Microscope-Cockpit: Python-based bespoke microscopy for bio-medical science

Area of Science:

• Microscopy
• Optical Engineering
• Software Development

Background:

• Traditional microscopy control systems can be complex and proprietary.
• There is a need for adaptable, open-source software for advanced microscopy.
• Bespoke microscope systems require flexible and user-friendly control environments.

Purpose of the Study:

• To develop an open-source, Python-based Graphical User Interface (GUI) for microscope control.
• To enable efficient, eyepiece-less navigation and automated image acquisition.
• To provide a platform for controlling both simple and complex bespoke microscope systems.

Main Methods:

• Developed "Microscope-Cockpit" (Cockpit), a Python GUI leveraging "Python-Microscope" (Microscope) for hardware control.
• Implemented abstracted device models for complex components like deformable mirrors and spatial light modulators.
• Demonstrated the platform on widefield, adaptive optics, and structured illumination microscopy systems.

Main Results:

• Cockpit provides near-instantaneous slide navigation and automated acquisition capabilities.
• The software successfully controls diverse hardware, including adaptive optics and structured illumination.
• The open-source Python base allows for easy customization and integration of future functionalities, such as machine learning.

Conclusions:

• Microscope-Cockpit offers a versatile and user-friendly solution for controlling bespoke microscopy systems.
• The platform streamlines advanced imaging techniques and facilitates future innovation in automated microscopy.
• Its open-source nature promotes accessibility and adaptability in scientific imaging research.