Principles of open source bioinstrumentation applied to the poseidon syringe pump system

Abstract

The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source files available at https://pachterlab.github.io/poseidon . We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.

Figure 1

Model of the poseidon system. (a) CAD rendering of the microscope station and (b) a single syringe pump loaded with a 60 mL syringe. (c) Exploded view of all the components needed for assembling three pumps.

Figure 2

Using the poseidon system. Configuration of the poseidon system for running an emulsion generation microfluidics experiment where only two pumps are used. (a) Side view (b) angled view (c) top view.

Figure 3

Overview of the tools used for developing the poseidon system. (a) The GUI was created using Qt Designer, an open source drag and drop application for organizing buttons that allows users to easily change the GUI interface when adding new functionalities. (b) The GUI interfaces with a Python script that controls both the microscope and Arduino via USB. The Arduino controls the stepper motors on each pump using the CNC shield and stepper motor drivers. (c) The system’s 3D printed components were designed using Fusion 360, a cloud enabled CAD software that streamlines collaboration and offers free licenses for academics, hobbyists and small businesses. To modify the 3D models users can either work with Fusion 360 or any other CAD software. (d) The 3D printed components can be fabricated on any fused filament fabrication (FFF) 3D printer.

Figure 4

Benchmarking the poseidon system against the Harvard Apparatus system. Using a droplet generation chip we compared the droplet diameters between two systems. (a) A droplet size of 58 μm in diameter is expected for the given flow rates. The variance in the sizes of the droplets created with the two systems is comparable. (b) A microfluidic droplet generation chip imaged using the poseidon microscope. (c) Example of a monodisperse emulsion produced by the poseidon system and imaged with a Motic AE31 Trinocular Inverted microscope.

Figure 5

Summary of the design principles for open source bioinstrumentation.