OpenSpinMicroscopy: An open-source platform for Scanning Light Sheet microscopy.


Emilio Gualda1, Gaby G Martins2, Hugo Pereira2, Nuno Martins2, Nuno Moreno3, and Tiago Vale3.

Estimated cost

~ 30.000 € (Highly dependent on configuration)


  • Hardware: Prototype/alpha version
  • Software: Prototype/alpha version

OpenSpinMicroscopy is an open-source platform to build digital Scanning Light Sheet Microscopes (SPIM/DSLM/OPT). It is a low-cost design that aims to help bring these technologies to imaging facilities with minimum technical capabilities, or allow adaptions to user’s specific needs. The image acquisition and analysis are all based on free software such as microManager and open source hardware such as Arduino micro-controllers.

Light Sheet Microscopy is a fluorescence microscopy technique. The technique shapes the illumination laser beam into a rectangle using a cylindrical lens (SPIM) or galvanometric mirrors (DSLM). This forms a thin “sheet of light” right illuminating the whole sample plane at the same time. This allows obtaining images of a big area in a fast way with a good sectioning of the sample and out-of-focus light suppression. Optical Projection Tomography (OPT) also takes advantage of the rotation of microscopic samples at different angles. LSM is especially well suited for the investigation of the development of large samples to study features (such as gene expression patterns) that require high resolution while being extended over a large volume and a long period of time.

According to the authors, the development of this method has been affected by marketing, investment recoupment or patent issues. Therefore, SPIM/DSLM has only been recently made available as a turnkey system while OPT is no longer available. Here, they present an open source setup using mainly Arduino boards and Micro-Manager for control of components. By combining the flexibility of Micro-Manager with the versatility and price of Arduino boards, the system provides a comprehensive framework for spinning microscopy that can be used either with SPIM, DSLM (1 or 2 photon) or OPT, and possibly other image acquisition techniques based on sample rotation.

A key component of this project is the custom Java plugin that has been designed for fully controlling DSLM/SPIM/OPT microscopes with a single window. It allows the capture of time lapse sequences, multicolor, z-stacks and multi-view recordings in an easy and intuitive manner. Regarding DSLM, the authors have designed a solution using an Arduino board to control the galvo speed and amplitude, modifying both the Micro-Manager device adapter for Arduino and the Micro-Manager firmware loaded on the Arduino board. The shutter state and the excitation/emission filters can be also controlled with this plugin.

This project provides technical hardware and software details to build and run the system. Focusing on price and standardization, the authors believe the OpenSpinMicroscopy plugin will help bring these cutting edge technologies to any imaging facility with minimum technical capabilities.



1Institute of Photonic Sciences ICFO – Spain

2Advanced Imaging Facility, Gulbenkian Institute of Science – Portugal

3Gulbenkian Institute of Science – Portugal