Index

_

__init__() (eda_plugin.actuators.micro_manager.DirectMMAcquisition method) (eda_plugin.actuators.micro_manager.MMAcquisition method) (eda_plugin.actuators.micro_manager.MMActuator method) (eda_plugin.actuators.micro_manager.MMActuatorGUI method) (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) (eda_plugin.actuators.pycro.PycroAcquisition method) (eda_plugin.analysers.image.ImageAnalyser method) (eda_plugin.analysers.image.ImageAnalyserWorker method) (eda_plugin.analysers.image.PycroImageAnalyser method) (eda_plugin.analysers.keras.KerasAnalyser method) (eda_plugin.analysers.keras.KerasSettingsGUI method) (eda_plugin.analysers.keras.KerasWorker method) (eda_plugin.examples.analysers.FtsWWorker method) (eda_plugin.examples.analysers.Keras1CWorker method) (eda_plugin.examples.analysers.KerasRescaleWorker method) (eda_plugin.examples.analysers.KerasTester method) (eda_plugin.examples.analysers.KerasTilingWorker method) (eda_plugin.examples.interpreters.FrameRateInterpreter method) (eda_plugin.interpreters.frame_rate.BinaryFrameRateInterpreter method) (eda_plugin.interpreters.frame_rate.BinaryFrameRateParameterForm method) (eda_plugin.interpreters.presets.ParameterForm method) (eda_plugin.interpreters.presets.PresetsInterpreter method) (eda_plugin.utility.data_structures.EDAEvent method) (eda_plugin.utility.data_structures.MMChannel method) (eda_plugin.utility.data_structures.ParameterSet method) (eda_plugin.utility.data_structures.PyImage method) (eda_plugin.utility.eda_gui.EDAMainGUI method) (eda_plugin.utility.eda_gui.EDAPlot method) (eda_plugin.utility.eda_gui.NapariImageViewer method) (eda_plugin.utility.eda_gui.NetworkImageViewer method) (eda_plugin.utility.event_bus.EventBus method) (eda_plugin.utility.ome_metadata.OME method) (eda_plugin.utility.qt_classes.QMainWindowRestore method) (eda_plugin.utility.qt_classes.QWidgetRestore method) (eda_plugin.utility.writers.NumpyEncoder method) (eda_plugin.utility.writers.Writer method) (eda_plugin.utility.writers.WriterGUI method)

A

acquire() (eda_plugin.actuators.micro_manager.DirectMMAcquisition method) (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) acquisition_ended_event (eda_plugin.utility.event_bus.EventBus attribute) acquisition_started_event (eda_plugin.actuators.pycro.PycroAcquisition attribute) (eda_plugin.utility.event_bus.EventBus attribute)

add_datapoint() (eda_plugin.utility.eda_gui.EDAPlot method) add_image() (eda_plugin.utility.eda_gui.NetworkImageViewer method) add_network_image() (eda_plugin.utility.eda_gui.NapariImageViewer method) (eda_plugin.utility.eda_gui.NetworkImageViewer method) add_plane_from_image() (eda_plugin.utility.ome_metadata.OME method)

B

basic() (in module eda_plugin.examples.main)

BinaryFrameRateInterpreter (class in eda_plugin.interpreters.frame_rate) BinaryFrameRateParameterForm (class in eda_plugin.interpreters.frame_rate)

C

calculate_interpretation() (eda_plugin.examples.interpreters.FrameRateInterpreter method) (eda_plugin.interpreters.frame_rate.BinaryFrameRateInterpreter method) (eda_plugin.interpreters.presets.PresetsInterpreter method) calculatePixel() (in module eda_plugin.utility.image_processing) calibrate() (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) call_action() (eda_plugin.actuators.micro_manager.MMActuator method) change_interval() (eda_plugin.actuators.micro_manager.DirectMMAcquisition method) (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) (eda_plugin.actuators.pycro.PycroAcquisition method) channels_from_settings() (eda_plugin.utility.ome_metadata.OME method) check_missing_channels() (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) closeEvent() (eda_plugin.actuators.micro_manager.MMActuatorGUI method) (eda_plugin.analysers.keras.KerasSettingsGUI method) (eda_plugin.interpreters.frame_rate.BinaryFrameRateParameterForm method) (eda_plugin.interpreters.presets.ParameterForm method) (eda_plugin.utility.eda_gui.EDAMainGUI method) (eda_plugin.utility.qt_classes.QMainWindowRestore method) (eda_plugin.utility.qt_classes.QWidgetRestore method) (eda_plugin.utility.writers.WriterGUI method)

configuration_settings_event (eda_plugin.utility.event_bus.EventBus attribute) connect_incoming_events() (eda_plugin.analysers.image.ImageAnalyser method) (eda_plugin.analysers.image.PycroImageAnalyser method) (eda_plugin.analysers.keras.KerasAnalyser method) connect_worker_signals() (eda_plugin.analysers.image.ImageAnalyser method) (eda_plugin.analysers.image.PycroImageAnalyser method) (eda_plugin.analysers.keras.KerasAnalyser method)

D

default() (eda_plugin.utility.writers.NumpyEncoder method) detector_from_settings() (eda_plugin.utility.ome_metadata.OME method)

DirectMMAcquisition (class in eda_plugin.actuators.micro_manager) download_data() (in module eda_plugin.utility.download_data)

E

eda_plugin.actuators module eda_plugin.actuators.micro_manager module eda_plugin.actuators.pycro module eda_plugin.analysers module eda_plugin.analysers.image module eda_plugin.analysers.keras module eda_plugin.examples module eda_plugin.examples.analysers module eda_plugin.examples.data module eda_plugin.examples.interpreters module eda_plugin.examples.main module eda_plugin.interpreters module eda_plugin.interpreters.frame_rate module eda_plugin.interpreters.presets module eda_plugin.utility module

eda_plugin.utility.data_structures module eda_plugin.utility.download_data module eda_plugin.utility.eda_gui module eda_plugin.utility.event_bus module eda_plugin.utility.image_processing module eda_plugin.utility.ome_metadata module eda_plugin.utility.qt_classes module eda_plugin.utility.settings module eda_plugin.utility.writers module EDAEvent (class in eda_plugin.utility.data_structures) EDAMainGUI (class in eda_plugin.utility.eda_gui) EDAPlot (class in eda_plugin.utility.eda_gui) encode() (eda_plugin.utility.writers.NumpyEncoder method) EventBus (class in eda_plugin.utility.event_bus) exposure_changed_event (eda_plugin.utility.event_bus.EventBus attribute) extract_decision_parameter() (eda_plugin.analysers.image.ImageAnalyserWorker method) (eda_plugin.analysers.keras.KerasWorker method) (eda_plugin.examples.analysers.FtsWWorker method) (eda_plugin.examples.analysers.Keras1CWorker method) (eda_plugin.examples.analysers.KerasRescaleWorker method) (eda_plugin.examples.analysers.KerasTester method) (eda_plugin.examples.analysers.KerasTilingWorker method)

F

finalize_metadata() (eda_plugin.utility.ome_metadata.OME method) flavour() (in module eda_plugin.examples.main)

FrameRateInterpreter (class in eda_plugin.examples.interpreters) FtsWWorker (class in eda_plugin.examples.analysers)

G

gather_images() (eda_plugin.analysers.image.ImageAnalyser method) (eda_plugin.analysers.image.PycroImageAnalyser method) (eda_plugin.analysers.keras.KerasAnalyser method) get_channel_information() (eda_plugin.actuators.micro_manager.DirectMMAcquisition method) (eda_plugin.actuators.micro_manager.MMAcquisition method) (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) (eda_plugin.actuators.pycro.PycroAcquisition method)

get_settings() (in module eda_plugin.utility.settings) getTilePositionsV2() (in module eda_plugin.utility.image_processing)

I

ImageAnalyser (class in eda_plugin.analysers.image) ImageAnalyserWorker (class in eda_plugin.analysers.image) init_from_settings() (eda_plugin.utility.ome_metadata.OME method)

install_mm_plugins() (in module eda_plugin.utility.settings) instrument_from_settings() (eda_plugin.utility.ome_metadata.OME method) iterencode() (eda_plugin.utility.writers.NumpyEncoder method)

K

keras() (in module eda_plugin.examples.main) Keras1CWorker (class in eda_plugin.examples.analysers) KerasAnalyser (class in eda_plugin.analysers.keras) KerasRescaleWorker (class in eda_plugin.examples.analysers)

KerasSettingsGUI (class in eda_plugin.analysers.keras) KerasTester (class in eda_plugin.examples.analysers) KerasTilingWorker (class in eda_plugin.examples.analysers) KerasWorker (class in eda_plugin.analysers.keras)

M

main() (in module eda_plugin.analysers.keras) (in module eda_plugin.utility.event_bus) main_isim() (in module eda_plugin.examples.main) mda_settings_event (eda_plugin.utility.event_bus.EventBus attribute) microscope_from_settings() (eda_plugin.utility.ome_metadata.OME method) MMAcquisition (class in eda_plugin.actuators.micro_manager) MMActuator (class in eda_plugin.actuators.micro_manager) MMActuatorGUI (class in eda_plugin.actuators.micro_manager) MMChannel (class in eda_plugin.utility.data_structures) module eda_plugin.actuators eda_plugin.actuators.micro_manager eda_plugin.actuators.pycro eda_plugin.analysers eda_plugin.analysers.image eda_plugin.analysers.keras eda_plugin.examples eda_plugin.examples.analysers eda_plugin.examples.data eda_plugin.examples.interpreters eda_plugin.examples.main eda_plugin.interpreters eda_plugin.interpreters.frame_rate eda_plugin.interpreters.presets eda_plugin.utility eda_plugin.utility.data_structures eda_plugin.utility.download_data eda_plugin.utility.eda_gui eda_plugin.utility.event_bus eda_plugin.utility.image_processing eda_plugin.utility.ome_metadata eda_plugin.utility.qt_classes eda_plugin.utility.settings eda_plugin.utility.writers

N

NapariImageViewer (class in eda_plugin.utility.eda_gui) NetworkImageViewer (class in eda_plugin.utility.eda_gui) new_acquisition_started_event (eda_plugin.utility.event_bus.EventBus attribute) new_decision_parameter (eda_plugin.analysers.image.ImageAnalyser attribute) (eda_plugin.analysers.image.PycroImageAnalyser attribute) (eda_plugin.analysers.keras.KerasAnalyser attribute) (eda_plugin.utility.event_bus.EventBus attribute) new_image (eda_plugin.actuators.pycro.PycroAcquisition attribute) new_interpretation (eda_plugin.examples.interpreters.FrameRateInterpreter attribute) (eda_plugin.interpreters.frame_rate.BinaryFrameRateInterpreter attribute) (eda_plugin.interpreters.presets.PresetsInterpreter attribute) (eda_plugin.utility.event_bus.EventBus attribute)

new_interval (eda_plugin.actuators.micro_manager.MMActuator attribute) new_magellan_settings (eda_plugin.utility.event_bus.EventBus attribute) new_mda_settings() (eda_plugin.analysers.keras.KerasAnalyser method) new_output_shape (eda_plugin.analysers.keras.KerasAnalyser attribute) (eda_plugin.utility.event_bus.EventBus attribute) new_parameters (eda_plugin.interpreters.frame_rate.BinaryFrameRateParameterForm attribute) (eda_plugin.interpreters.presets.ParameterForm attribute) (eda_plugin.interpreters.presets.PresetsInterpreter attribute) new_save_location() (eda_plugin.utility.writers.Writer method) new_settings (eda_plugin.analysers.keras.KerasSettingsGUI attribute) new_settings() (eda_plugin.analysers.keras.KerasAnalyser method) NumpyEncoder (class in eda_plugin.utility.writers)

O

OME (class in eda_plugin.utility.ome_metadata)

P

ParameterForm (class in eda_plugin.interpreters.presets) ParameterSet (class in eda_plugin.utility.data_structures) pixels_after_acqusition() (eda_plugin.utility.ome_metadata.OME method) post_hardware() (eda_plugin.actuators.pycro.PycroAcquisition method) post_process_output() (eda_plugin.analysers.keras.KerasWorker method) (eda_plugin.examples.analysers.FtsWWorker method) (eda_plugin.examples.analysers.Keras1CWorker method) (eda_plugin.examples.analysers.KerasRescaleWorker method) (eda_plugin.examples.analysers.KerasTester method) (eda_plugin.examples.analysers.KerasTilingWorker method) prepare_1c() (in module eda_plugin.utility.image_processing) prepare_ftsw() (in module eda_plugin.utility.image_processing) prepare_images() (eda_plugin.analysers.keras.KerasWorker method) (eda_plugin.examples.analysers.FtsWWorker method) (eda_plugin.examples.analysers.Keras1CWorker method) (eda_plugin.examples.analysers.KerasRescaleWorker method) (eda_plugin.examples.analysers.KerasTester method) (eda_plugin.examples.analysers.KerasTilingWorker method)

prepare_nn_image() (eda_plugin.utility.writers.Writer method) prepare_wo_tiling() (in module eda_plugin.utility.image_processing) prepareNNImages() (in module eda_plugin.utility.image_processing) presets() (in module eda_plugin.examples.main) PresetsInterpreter (class in eda_plugin.interpreters.presets) PycroAcquisition (class in eda_plugin.actuators.pycro) PycroImageAnalyser (class in eda_plugin.analysers.image) PyImage (class in eda_plugin.utility.data_structures) pyro() (in module eda_plugin.examples.main) pyro_keras() (in module eda_plugin.examples.main)

Q

QMainWindowRestore (class in eda_plugin.utility.qt_classes)

QWidgetRestore (class in eda_plugin.utility.qt_classes)

R

receive_image() (eda_plugin.actuators.pycro.PycroAcquisition method) reset_thread() (eda_plugin.actuators.micro_manager.MMActuator method) run() (eda_plugin.analysers.image.ImageAnalyserWorker method) (eda_plugin.analysers.keras.KerasWorker method) (eda_plugin.examples.analysers.FtsWWorker method) (eda_plugin.examples.analysers.Keras1CWorker method) (eda_plugin.examples.analysers.KerasRescaleWorker method) (eda_plugin.examples.analysers.KerasTester method) (eda_plugin.examples.analysers.KerasTilingWorker method)

S

save_decision_parameter() (eda_plugin.utility.writers.Writer method) save_image() (eda_plugin.utility.writers.Writer method) save_imagej_metadata() (eda_plugin.utility.writers.Writer method) save_metadata() (eda_plugin.utility.writers.Writer method) save_mmacq_settings() (eda_plugin.utility.writers.Writer method) save_mmdev_settings() (eda_plugin.utility.writers.Writer method) save_network_image() (eda_plugin.utility.writers.Writer method) save_ome_metadata() (eda_plugin.utility.writers.Writer method) save_thresholds() (eda_plugin.utility.writers.Writer method) screen_images() (eda_plugin.utility.eda_gui.NetworkImageViewer method) set_settings() (in module eda_plugin.utility.settings) setup_logging() (in module eda_plugin.utility.settings) start() (eda_plugin.actuators.micro_manager.DirectMMAcquisition method) (eda_plugin.actuators.micro_manager.MMAcquisition method) (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) (eda_plugin.actuators.pycro.PycroAcquisition method)

start_acq() (eda_plugin.actuators.micro_manager.DirectMMAcquisition method) (eda_plugin.actuators.micro_manager.MMAcquisition method) (eda_plugin.actuators.micro_manager.MMActuator method) (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) (eda_plugin.actuators.pycro.PycroAcquisition method) start_acq_signal (eda_plugin.actuators.micro_manager.MMActuator attribute) start_analysis() (eda_plugin.analysers.image.ImageAnalyser method) (eda_plugin.analysers.image.PycroImageAnalyser method) (eda_plugin.analysers.keras.KerasAnalyser method) stitchImage() (in module eda_plugin.utility.image_processing) stop_acq() (eda_plugin.actuators.micro_manager.TimerMMAcquisition method) (eda_plugin.actuators.pycro.PycroAcquisition method)

T

TimerMMAcquisition (class in eda_plugin.actuators.micro_manager)

U

update_parameters() (eda_plugin.examples.interpreters.FrameRateInterpreter method) (eda_plugin.interpreters.frame_rate.BinaryFrameRateInterpreter method) (eda_plugin.interpreters.presets.PresetsInterpreter method) (eda_plugin.utility.writers.Writer method)

W

Writer (class in eda_plugin.utility.writers)

writer() (in module eda_plugin.examples.main) WriterGUI (class in eda_plugin.utility.writers)