Hardware: Transformer Mark 3

Hardware Guide


Our Sequencing instrument, “Transformer Mark 3.0”, is a custom-built total internal reflection fluorescence (TIRF) imaging system, specifically designed to support the innovative Lightning Terminators™ (LT) one pot sequencing. This system combines advanced optical engineering with the versatile control offered by a Raspberry Pi 4, augmented with stackable HAT (Hardware Attached on Top) boards for enhanced functionality.

Key functionalities

Temperature control and monitoring

The Transformer Mark 3.0 ensures optimal environmental conditions for sequencing reactions. Precision temperature control is crucial for accurate and reliable sequencing results.

Waveguide-based TIRF imaging module

At the heart of the system is the TIRF imaging module. Utilizing a waveguide approach, this module excites the fluorescent molecules linked to incorporated LTs a few hundreds of nanometers from the sequencing substrate surface. This module also performs effective UV cleavage of the terminating groups for continuous sequencing.

Motorized imaging filter switching and focus adjustment

To adapt to various imaging requirements, the Transformer Mark 3.0 includes a motorized filter wheel and focus adjustment mechanism. This allows for rapid and precise changes between different fluorescence channels and focus levels, ensuring sharp images and accurate data capture.


The Transformer Mark 3.0 is assembled in four main sections. The process is detailed in the subpages below — we recommend assembling in this order (generally from bottom to top):

Laboratory Stand

Laboratory Stand Guide

Camera and focus

This section houses the core imaging components, including the high-resolution CMOS camera and the mechanisms for focus adjustment.

Filter wheel and optics

Situated above the camera assembly, this section contains the motorized filter wheel with optical tubing and an imaging lens, allowing for 4x magnification with seamless switching between different fluorescent channels.

TIRF LED and temperature control assemblies

Heat sink and LED mounting assemblies. These are installed into the main body.

Main body

The topmost section forms the main body of the Transformer Mark 3.0. It integrates all the components into a cohesive unit, housing the sequencing reservoir, LED and heat sinks, heaters, temperature sensors, and providing structural integrity to the entire assembly.