_parameters gui gui.advancedsettings_window gui.main_window gui.run_window gui.smart_window gui.stages_window gui.Welcome_window multiScale_main multiScope src src.camera src.camera.Photometrics_camera src.camera.Synthetic_camera src.filter_wheel src.filter_wheel.ludlcontrol src.filter_wheel.Synthetic_Filterwheel src.ni_board src.ni_board.ni_synthetic src.ni_board.vni src.slit src.slit.slit_cmd src.stages src.stages.rotation_stage_cmd src.stages.synthetic_rotation_stage src.stages.synthetic_translation_stage src.stages.translation_stage_cmd

move_to_position() (multiScope.multiScopeModel method) movestage() (multiScale_main.MultiScale_Microscope_Controller method) movestageToPosition() (multiScale_main.MultiScale_Microscope_Controller method) moveToAngle() (src.stages.rotation_stage_cmd.SR2812_rotationstage method) (src.stages.synthetic_rotation_stage.Synthetic_rotationstage method) moveToPosition() (src.stages.synthetic_translation_stage.Synthetic_translationstage method) (src.stages.translation_stage_cmd.SLC_translationstage method) mSPIM_mirror_line (auxiliary_code.constants.NI_board_parameters attribute) mSPIM_mirror_voltage (auxiliary_code.constants.NI_board_parameters attribute) multiScale_main module MultiScale_Microscope_Controller (class in multiScale_main) multiScope module MultiScope_MainGui (class in gui.main_window) multiScopeModel (class in multiScope)

N

ni_board (auxiliary_code.constants.microscope_configuration attribute)

NI_board_parameters (class in auxiliary_code.constants)

O

ObjectInSubprocess (class in auxiliary_code.concurrency_tools)

open() (src.camera.Synthetic_camera.Synthentic_cam_object method)

P

p2s() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) parentdir (auxiliary_code.constants.microscope_configuration attribute) Photo_Camera (class in src.camera.Photometrics_camera) play_voltages() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) poll_frame() (src.camera.Synthetic_camera.Synthentic_cam_object method) power_488_line (auxiliary_code.constants.NI_board_parameters attribute) power_552_line (auxiliary_code.constants.NI_board_parameters attribute) power_594_line (auxiliary_code.constants.NI_board_parameters attribute) power_640_line (auxiliary_code.constants.NI_board_parameters attribute)

prepare_acquisition() (multiScope.multiScopeModel method) prepare_ASLM_acquisition() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) prepare_stack_acquisition_highres() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) prepare_stack_acquisition_lowres() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) preview_change() (gui.run_window.Run_Tab method) preview_filter_select() (gui.run_window.Run_Tab method) preview_highres_ASLM() (multiScope.multiScopeModel method) preview_highres_static() (multiScope.multiScopeModel method) preview_lowres() (multiScope.multiScopeModel method)

R

random() (in module automated_microscopy.template_matching) rate (auxiliary_code.constants.NI_board_parameters attribute) register_image() (automated_microscopy.drift_correction.drift_correction method) remote_mirror_maxVol (auxiliary_code.constants.ASLM_parameters attribute) remote_mirror_minVol (auxiliary_code.constants.ASLM_parameters attribute) replaceImage() (automated_microscopy.image_deposit.images_InMemory_class method) reset() (automated_microscopy.image_deposit.images_InMemory_class method) reset_rois() (src.camera.Synthetic_camera.Synthentic_cam_object method) ResultThread (class in auxiliary_code.concurrency_tools) reverthighresList() (gui.stages_window.Stages_Tab method) revertlowresList() (gui.stages_window.Stages_Tab method) rotationstage (auxiliary_code.constants.microscope_configuration attribute)

run() (auxiliary_code.concurrency_tools.ResultThread method) (multiScale_main.MultiScale_Microscope_Controller method) run_highrespreview() (multiScale_main.MultiScale_Microscope_Controller method) run_lowrespreview() (multiScale_main.MultiScale_Microscope_Controller method) run_preview_highres() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) run_preview_lowres() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) run_stack_acquisition_buffer_fast() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) run_stop_preview() (multiScale_main.MultiScale_Microscope_Controller method) Run_Tab (class in gui.run_window)

S

s2p() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) s2s() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) save_currentpositionToFile() (multiScope.multiScopeModel method) savehighresPosList() (gui.stages_window.Stages_Tab method) savelowresPosList() (gui.stages_window.Stages_Tab method) scaling_templateMatching() (automated_microscopy.template_matching.automated_templateMatching method) scaling_templateMatching_multiprocessing() (automated_microscopy.template_matching.automated_templateMatching method) set_filter() (src.filter_wheel.ludlcontrol.LudlFilterwheel method) (src.filter_wheel.Synthetic_Filterwheel.Synthetic_Filterwheel method) set_imageroi() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) set_laserpower() (multiScope.multiScopeModel method) set_rate() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) set_roi() (src.camera.Synthetic_camera.Synthentic_cam_object method) set_up_highrespreview() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) set_up_lowres_preview() (src.camera.Photometrics_camera.Photo_Camera method) (src.camera.Synthetic_camera.Synthetic_Photo_Camera method) set_verbose() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) setconstantvoltage() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method) shape() (src.camera.Synthetic_camera.Synthentic_cam_object method) SharedNDArray (class in auxiliary_code.concurrency_tools) simple_templateMatching() (automated_microscopy.template_matching.automated_templateMatching method) simultaneous_lines (auxiliary_code.constants.ASLM_parameters attribute) SLC_translationstage (class in src.stages.translation_stage_cmd) slit_closing() (src.slit.slit_cmd.slit_ximc_control method) slit_get_position() (src.slit.slit_cmd.slit_ximc_control method) slit_get_speed() (src.slit.slit_cmd.slit_ximc_control method) slit_info() (src.slit.slit_cmd.slit_ximc_control method) slit_move() (src.slit.slit_cmd.slit_ximc_control method) slit_serial() (src.slit.slit_cmd.slit_ximc_control method) slit_set_microstep_mode_256() (src.slit.slit_cmd.slit_ximc_control method) slit_set_speed() (src.slit.slit_cmd.slit_ximc_control method) slit_status() (src.slit.slit_cmd.slit_ximc_control method) slit_wait_for_stop() (src.slit.slit_cmd.slit_ximc_control method) slit_ximc_control (class in src.slit.slit_cmd) SmartMicroscopySettings_Tab (class in gui.smart_window) smooth_sawtooth() (multiScope.multiScopeModel method) SR2812_rotationstage (class in src.stages.rotation_stage_cmd) src module src.camera module

src.camera.Photometrics_camera module src.camera.Synthetic_camera module src.filter_wheel module src.filter_wheel.ludlcontrol module src.filter_wheel.Synthetic_Filterwheel module src.ni_board module src.ni_board.ni_synthetic module src.ni_board.vni module src.slit module src.slit.slit_cmd module src.stages module src.stages.rotation_stage_cmd module src.stages.synthetic_rotation_stage module src.stages.synthetic_translation_stage module src.stages.translation_stage_cmd module stack_acquisition_master() (multiScope.multiScopeModel method) stage (auxiliary_code.constants.NI_board_parameters attribute) stage_id_rot (auxiliary_code.constants.Stage_parameters attribute) stage_id_XYZ (auxiliary_code.constants.Stage_parameters attribute) Stage_parameters (class in auxiliary_code.constants) Stages_Tab (class in gui.stages_window) start() (auxiliary_code.concurrency_tools.ResultThread method) start_live() (src.camera.Synthetic_camera.Synthentic_cam_object method) streamStackAcquisition_externalTrigger_setup() (src.stages.synthetic_translation_stage.Synthetic_translationstage method) (src.stages.translation_stage_cmd.SLC_translationstage method) streamStackAcquisition_externalTrigger_waitEnd() (src.stages.synthetic_translation_stage.Synthetic_translationstage method) (src.stages.translation_stage_cmd.SLC_translationstage method) Synthentic_cam_object (class in src.camera.Synthetic_camera) Synthetic_Filterwheel (class in src.filter_wheel.Synthetic_Filterwheel) Synthetic_Photo_Camera (class in src.camera.Synthetic_camera) Synthetic_rotationstage (class in src.stages.synthetic_rotation_stage) Synthetic_translationstage (class in src.stages.synthetic_translation_stage)

T

template_processing_subprocess() (automated_microscopy.template_matching.automated_templateMatching method)

translationstage (auxiliary_code.constants.microscope_configuration attribute)

U

update_ASLMParameters() (multiScale_main.MultiScale_Microscope_Controller method) update_bufferSize() (multiScope.multiScopeModel method) update_stack_aq_parameters() (multiScale_main.MultiScale_Microscope_Controller method) update_stage_trans_stepsize() (gui.stages_window.Stages_Tab method) updateDriftCorrectionSettings() (multiScale_main.MultiScale_Microscope_Controller method)

updateExposureParameters() (multiScale_main.MultiScale_Microscope_Controller method) updatefilename() (multiScale_main.MultiScale_Microscope_Controller method) updateHighResLaserParameters() (multiScale_main.MultiScale_Microscope_Controller method) updateLowResLaserParameters() (multiScale_main.MultiScale_Microscope_Controller method) updatepreview() (multiScale_main.MultiScale_Microscope_Controller method) updateTimesTimelapse() (gui.run_window.Run_Tab method)

V

voicecoil (auxiliary_code.constants.NI_board_parameters attribute)

W

Welcome_Tab (class in gui.Welcome_window) write_Params (class in auxiliary_code.write_parameters)

write_to_textfile() (auxiliary_code.write_parameters.write_Params method) write_voltages() (src.ni_board.ni_synthetic.Analog_Out method) (src.ni_board.vni.Analog_Out method)

X

xy_pixelsize_highres_um (auxiliary_code.constants.Image_parameters attribute)

xy_pixelsize_lowres_um (auxiliary_code.constants.Image_parameters attribute)