Team:Cambridge-JIC/Software

CAMBRIDGE-JIC

Microscopy Server

Turn your Raspberry Pi into a web-accessible microscope.

Look and control your microscope from your computer, phone, table or with a monitor connected to the Pi itself. You can connect to the microscope just like another computer over SFTP. After installing WinSCP (Windows) or Cyberduck (Mac) or Nautilus (Linux), it is easy to connect to the Pi (default username: pi, password: raspberry). Download your images as if they were on another folder.

Our software runs on nginx, a widely used lightweight web server. Behind this, we run an image streamer (mjpg-streamer) and our own python scripts. nginx deals with the user control and load balancing, leaving us to implement the various features of our microscope.

Visit our github

Webshell

Microscopy in a nutshell.

Everything you expect from a standard microscope. And more. WebShell shows the live stream from the microscope, while allowing control over the light sources and motorised axes. Apply sample recognition algorithms with opencv. Measure your cells by dragging a line across. Set up timelapses. Control it all from the keyboard like a video game. #gamifyingmicroscopy

ImageJ

OpenScope integrates with your favourite image processing tool.

For many years, scientists have used ImageJ to process microscope images. Our ImageJ plugin allows you to remotely connect to the microscope, see the live view, control the microscope lights and motors, while also letting you take pictures and import them straight into ImageJ. One click, no hassle.

Autofocus

Crisp, sharp images every time.

Focusing on samples is typically very fiddly. OpenScope supports autofocus. Find out more about the algorithms we used and see how they compare.

MicroMaps

Never get lost on your slide again.

MicroMaps performs image stitching in the background, allowing you to navigate your slide, just like exploring an online map.