Patterned Structure Imaging for Overlapping Fluorescent Signals

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Solution Overview

Problem

Next-generation sequencing methods face challenges in accurately detecting genomic fragments due to significant spatial overlap of fluorescent signals between neighboring features in high-density arrays, leading to inaccurate detection and quantification.

Innovation Solution

A method and system for image analysis that registers and quantifies features in a repeating pattern by partitioning images into subimages, detecting features, and assigning index addresses, using algorithms to determine signal levels, and employing a processor and storage device for data processing.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Quantity of substance

If the distance between neighboring features is reduced to increase array density, then the array capacity increases, but the spatial overlap of fluorescent signals between neighboring features increases leading to detection errors

Engineering Contradiction:

Improvearray densityVSAvoidsignal detection accuracy

Core Design Contradiction:

Quantity of substanceVSMeasurement precision

Solution Approach 1:

The patent applies segmentation by dividing the image analysis process into distinct stages: initial feature detection, pattern recognition, and signal quantification. The image is processed in multiple passes with different algorithms optimized for each stage, allowing accurate separation of overlapping signals from high-density features

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent transitions from analyzing individual 2D images to processing 4D data (x, y coordinates, multiple fluorescent channels, and multiple image cycles). This dimensional expansion allows the system to distinguish overlapping features by their temporal and spectral characteristics, resolving signals that are spatially overlapping but distinguishable in other dimensions

Inventive Principle:

Principle #17Another dimension (Dimensionality change)

2Quantity of substance

If the feature size is reduced to increase array density, then more features can be accommodated, but accurate detection becomes problematic due to signal overlap

Engineering Contradiction:

Improvenumber of featuresVSAvoidfeature detection difficulty

Core Design Contradiction:

Quantity of substanceVSDifficulty of detecting and measuring

Solution Approach 1:

The patent performs preliminary pattern recognition and feature localization before full signal quantification. By pre-identifying feature locations and establishing their spatial relationships, the system prepares the data structure needed for accurate signal decomposition, making the subsequent detection of small features more reliable

Inventive Principle:

Principle #10Preliminary action

Solution Approach 2:

The patent introduces pattern templates as intermediaries between the raw image data and feature detection. These templates represent expected feature patterns and are used to guide the detection algorithm, allowing accurate identification of small features even when their signals overlap with neighbors

Inventive Principle:

Principle #24Intermediary (Mediator)

3Measurement precision

If the pixel pitch of the camera is reduced to increase resolution, then the optical resolution improves, but the signal-to-noise ratio decreases

Engineering Contradiction:

Improveoptical resolutionVSAvoidsignal-to-noise ratio

Core Design Contradiction:

Measurement precisionVSReliability

Solution Approach 1:

The patent merges information from multiple image cycles and multiple fluorescent channels to improve the signal-to-noise ratio. By accumulating signals across time and combining data from different spectral channels, the system achieves high reliability measurements even with small features that produce weak signals at high pixel pitches

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The patent performs continuous imaging across multiple cycles, capturing the same features repeatedly. This continuous observation allows the system to accumulate signal information over time while averaging out random noise, maintaining high signal-to-noise ratios even when individual images have low signal levels

Inventive Principle:

Principle #20Continuity of useful action

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 the accuracy of feature detection and quantification in high-density arrays by reducing computational load and improving signal extraction, even in conditions with spatial overlap, thereby enhancing the reliability of nucleic acid sequencing.

Implementation Method 1

fluorescently labeled nucleotides are added to an array of polynucleotide primers and are detected upon incorporation

Methodology Applied

Scientific EffectFluorescence: Fluorescence

Implementation Method 2

obtaining an image of an object using a detection apparatus

Methodology Applied

Scientific EffectPhotoelectric Effect: Photoelectric Effect

Data Source

PatentUS12573039B2Imaging systems and methods useful for patterned structures

Publication Date: 2026.03.10 SINGULAR GENOMICS SYSTEMS INC

AI summary

Disclosed herein, inter alia, are methods and systems of image analysis useful for identifying and/or quantifying features in patterns.