Solid-State Optical Test Targets for Flow Cell Image Registration
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Solution Overview
Problem
Existing systems face challenges in accurately imaging and registering images of flow cells during sequencing processes, particularly in next-generation sequencing (NGS), due to the need for precise alignment and calibration across multiple imaging cycles.
Innovation Solution
The use of solid-state optical test targets with configurable substrates and micropatterns, simulating flow cell channels, to facilitate accurate imaging and registration by mimicking the optical properties of flow cells, and incorporating fluorescent dyes for enhanced calibration and alignment.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If traditional flow cells with liquid are used for imaging, then the actual sequencing process can be performed, but imaging accuracy and registration precision deteriorate due to refractive index variations and fluid dynamics
Solution Approach 1:
The patent creates a solid-state copy of the flow cell channel structure using a transparent substrate with micropatterns that replicate the optical path and geometric features of the actual flow cell. This solid-state replica eliminates fluid-related imaging variations while preserving the structural characteristics needed for accurate registration and alignment during sequencing operations.
2Productivity
If multiple imaging cycles are performed during sequencing, then complete sequencing data can be obtained, but alignment and calibration accuracy deteriorate due to cumulative errors and drift
Solution Approach 1:
The patent incorporates calibration features and reference markers into the solid-state substrate before imaging begins. These pre-integrated reference elements provide stable alignment targets that can be used across multiple imaging cycles to correct for drift and maintain consistent positioning accuracy throughout the sequencing process.
3Ease of operation
If flow cell channels with fluid are imaged, then the sequencing sample can be observed, but optical stability deteriorates due to refraction and light scattering
Solution Approach 1:
The patent creates a solid-state copy of the flow cell channel structure using a transparent substrate with micropatterns that replicate the optical path and geometric features of the actual flow cell. This solid-state replica eliminates fluid-related imaging variations while preserving the structural characteristics needed for accurate registration and alignment during sequencing operations.
Solution Approach 2:
The patent changes the physical state of the imaging medium from liquid (flow cell fluid) to solid (transparent substrate), thereby eliminating refraction and scattering issues associated with fluid while maintaining the necessary optical transparency for imaging.
4Ease of manufacture
If conventional test targets are used for calibration, then simple alignment can be achieved, but they fail to simulate the complex optical properties of flow cells
Solution Approach 1:
The patent uses a composite structure combining a transparent substrate material with integrated micropattern features and calibration markers. This composite design simultaneously provides the optical transparency needed for imaging and the geometric patterns needed for calibration, creating a single element that serves multiple functions.
Solution Approach 2:
The solid-state substrate serves multiple functions: it acts as the imaging medium, provides calibration reference features, simulates flow cell geometry, and enables alignment registration. This multi-functional design replaces what would traditionally require multiple separate components.
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
Enables precise imaging and registration of flow cell images, improving the accuracy and efficiency of sequencing systems by providing a standardized reference for optical alignment and calibration, thereby enhancing the performance of optical imaging systems.
Implementation Method 1
a first substrate comprising a transparent medium... the thickness of the first substrate is configured to permit imaging of the bottom surface of the first channel of the first hypothetical flow cell
Implementation Method 2
at least a portion of the top surface of the second substrate comprises an opaque coating that forms a micropattern, the micropattern configured to include opaque portions and transparent portions
Implementation Method 3
the first substrate having a refractive index of [n-top substrate(1)]... the thickness of the first substrate simulates the presence of a first hypothetical flow cell... the first fluid has a refractive index of [n-fluid(1)]
Data Source
AI summary
The present disclosure provides solid-state optical test targets useful for evaluating the performance of an optical imaging system. The solid-state optical test targets comprise at least a first substrate made from a flat transparent material. In some embodiments, the solid-state optical test targets further comprise an opaque coating that forms a micropattern. The first substrate is positioned in direct contact with the micropattern. The optical test targets described herein lack a flow cell and lack a liquid, and are therefore solid-state apparatus. Since the solid-state optical test targets lack a flow cell and liquid, the thickness of the first substrate is adjusted to simulate the presence of a hypothetic flow cell which could be located for example below the first substrate. The adjusted thickness of the first substrate can simulate the collective effects of the first substrate and the hypothetical flow cell containing a fluid/liquid. The disclosure also provides flow cells comprising pluralities of fluorescent beads for use as fiducials, and methods of using same in high throughput sequencing applications.