microEye 0.1.3

A python toolkit for fluorescence microscopy that features multi IDS uEye industrial-grade CMOS cameras and Integrated Optics laser combiner MatchBox.

microEye

A python toolkit for fluorescence microscopy that features IDS uEye industrial-grade CMOS cameras.

The Acquisition Module allows multi-cam image acquisition within one graphical user interface.

The Control Module allows setting the laser excitation presets, manual focus and automatic focus stabilization by monitoring the peak position of a totally internally reflected IR beam and moving the piezo stage accordingly.

This toolkit is compatible with the hardware we are using in our microscope. For further details check our microscope's github (TBA)

Uses Packages

• Numpy
• scipy
• pyueye
• cv2
• tifffile
• PyQt5
• pyqtgraph
• qdarkstyle
• ome-types
• lmfit

How to Install Package

> pip install microEye

Microscope Scheme

Hardware

• IDS uEye industrial-grade CMOS cameras, specifically UI-3060CP Rev. 2.
• Thorlabs DCx cameras using the UC480 driver, specifically DCC1545M.
• Integrated Optics Multi-wavelength Laser Combiner MatchBox.
• Piezo Concept nanopositioner for microscope objectives FOC.
• Parallax Linescan Camera Module used for IR autofocus stabilization tracking TSL1401-DB (#28317) acquisition done by an Arduino LineScanner.
• RelayBox arduino for laser control using the camera flash signal with different presets.
• Parts list related to our iteration of hohlbeinlab miCube (TBA).

Acquisition Module

How to use

from microEye.acquisition_module import acquisition_module

try:
    app, window = acquisition_module.StartGUI()
    app.exec_()
except Exception as e:
    traceback.print_exc()
finally:
    # dispose camera adapters
    for cam in window.ids_cams:
        cam.dispose()

    # Destroys the OpenCv windows
    cv2.destroyAllWindows()

Control Module

How to use

from microEye.control_module import control_module

app, window = control_module.StartGUI()
app.exec_()

Authors

Mohammad Nour Alsamsam

People Involved

Dr. Marijonas Tutkus (supervision)

Aurimas Kopūstas (sample preparation and experiments)

Acknowledgement