Three-dimensional imaging systems and methods for determining nucleic acids in thick tissues
AssigneePresident and Fellows of Harvard College
InventorsXiaowei Zhuang, Rongxin Fang, Aaron Halpern
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Abstract
The present disclosure generally relates to microscopy, including confocal microscopy. In some cases, techniques such as MERFISH can be used to determine nucleic acids within a sample, with images acquired using confocal microscopy. In some cases, the nucleic acids may be determined in 3 dimensions. In some cases, relatively thick samples, e.g., at least 100 micrometers thick, may be determined. In some embodiments, deep learning or other machine learning techniques may be used to enhance the image quality and/or speed up the confocal imaging process.
Claims27
A method, comprising:
- using a confocal microscope to acquire images of a sample;
- and
- determining nucleic acids within the sample using MERFISH.
The method of any previous claim, wherein the confocal microscope is a spinning disk confocal microscope.
The method of any previous claim, further comprising using machine learning to enhance the images of the sample.
The method of any previous claim, further comprising executing a machine learning model, trained on confocal images, to accept an input image and output an enhanced images based on at least signal-to-noise ratio.
The method of any previous claim, further comprising executing a machine learning model, trained on confocal images, to accept an input image and output an enhanced images based on at least signal-to-background ratio.
The method of any previous claim, further comprising executing a machine learning model, trained on confocal image properties, to accept an input image and output an enhanced images based on at least signal-to-noise ratio.
The method of any previous claim, further comprising executing a machine learning model, trained on confocal image properties, to accept an input image and output an enhanced images based on at least signal-to-background ratio.
The method of any previous claim, wherein the sample has a thickness of at least 100 micrometers.
A method, comprising:
- using a confocal microscope to acquire images of a sample;
- and
- determining nucleic acids within the sample in 3 dimensions using the images.
A method, comprising:
- exposing a sample to a plurality of nucleic acid probes;
- for each of the nucleic acid probes, determining binding of the nucleic acid probes within the sample by acquiring images of the sample using a confocal microscope;
- creating codewords based on the binding of the nucleic acid probes;
- and
- for at least some of the codewords, matching the codeword to a valid codeword wherein, if no match is found, applying error correction to the codeword to form a valid codeword.
A method, comprising:
- using a confocal microscope to acquire images of a sample;
- enhancing the images using machine learning;
- and
- determining nucleic acids within the sample using MERFISH.
A method, comprising:
- using a confocal microscope to acquire images of a sample;
- enhancing the images using machine learning;
- and
- determining nucleic acids within the sample.
A method, comprising:
- using a confocal microscope to acquire images of a sample;
- and
- determining nucleic acids within the sample by exposing the sample to a plurality of nucleic acid probes and determining binding of the plurality of the nucleic acid probes to the sample.
A method, comprising:
- using a confocal microscope to acquire images of a sample;
- enhancing the images using machine learning;
- and
- determining nucleic acids within the sample by exposing the sample to a plurality of nucleic acid probes and determining binding of the plurality of the nucleic acid probes to the sample.
A method, comprising:
- acquiring a plurality of images of the sample contained in a gel using a spinning disk confocal microscope, wherein between the acquisition of images, the gel exhibits a linear expansion of no more than 5%;
- determining nucleic acids within the sample using MERFISH.
A method, comprising:
- acquiring a plurality of images of the sample contained in a gel using a spinning disk confocal microscope, wherein between the acquisition of images, the gel exhibits a linear expansion of no more than 5%;
- determining nucleic acids within the sample;
- and
- using machine learning to enhance the images of the sample.
Dependencies are inferred from the claim text.