OpenFlexure Raspbian - The OpenFlexure Project

Installing the operating system

Choose a version of OpenFlexure Raspbian

For your microscope, you will need to download OpenFlexure Raspbian, our custom operating system for the Raspberry Pi. It comes with all necessary software pre-installed.

There are two key decisions to make:

A Full or a Lite OS?

Full OS

The best option for new users.

A full desktop OS
Control directly from the microscope*
Remote control over the network^†
Uses more RAM and Storage

*Requires a keyboard, mouse, and monitor
^†Control from your computer, laptop, or tablet.

Lite OS

The best performance for advanced use.

Remote control over the network^† only
Maximises RAM and Storage availability for microscopy

^†Control from your computer, laptop, or tablet.

Development or Stable Release?

v3.0.0-Beta - Development

The best experience for automated microscopy

Automated scanning with live preview
Improved user experience
Modern OS, with active maintenance
Does not support:
- Raspberry Pis older than the Pi 4, nor Pi 5
- The Delta stage (support planned)
- Motor boards other than Sangaboard v0.5 with Firmware v1.3 or later (support for “Workaround” motor boards is planned)
- Server extensions (support planned)

Requirements

Raspberry Pi 4 with 4GB of RAM (or higher RAM)
We do not yet support the Raspberry Pi 5
2GB of RAM can be used for the Lite OS, but may affect performance.

v2.11.0 - Stable

Supports a wider number of variations

Older OS, no longer gets updates
The maximum RAM is 4GB. 8GB Raspberry Pis will work, but will only use 4GB of RAM
Recommended if:
- You only have older Raspberry Pis available
- You use the Delta Stage
- You use a workaround motor board
- You need a specific v2 extension

Requirements

Raspberry Pi 2 Model B (1GB RAM) (or better*)
Raspberry Pi 4 Model B (2GB RAM) is recommended for the Full OS
Raspberry Pi 1 Model B (512MB RAM) can be used for the Lite OS, but may affect performance.

*We do not yet support the Raspberry Pi 5

Write your SD card

To write the OS you will need version 2 of the Raspberry Pi imager software. Version 1.9.X doesn’t always customise the OS correctly.

To write the OS:

Open Imager2
Select App options
Click the edit button next to “Content Repository”
Select “Use custom URL” and paste in the following URL: https://build.openflexure.org/raspbian-openflexure/manifest.json
Select Apply & Restart
Now you can select the model of Raspberry Pi you have (e.g. Raspberry Pi 4)
Choose your OS. See above for more information on which OS to choose.
- Select either the v3.0.0 beta release of OpenFlexure Raspbian (For Raspberry Pi 4 only), or v2.11.0.
- You then need to select either the Full or the Lite version of the OS.
Select your SD card from the list
Give your microscope a name, and select Next
Leave the localisation settings as they are and click Next
Choose a user name and password then click Next
Optionally enter your Wifi details, but you can skip this (you may need to delete the SSID for it to let you click Next)
Turn Enable SSH on and click Use Password Authentication (Unless you understand SSH keys and how to manage them)
Finally, click Write and wait for it to finish

Managing the microscope server

Our installer includes various commands to simplify common tasks when using the OpenFlexure Microscope. From the terminal on your Raspberry Pi, you will have available commands such as:

ofm start - Start the server background service

ofm stop - Stop the server background service

ofm update - Pull and install the latest version of the OFM CLI itself (v2 only)

ofm upgrade - Pull and install the latest version of the server (v2 only)

For a complete list of available commands, run ofm help

Raspberry Pi configuration

Additional Raspberry Pi configuration options, such as network and interface settings, can be accessed by running sudo raspi-config from your terminal.

Source

Source code for the OpenFlexure Microscope server is available on GitLab.

Legacy versions

Previous versions of the OpenFlexure Microscope server can be found on the build server. Previous versions of OpenFlexure Raspbian can also be found on the build server.