Microscope-Scanner Focus Stacking for Biological Sample Imaging
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Solution Overview
Problem
Traditional microscopy techniques face challenges in capturing high-quality 2D images of biological samples with enhanced depth of field, as they often result in parts of the sample being out of focus due to limited depth of field, leading to the need for extensive data acquisition and storage.
Innovation Solution
A system and method utilizing a microscope-scanner and processing unit that acquires image data at multiple depths and lateral positions, applying focus stacking algorithms to generate a synthetic 2D image with enhanced depth of field in real-time, allowing features at different depths to be in focus across the image without requiring extensive data storage.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Manufacturing precision
If traditional microscopy is used to capture images of biological samples, then the imaging process is simple, but the depth of field is limited causing parts of the sample to be out of focus
Solution Approach 1:
The imaging process is segmented into multiple focal planes, where the system captures images at different depths separately and then combines them through focus stacking to achieve extended depth of field while maintaining image quality
Solution Approach 2:
The system transitions from 2D single-plane imaging to 3D multi-plane imaging by capturing images at different focal depths along the z-axis, then synthesizing them into a 2D image with extended depth of field
2Manufacturing precision
If the tissue is scanned at multiple depths to ensure all parts are in focus, then image quality improves, but the amount of data to be acquired and stored increases significantly
Solution Approach 1:
The system extracts only the in-focus portions from each captured image at different depths and combines them, discarding out-of-focus data to reduce overall data volume while maintaining focus accuracy
Solution Approach 2:
The system creates a synthetic 2D image that copies and combines the best in-focus regions from multiple depth images, producing a final image with extended depth of field without storing all intermediate depth images
3Ease of operation
If digital microscope scanning is automated to reduce manual operation, then operation efficiency improves, but the limited depth of field causes not all tissue parts to be in focus
Solution Approach 1:
The system performs preliminary automated scanning at multiple predetermined focal planes before synthesis, ensuring all tissue regions are captured at appropriate depths without manual intervention
Solution Approach 2:
The system introduces focus stacking algorithm as an intermediary processing step that automatically combines multiple depth images, bridging the gap between automated single-depth scanning and comprehensive multi-depth focus coverage
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 the generation of 2D images with enhanced depth of field on the fly, reducing data storage needs and improving image quality by ensuring that features at various depths are in focus, facilitating more efficient analysis of biological samples.
Implementation Method 1
a microscope-scanner... acquire first image data at a first lateral position... third image data at the first lateral position... wherein the third image data is acquired at a depth that is different than that for the first image data
Data Source
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AI summary
The present invention relates to a system for generating a synthetic 2D image with an enhanced depth of field of a biological sample. It is described to acquire (110) with a microscope-scanner (20) first image data at a first lateral position of the biological sample and second image data at a second lateral position of the biological sample. The microscope-scanner is used to acquire (120) third image data at the first lateral position and fourth image data at the second lateral position, wherein the third image data is acquired at a depth that is different than that for the first image data and the fourth image data is acquired at a depth that is different than that for the second image data. First working image data is generated (130) for the first lateral position, the generation comprising processing the first image data and the third image data by a focus stacking algorithm. Second working image data is generated (140) for the second lateral position, the generation comprising processing the second image data and the fourth image data by the focus stacking algorithm. The first working image data and the second working image data are combined (150), during acquisition of image data, to generate the synthetic 2D image with an enhanced depth of field of the biological sample.