Sequencer Mask Optimization for Extended Depth of Field
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing nucleic acid sequencers face challenges in maintaining optical signal-to-noise ratio due to point spread function degradation from defocus, which affects focus accuracy and increases noise, limiting throughput and increasing costs.
Innovation Solution
Implementing a nucleic acid sequencer with a detection system that includes an objective lens, a set of detection pixels, and a mask, such as a phase or amplitude mask, to extend the depth of field by optimizing the mask using iterative optimization steps based on discrepancies between actual and ideal point spread functions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If a conventional objective lens is used without a mask, then the device complexity is low, but the depth of field is limited and point spread function degrades with defocus
Solution Approach 1:
A mask is introduced as an intermediary optical element positioned between the objective lens and the detection pixels. This mask modifies the optical path and point spread function to extend depth of field, acting as a mediator that enables improved focus tolerance without requiring complex mechanical focusing mechanisms or multiple lenses.
Solution Approach 2:
The mask changes the optical parameters of the detection system by modifying the point spread function through its transmission function. This parameter change allows the system to maintain acceptable image quality over a larger range of defocus amounts, effectively extending the depth of field without altering the fundamental lens structure.
2Reliability
If the depth of field is extended using a mask, then the optical signal to noise ratio is improved, but the device complexity increases
Solution Approach 1:
The mask serves as a simple intermediary optical element that improves signal quality by shaping the point spread function. Rather than using complex signal processing or multiple detection systems, the mask provides a passive optical solution that enhances the optical signal to noise ratio through its spatial filtering function.
Solution Approach 2:
The solution replaces potential mechanical focusing adjustments with an optical mask-based approach. Instead of mechanically moving the lens or sample to achieve focus, the mask provides an optical field of view extension that maintains signal quality across a range of positions, substituting mechanical complexity with optical design.
3Productivity
If the depth of field is increased to +/â300 nm or greater, then the throughput is increased, but the manufacturing precision requirements for the mask increase
Solution Approach 1:
The mask design utilizes parameter changes in the transmission function to achieve depth of field extension. By carefully designing the transmission function parameters (such as aperture size, shape, and transmission values at different radial positions), the system achieves extended depth of field while maintaining manufacturability through standard fabrication techniques.
Solution Approach 2:
The mask implements local quality variations through its spatially varying transmission function. Different regions of the mask have different transmission properties, with the transmission value varying as a function of radial distance from the optical axis. This local differentiation allows the mask to correct optical aberrations and extend depth of field across the field of view.
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
The solution enhances focus accuracy, reduces noise, and increases throughput by extending the depth of field to greater than +/â300 nm, improving sequencing accuracy and reducing costs.
Implementation Method 1
a mask, such as a phase or amplitude mask, to extend the depth of field by optimizing the mask using iterative optimization steps based on discrepancies between actual and ideal point spread functions
Data Source
AI summary
A method for extending a depth of field of a nucleic acid sequencer may comprise optimization steps which are repeated one or more times, in which a result of passing light through an objective lens and a mask is compared with an ideal result, and any discrepancy is used to update the mask. Such a mask may be incorporated into a nucleic acid sequencer which adds fluorescent tags to nucleic acid sites and then detect light emitted from the fluorescent tags, thereby extending the sequencer's depth of field.