Package: microEye
microEyemicroEyeis a python toolkit for fluorescence microscopy that features hardware control, data analysis and vizualization for super-resolution single-molecule localization microscopy and single-partical tracking.ModulesmiEye Module:Provides the primary GUI for microscope control and data acquisition, combining previous functionalities implemented withinAcquisitionandControlmodules.Multi Viewer Module:An improved GUI replacingTiff Viewermodule that allows processing multiple files providing data analysis and visualization tools.Note: The following modules are deprecated, and support has been halted. Please consider the alternatives above.Acquisition Module:Enables multi-camera image acquisition within a unified graphical user interface.Control Module:Allows users to set laser excitation presets, manually focus, and perform automatic focus stabilization by monitoring the peak position of a totally internally reflected IR beam and adjusting the piezo stage accordingly.Tiff Viewer Module:Provides access to TIFF images (single files and sequences) of order TYX (2D SMLM) and facilitates visualizing the filtering-localization process (WYSIWYG).This toolkit is compatible with thehardwareused in our microscope. For further details, refer to themiEye microscope paperandOSF project.Uses Packagesautopep8daskh5pyhidapimatplotlibnumbanumpyome_typesopencv_pythonpandaspyflakesPyQt5PyQt5_sippyqtgraphpyserialpyueyeQDarkStyleQScintillascikit_imagescikit_learnscipysetuptoolstablestifffileVimbaPython (Included inVimba SDKand installed manually)zarrHow to InstallPackageDownload and install the latestPython3.9 stable release.Open a terminal and install themicroEyepackage usingpip.pipinstallmicroEyeDownload therequirements.txtfile and install the required packages formicroEyeby executing: (This may take a while)pipinstall-r/path/to/requirements.txtInstall the specific hardware drivers for the cameras:Integrated OpticsLaser control software.IDS uEye CMOS cameras:InstallIDS Software Suite 4.96.1for Windows 32/64-bit.Allied Vision CMOS cameras:InstallVimba SDK5.0 or 6.0 outside the Program Files to skip the run-as-admin requirement. In a terminal navigate to directory [.../Allied Vision/Vimba_5.0/VimbaPython/] where [setup.py] is located and execute:python-mpipinstall.Thorlabs CMOS cameras:InstallThorcamin its default directory. Note, someThorlabscameras can get identified byWindowsasIDS uEyecameras and run without this software.Other hardware used by the miEye microscope:ThorlabsKinesis® SoftwareandElliptec™ Software.Download and run examples to start using microEye! :partying_face:Note:microEyemight not function as expected in case drivers are missing.Microscope SchemeSchematic overview of the miEye instrument. A) The excitation path via single-mode fiber (SMF) for TIRF-, HILO-, and Epi-mode. B) The excitation path via multi-mode fiber (MMF) for Epi-mode when imaging MMF output on the sample plane. C) The fluorescence emission path. D) IR laser-based autofocusing path. AC: achromat lens, AS: aspheric lens, BFP: back-focal plane, TL: tube lens, B: B-coated N-BK7 optics, BS: beamsplitter.Scheme 1Scheme 2HardwareSupported CamerasIDS uEye industrial-grade CMOS cameras, specificallyUI-3060CP Rev. 2.Thorlabs DCx cameras using the UC480 driver, specificallyDCC1545M.Allied Vision cameras using Vimba SDK, specificallyAlvium 1800 U-158m.Additional HardwareIntegrated Optics Multi-wavelength Laser CombinerMatchBox.Piezo Concept nanopositioner for microscope objectivesFOC.Thorlab's Elliptec Dual-Position/Four-Position (ELL6/ELL9) support.Thorlab's KinesisKDC101controller forZ825B25mm motorized actuators used for the XY stage instead of manual micrometers. (Requires activating USB VCP to access the COM port from device manager)Parallax Linescan Camera Module used for IR autofocus stabilization trackingTSL1401-DB (#28317)acquisition done by an ArduinoLineScanner.RelayBoxArduino for laser control using the camera flash signal with different presets.Parts list of ourmiEye OSF Project– an iteration ofhohlbeinlab miCube.miEye ModulemiEye moduleAcquisition CameraHow to useFor Vimba SDK to work, the script should be executed as an administrator on Windows and wrapped in awithstatement:frommicroEye.hardwareimportmiEye_moduletry:importvimbaasvbexceptException:vb=Noneifvb:withvb.Vimba.get_instance()asvimba:app,window=miEye_module.StartGUI()app.exec_()else:app,window=miEye_module.StartGUI()app.exec_()Multi Viewer ModuleRaw DataLocalizationsHow to usefrommicroEyeimportmulti_viewerapp,window=multi_viewer.StartGUI('')app.exec_()Acquisition Module (Deprecated)How to useFor Vimba SDK to work, the script should be executed as an administrator on Windows and wrapped in awithstatement:frommicroEye.hardwareimportacquisition_moduletry:importvimbaasvbexceptException:vb=Noneifvb:withvb.Vimba.get_instance()asvimba:app,window=acquisition_module.StartGUI()app.exec_()else:app,window=acquisition_module.StartGUI()app.exec_()Control Module (Deprecated)How to usefrommicroEye.hardwareimportcontrol_moduleapp,window=control_module.StartGUI()app.exec_()Tiff Viewer Module (Deprecated)File SystemData FittingLocalizations Visualization & AnalysisHow to usefrommicroEyeimporttiff_viewerapp,window=tiff_viewer.StartGUI('')app.exec_()AuthorsMohammad Nour Alsamsam, PhD student @ Vilnius University.People InvolvedPhD supervision:Dr. Marijonas TutkusSample preparation, experiments and testing:Aurimas KopūstasTutkus Lab TeamAcknowledgementResearch and access to intruments and samples is credited to:Vilnius University, Lithuania.Center For Physical Sciences and Technology, Vilnius, Lithuania.Research Council of Lithuania.