Non-linear deskewing for light sheet microscopy volumetric images
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Solution Overview
Problem
Current oblique plane microscopy methods using light sheet microscopes suffer from residual geometric distortions in volumetric images due to the oblique orientation of the light sheet, which cannot be corrected by simple linear transformations.
Innovation Solution
A method that employs a non-linear transformation to deskew and correct the geometric distortions in volumetric images, parameterizing both the shear caused by the tilt of the light sheet and the optical distortions induced by the system, thereby providing a more accurate representation of the imaged volume.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Ease of manufacture
If a simple linear transformation is used to deskew the image data, then the transformation process is simple and fast, but residual geometric distortions remain in the volumetric images
Solution Approach 1:
The patent transforms the image data from a linear transformation approach to a non-linear transformation approach. Specifically, it applies a non-linear mapping that accounts for the oblique angle of the light sheet and the curvature of the sample, using parameters such as the oblique angle and radial distance from the optical axis to correct geometric distortions accurately.
Solution Approach 2:
The patent introduces a curvature correction term in the transformation equation that accounts for the spherical shape of the sample. The transformation includes a radial component that adjusts for the curvature of the sample surface, ensuring that points on the curved surface are correctly mapped to the flattened image plane.
2Volume of moving object
If the light sheet is oriented oblique to the optical axis to enable single-objective imaging, then space constraints are resolved, but the image stack becomes sheared and requires complex deskewing
Solution Approach 1:
The patent performs preliminary correction of the geometric distortions during the image acquisition and processing stage. By applying the non-linear transformation early in the workflow, the sheared image stack is corrected before further analysis or visualization, simplifying subsequent processing steps.
Solution Approach 2:
The patent replaces the need for mechanical rearrangement of optical components with a computational transformation approach. Instead of physically reorienting the light sheet or detector to achieve proper alignment, the patent uses mathematical transformation to correct the oblique imaging geometry, reducing mechanical complexity.
3Measurement precision
If conventional light sheet microscopy with separate illumination and detection objectives is used, then optimal illumination and detection are achieved, but the setup requires more space and is less adaptable
Solution Approach 1:
The patent makes a single objective lens serve dual functions: both illumination and detection. By configuring the single objective to both deliver the oblique light sheet and collect the emitted light, the system achieves functionality equivalent to separate objectives while reducing the number of components and increasing adaptability to constrained environments.
Solution Approach 2:
The patent merges the illumination and detection pathways into a single optical path using one objective lens. The objective lens simultaneously focuses the illumination light sheet and collects the emitted photons, combining functions that are typically separated in conventional light sheet microscopy setups.
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 proposed method significantly improves the accuracy of volumetric image representation by effectively correcting residual geometric distortions, resulting in a more faithful reconstruction of the imaged volume compared to current methods.
Implementation Method 1
Generating a light sheet, said light sheet extending along a light propagation direction and an extension direction perpendicular thereto
Implementation Method 2
Fluorescent light emitted by the sample is then imaged onto a detector by a detection objective
Data Source
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AI summary
A method for generating a volumetric image of a sample (118) using a light sheet microscope (100, 300) comprises: Illuminating a plurality of layers (202) of the sample (118) arranged along a scanning direction (C) using the light sheet, wherein a light propagation direction (A) of the light sheet is tilted by a tilt angle (α) less than 90° with respect to the scanning direction (C). Generating layer images from the illuminated layers (202). Generating raw image data corresponding to an image stack comprising the layer images, the image stack being sheared by the tilt angle (α) or by 90° minus the tilt angle (α) and being distorted by the optical properties of the optical system (104). The method further comprises generating processed image data from the raw image data by defining an image space comprising voxel and corresponding to the imaged volume (200, 400) of the sample (118), and assigning at least one value to each voxel of the image space based on at least one value of at least one voxel of the image stack, wherein the voxel of the image space and the at least one voxel of the image stack are related by a non-linear transformation. Alternatively, the method comprises generating processed image data from the raw image data by applying the inverse of the non-linear transformation to the raw image data.