The microEye

The microEye is a Python toolkit for fluorescence microscopy that supports super-resolution single-molecule localization microscopy and single-particle tracking. It features hardware control, data analysis, and visualization.

This toolkit is compatible with the hardware used in our microscope. For further details, refer to the miEye microscope paper and OSF project.

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Modules

The miEye Module

The miEye_module provides the primary graphical user interface (GUI) for microscope control and data acquisition, combining the functionalities of the deprecated Acquisition and Control modules.

miEye module	Acquisition Camera

How to use:

For Vimba SDK to work, the script should be executed as an administrator on Windows and wrapped in a with statement:

from microEye.hardware import miEye_module

try:
    import vimba as vb
except Exception:
    vb = None

if vb:
    with vb.Vimba.get_instance() as vimba:
        app, window = miEye_module.StartGUI()
        app.exec_()
else:
    app, window = miEye_module.StartGUI()
    app.exec_()

The Multi Viewer Module

The multi_viewer Module is an improved GUI that replaces the deprecated tiff_viewer module. It allows users to process multiple files and provides data analysis and visualization tools for super-resolution single-molecule localization microscopy and single-particle tracking.

Raw Data	Localizations

How to use:

from microEye import multi_viewer

app, window = multi_viewer.StartGUI('')

app.exec_()

Uses Packages

The microEye uses the following Python packages:

Data Analysis and Visualization	GUI and UI Development	Code Quality and Formatting	Image and Video Processing	File and Data Storage	Other Utilities
dask	PyQt5	autopep8	opencv-python	ome-types	hidapi
h5py	pyqtdarktheme	pyflakes		tables	pyfiglet
matplotlib	pyqtgraph			zarr	pyserial
numba	QDarkStyle				pyueye
numpy	QScintilla				setuptools
pandas					tabulate
scikit-image					VimbaPython
scikit-learn
scipy
tifffile
vispy

Note: VimbaPython is included in Vimba SDK and needs to be installed manually.

How to Install microEye

1. Install Python:

   Download and install the latest Python 3.9 stable release.

2. Install microEye package:

   Open a terminal and execute the following command to install microEye using pip:

   pip install microEye

3. Install required packages:

   Download the requirements.txt file. Navigate to the directory containing the requirements file in your terminal and run:

   pip install -r requirements.txt

   Note: This step might take a while.

4. Install specific hardware drivers: (Optional)

   • For Integrated Optics: Download and install Laser control software.

   • For IDS uEye CMOS cameras: Install IDS Software Suite 4.96.1 for Windows 32/64-bit.

   • For Allied Vision CMOS cameras: Install Vimba SDK 5.0 or 6.0 outside the Program Files. Navigate to the directory containing setup.py and run:

     python -m pip install .

   • For Thorlabs CMOS cameras: Install Thorcam in its default directory. Note: Some Thorlabs cameras may be identified as IDS uEye cameras by Windows and may run without Thorcam.

   • For Thorlabs hardware, install Kinesis® Software and Elliptec™ Software.

5. Download and run examples: Download examples to start using microEye!

🥳 Note: Ensure all necessary drivers are installed for microEye to function properly.

Microscope Scheme

Schematic overview of the miEye instrument:

• A) Single-Mode Fiber (SMF): Excitation path for TIRF-, HILO-, and Epi-mode.
• B) Multi-Mode Fiber (MMF): Excitation path for Epi-mode when imaging MMF output on the sample plane.
• C) Fluorescence Emission: Path for fluorescence emission.
• D) Automatic Focus Stabilization: the automatic focus stabilization path using an IR laser in TIRF setting.

Scheme 1	Scheme 2

Key Components: AC: Achromat lens, AS: Aspheric lens, BFP: Back-focal plane, TL: Tube lens, B: B-coated N-BK7 optics, BS: Beamsplitter.

Hardware

Supported Cameras

Camera	Description	Link
IDS uEye UI-3060CP Rev. 2	IDS industrial-grade CMOS cameras	Link
Thorlabs DCC1545M	DCx camera using UC480 driver	Link
Allied Vision Alvium 1800	Allied Vision industrial-grade CMOS cameras (U-158m, U-511m)	Link

Additional Hardware

Hardware	Description	Link
Integrated Optics MatchBox	Multi-wavelength Laser Combiner, Single Laser MatchBox	Link
Piezo Concept FOC	Nanopositioner for microscope objectives	Link
Thorlabs Elliptec ELL6/ELL9	Dual/Four-Position Support	ELL6, ELL9
Thorlabs KDC101	Kinesis Controller for Z825B/Z925B actuators (Activate USB VCP to access the COM port in device manager)	Link
Parallax TSL1401-DB (#28317)	Linescan Camera Module	Link
RelayBox Arduino	For laser control using camera GPIO signals	RelayBox
miEye OSF Project Parts List	Parts list of miEye OSF Project	Link

Authors

Mohammad Nour Alsamsam, PhD student @ Vilnius University.

People Involved

PhD supervision: Dr. Marijonas Tutkus

Sample preparation, experiments and testing:

• Aurimas Kopūstas
• Tutkus Lab Team

Acknowledgement

Research and access to intruments and samples is credited to:

• Vilnius University, Lithuania.
• Center For Physical Sciences and Technology, Vilnius, Lithuania.
• Research Council of Lithuania.