Sequencing Illumination Optics for Wide-Field Uniformity and Low Speckle
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Solution Overview
Problem
Next generation sequencing (NGS) systems face challenges in achieving increased throughput, flexibility, and uniform illumination power while reducing speckle noise and system complexity.
Innovation Solution
Optical systems with wide field-of-view illumination and integrated despecklers, along with a rotary sample stage design, enable uniform illumination and efficient imaging of multiple surfaces without moving optical components, reducing speckle noise and system complexity.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Illumination intensity
If conventional illumination systems are used, then system complexity is reduced, but illumination uniformity and field-of-view are insufficient
Solution Approach 1:
The illumination system is segmented into multiple independent components: a light source module, a beam-shaping module with multiple optical elements (freeform lens, cylindrical lens, diffuser), and an illumination module. Each segment performs a specific function to progressively shape and distribute light, achieving uniform illumination across a wide field-of-view through coordinated action of these modular segments.
2Productivity
If wide field-of-view illumination is implemented, then sequencing throughput is improved, but speckle noise increases
Solution Approach 1:
A vibration element is introduced into the optical path to mechanically vibrate light waves. This vibration disrupts the coherent interference patterns that generate speckle noise, converting structured interference patterns into randomized intensity distributions that average out to uniform illumination, thereby eliminating speckle artifacts while maintaining wide field-of-view capability.
Solution Approach 2:
A diffuser element is positioned between the beam-shaping module and the flow cell to act as an intermediary. This diffuser scatters light waves, breaking up coherent beams into incoherent rays that illuminate the wide field-of-view without generating speckle patterns, serving as a mediator between the illumination source and the sample.
3Illumination intensity
If multiple optical components are used, then illumination quality is improved, but system alignment and manufacturing burden increase
Solution Approach 1:
The optical elements are designed with multi-functionality: the freeform lens simultaneously performs beam shaping and field flattening, the cylindrical lens provides both divergence control and uniformity enhancement, and the diffuser serves both speckle reduction and illumination broadening. This multi-functionality reduces the total number of components needed while maintaining high illumination quality.
Solution Approach 2:
The optical elements utilize varying geometric parameters and material properties to achieve multiple functions. The freeform lens employs complex surface curvature variations to shape beams and flatten the illumination field simultaneously. The diffuser uses controlled particle size distributions and material compositions to optimize both scattering performance and speckle reduction, allowing parameter optimization for multiple objectives within single components.
4Reliability
If stage movement in z-direction is eliminated, then system reliability is improved, but focusing capability is reduced
Solution Approach 1:
The mechanical z-stage focusing system is replaced with an optical focusing mechanism. A movable lens element within the illumination module adjusts its position along the optical axis to change the focal plane, substituting mechanical sample stage movement with optical element repositioning. This maintains focusing capability while eliminating the need for complex z-stage mechanisms, thereby improving system reliability.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
Enhances sequencing throughput and reduces speckle noise, allowing for higher efficiency and flexibility in NGS analysis with simpler setups and reduced system volume.
Implementation Method 1
a light source configured to illuminate said solid support; and an optical assembly disposed at least partly within an optical path from said stage to said light source
Implementation Method 2
said optical assembly is configured to receive an emission light from said solid support
Data Source
AI summary
The present disclosure describes illumination methods and systems for illumination and sequencing applications that can be utilized for, for example, microscopy and sequencing platforms. The methods and systems of the present disclosure can provide wide area, flat illumination, which can reduce error and improve system throughputs.