Pi-seq—A customizable multichannel syringe pump for microfluidics

The advent of single cell technologies resulted in growing demand for microfluidics in the biological sciences. Commercial platforms have remained expensive, inflexible, and non-customizable black boxes. We developed an open source, multichannel, zero-backflow microfluidics device based on syringe pumps controlled by a Raspberry Pi computer. It uses both readily available and 3D-printed parts as well as a custom PCB and is easily serviceable. Moreover, it is fully customizable for various applications. Total cost is under €600. We equipped one channel with a custom Peltier-based temperature controller for precise heating or cooling and a mixer mechanism to prevent sedimentation of the cells within the syringe. Depending on the cells in the sample, heating and cooling can be useful to maintain a beneficial environment or to slow down cellular processes and cell death, respectively. Combined with microfluidics consumables and a microscope, the device is capable of integration into a high quality droplet-based single cell RNA sequencing workflow as shown here. Analysis of a mixture of human and insect cells resulted in a dataset of 17,769 single cells and demonstrates reliable operation and separation.