Tube lens design for improved depth-of-field

Abstract

Imaging systems and methods comprising imaging a first interior surface and a second interior surface of a flow cell are described. In some embodiments, the imaging systems may comprise: a) an objective lens; b) at least one image sensor; and c) at least one tube lens disposed in an optical path between the objective lens and the at least one image sensor; wherein the at least one tube lens is configured to correct imaging performance such that images of the first interior surface of the flow cell and the second interior surface of the flow cell have substantially the same optical resolution.

What is claimed is: 
     
         1 . An imaging system configured to image a first interior surface and a second interior surface of a flow cell, the imaging system comprising:
 a) an objective lens;   b) at least one image sensor; and   c) at least one tube lens disposed in an optical path between the objective lens and the at least one image sensor;   wherein said optical system has a numerical aperture (NA) of less than 0.6 and a field-of-view (FOV) of greater than 1.0 mm 2 ; and   wherein the at least one tube lens is configured to correct imaging performance such that images of the first interior surface of the flow cell and the second interior surface of the flow cell have substantially the same optical resolution.   
     
     
         2 . The imaging system of  claim 1 , wherein the flow cell has a wall thickness of at least 700 μm and a fluid-filled gap between the first interior surface and the second interior surface of at least 50 μm. 
     
     
         3 . The imaging system of  claim 1 , wherein the images of the first interior surface and the second interior surface are acquired without moving an optical compensator into an optical path between said objective lens and said at least one image sensor. 
     
     
         4 . The imaging system of  claim 1 , wherein the imaging system has a numerical aperture (NA) of less than 0.6. 
     
     
         5 . The imaging system of  claim 1 , wherein the imaging system has a numerical aperture (NA) of greater than 0.3. 
     
     
         6 . The imaging system of  claim 1 , wherein the imaging system has a field-of-view (FOV) of greater than 1.5 mm 2 . 
     
     
         7 . The imaging system of  claim 6 , wherein the optical resolution of images of the first interior surface and the second interior surface are diffraction-limited across the entire field-of-view (FOV). 
     
     
         8 . The imaging system of  claim 1 , wherein the at least one tube lens comprises, in order, an asymmetric convex-convex lens, a convex-plano lens, an asymmetric concave-concave lens, and an asymmetric convex-concave lens. 
     
     
         9 . The imaging system of  claim 1 , wherein the imaging system comprises two or more tube lenses which are designed to provide optimal imaging performance for the first interior surface and the second interior surface at two or more fluorescence wavelengths. 
     
     
         10 . The imaging system of  claim 1 , further comprising a focusing mechanism configured to refocus the optical system between acquiring images of the first interior surface and the second interior surface. 
     
     
         11 . The imaging system of  claim 1 , wherein the imaging system is configured to image two or more fields-of-view on at least one of the first interior surface or the second interior surface. 
     
     
         12 . The imaging system of  claim 1 , wherein the first interior surface and second interior surface of the flow cell are coated with a hydrophilic coating layer, and wherein said hydrophilic coating layer further comprises labeled nucleic acid colonies disposed thereon at a surface density of >10,000 nucleic acid colonies/mm 2 . 
     
     
         13 . The imaging system of  claim 12 , wherein an image of the first interior surface or second interior surface acquired using the imaging system shows a contrast to noise ratio (CNR) of at least 5 when the nucleic acid colonies are labeled with cyanine dye 3 (Cy3), the imaging system comprises a dichroic mirror and bandpass filter set optimized for Cy3 emission, and the image is acquired under non-signal saturating conditions while the surface is immersed in 25 mM ACES, pH 7.4 buffer. 
     
     
         14 . The imaging system of  claim 12 , wherein said imaging system comprises 1, 2, 3, or 4 imaging channels configured to detect nucleic acid colonies disposed on at least one of said two distinct surfaces that have been labeled with 1, 2, 3, or 4 distinct detectable labels. 
     
     
         15 . The imaging system of  claim 12 , wherein the imaging system is used to monitor a sequencing-by-avidity, sequencing-by-nucleotide base-pairing, sequencing-by-nucleotide binding, or sequencing-by-nucleotide incorporation reaction on at least one of the first interior surface and the second interior surface and detect a bound or incorporated nucleotide base. 
     
     
         16 . The imaging system of  claim 12 , wherein the imaging system is used to perform nucleic acid sequencing. 
     
     
         17 . The imaging system of  claim 12 , wherein the imaging system is used to determine a genotype of a sample, wherein determining the genotype of the sample comprises preparing a nucleic acid molecule extracted from the sample for sequencing, and then sequencing the nucleic acid molecule. 
     
     
         18 . The imaging system of  claim 1 , wherein the at least one image sensor comprises pixels having a pixel dimension chosen such that a spatial sampling frequency for the imaging system is at least twice an optical resolution of the imaging system. 
     
     
         19 . The imaging system of  claim 1 , wherein a combination of the objective lens and the at least one tube lens is configured to optimize a modulation transfer function in the spatial frequency range from 700 cycles per mm to 1100 cycles per mm in the sample plane. 
     
     
         20 . The imaging system of  claim 1 , wherein the at least one tube lens is designed to correct modulation transfer function (MTF) at one or more specified spatial frequencies, defocus, spherical aberration, chromatic aberration, coma, astigmatism, field curvature, image distortion, image contrast-to-noise ratio (CNR), or any combination thereof, for a combination of the objective lens and the at least one tube lens.