Microscope-Cockpit

Examples of Unique Microscope systems controlled by Cockpit and Microscope 

• Cryo-SIM:   Applications paper.   Engineering paper
• Deep-SIM
• Aurox-AO   Optical design paper
• Olympus-Aurox 
• Zaber
• Prior-based hardware microscopes

Our general philosophy

A key challenge facing all microscope users is the time spent familiarising themselves with the software interface. Due to the complex nature of advanced imaging systems and the wide range of software both within and between the different manufacturers systems this can become confusing and lead to lost time and effort. If you add in bespoke systems then control for the non-expert is extremely challenging and difficult to customise to the user's needs. 

We have developed "Microscope-Cockpit", a Python-based GUI environment that is intuitive enough for users with little experience while maintaining a high level of functionality and adaptability. Based on software developed by John Sedat and his colleagues in UCSF, the Micron team have created a piece of software that is both functional and straightforward to use. The user environment is centred on the concept of the entire specimen landscape rather than the traditional small field of view. Simple and speedy navigation of the whole slide or dish makes specimen selection extremely efficient while also enabling integration of AI-led specimen selection. Microscope-Cockpit uses Python-Microscope to drive and control a broad range of hardware devices. 

Python-Microscope (Microscope) allows users to access hardware that is currently used only rarely in the biological sciences, such as adaptive optics and spatial light modulators. By controlling components such as deformable mirrors it is possible to correct artefacts such as chromatic aberration and to focus remotely without moving the specimen. This level of optical control opens up a whole avenue of more sophisticated experiments that may otherwise be out of reach.