3D Image Registration Using Dense Staining in Sparse Tissue
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Solution Overview
Problem
Existing image registration methods using fiducial markers within cell nuclei suffer from non-linear deformities due to repeated antibody and DNA probe labeling, leading to low accuracy in tissue structures with sparsely packed cell nuclei.
Innovation Solution
A method involving dense staining and expansion microscopy, where fiducial markers are placed within a biological sample using a hydrogel-sample complex, followed by decalcification and expansion to achieve uniform expansion, allowing for high-density chemical labeling and improved image registration accuracy.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If cell nuclei are used as fiducial markers for image registration, then the registration process can be performed, but the accuracy is low in tissue structures with sparsely packed cell nuclei due to non-linear deformities
Solution Approach 1:
The patent introduces a hydrogel matrix as an intermediary substance that is uniformly distributed throughout the tissue sample. This hydrogel serves as a stable reference framework that mediates the registration process, replacing the unreliable cell nuclei in sparse tissues with a consistent artificial structure that maintains its position and properties throughout repeated imaging cycles.
Solution Approach 2:
The patent changes the fundamental parameter of fiducial marker selection from biological structures (cell nuclei) to synthetic structures (hydrogel matrix). This parameter change transforms the registration system from one dependent on variable biological features to one based on stable, uniformly distributed synthetic features, thereby improving accuracy and reliability.
2Adaptability or versatility
If repeated antibody and DNA probe labeling is performed to achieve multiplexed imaging, then multiple markers can be observed, but non-linear nanometer deformation occurs within the biological specimen
Solution Approach 1:
The patent performs preliminary embedding of the tissue sample in a hydrogel matrix before the repeated labeling process. This preliminary action creates a stable structural framework that prevents deformation during subsequent antibody and DNA probe labeling operations, allowing multiple markers to be observed without compromising specimen integrity.
Solution Approach 2:
The hydrogel matrix acts as an intermediary between the repeated labeling operations and the biological specimen. It absorbs and distributes mechanical stresses from repeated handling and labeling, preventing these stresses from causing non-linear deformation of the delicate biological structures within the sample.
3Measurement precision
If fiducial markers are placed within cell nuclei, then image registration can be performed, but signal distortion occurs during repeated labeling affecting registration accuracy
Solution Approach 1:
The hydrogel matrix serves as an intermediary fiducial marker system that is chemically inert and physically stable during repeated labeling operations. Unlike cell nuclei that can undergo signal distortion, the synthetic hydrogel structure maintains consistent fluorescent signal properties throughout the multiplexed imaging process, eliminating signal distortion-related registration errors.
Solution Approach 2:
The patent creates an artificial copy of the fiducial marker system using hydrogel with embedded fluorescent features, replacing the original cell nucleus-based system. This synthetic copy provides the same registration function without the vulnerabilities of biological structures, including signal distortion during repeated labeling.
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
This approach achieves image registration accuracy of around 10 nm, enabling effective super-resolution multiplexed imaging with improved accuracy by minimizing signal distortion during repeated labeling.
Implementation Method 1
synthesizing a hydrogel-sample complex from an organism sample
Implementation Method 2
expanding the hydrogel-sample complex
Implementation Method 3
staining a target molecule within a biological sample by using a hydrophilic fluorescent material and a hydrophobic fluorescent material together
Implementation Method 4
staining a target molecule within a biological sample by using a hydrophilic fluorescent material and a hydrophobic fluorescent material together
Implementation Method 5
staining a target molecule within a biological sample by using a hydrophilic fluorescent material and a hydrophobic fluorescent material together
Data Source
AI summary
Disclosed are three-dimensional image registration via dense staining and a super-resolution multiplexed imaging method using the same. The three-dimensional image registration includes: placing at least one fiducial marker in an internal structure of a biological sample via dense staining; obtaining a plurality of images by repeatedly imaging the biological sample while replacing a fluorescent label attached to at least one target molecule within the biological sample where the fiducial marker is placed; and registering the images using the fiducial marker as a reference to obtain a final image of the target molecule.