Sample handling apparatus and image registration methods

Abstract

A method for aligning a sample to an array is provided. An image of sample image of a sample can be received by a data processor. The sample image having a first resolution. An array image including an overlay of an array with the sample and an array fiducial can be received by the data processor. The array image having a second resolution lower than the first resolution of the sample image. The sample image can be registered to the array image by aligning the sample image and the array image. An aligned image can be generated based on the registering. The aligned image can include an overlay of the sample image with the array. The aligned image can be provided by the data processor. A method for detecting fiducials associated with an array is provided. Systems and non-transitory computer readable mediums performing the method are also provided.

1 - 82 . (canceled) 
     
     
         83 . A method for detecting fiducials associated with an array, the method comprising:
 receiving, by a data processor, first array image data comprising a first array image comprising an array and an array fiducial;   receiving, by the data processor, second array image data comprising a second array image comprising an overlay of the array with a sample and the array fiducial, wherein the sample obscures the array fiducial in the overlay;   determining, by the data processor, the location of the array fiducial in the first array image based on a first coordinate system;   determining, by the data processor, a location of the sample in the second array image based on the first coordinate system;   comparing, by the data processor, the location of the array fiducial in the first array image and the location of the sample in the second array image; and   providing, by the data processor, the location of the array fiducial relative to the location of the sample based on the comparing.   
     
     
         84 . The method of  claim 83 , wherein the first array image is taken when the sample is not in contact with the array and wherein the second array image is taken when the sample is in contact with the array. 
     
     
         85 . The method of  claim 83 , wherein the first array image and the second array image are taken when the sample is in contact with the array. 
     
     
         86 . The method of  claim 85 , wherein the first array image is acquired at a first focal depth so as to exclude the sample from the first array image, and wherein the second array image is acquired at a second focal depth as to include the sample overlaid with the array. 
     
     
         87 . The method of  claim 85 , wherein the first array image is acquired at a first illumination causing a contrast of the sample to be lower than a contrast of the array fiducial, and wherein the second array image is acquired at a second illumination causing a contrast of the sample to be higher than a contrast of the array fiducial. 
     
     
         88 . The method of  claim 83 , wherein the first array image further comprises a first instrument fiducial, the method further comprising
 receiving, by the data processor, the second array image data further comprising the first instrument fiducial in the second array image, wherein the sample obscures the array fiducial and the first instrument fiducial in the overlay;   determining, by the data processor, the location of the array fiducial relative to the first instrument fiducial in the first array image based on the first coordinate system;   determining, by the data processor, the location of the sample relative to the first instrument fiducial in the second array image based on a second coordinate system; and   comparing, by the data processor, the location of the array fiducial in the first array image and the location of the sample in the second array image.   
     
     
         89 . The method of  claim 83 , wherein the first array image further comprises a first applied fiducial, the method further comprises
 receiving, by the data processor, the second array image data further comprising the first applied fiducial in the second array image, wherein the sample obscures the array fiducial and the first applied fiducial in the overlay;   determining, by the data processor, the location of the array fiducial relative to the first applied fiducial in the first array image based on the first coordinate system;   determining, by the data processor, the location of the sample relative to the first applied fiducial in the second array image based on the second coordinate system; and   comparing, by the data processor, the location of the array fiducial in the first array image and the location of the sample in the second array image.   
     
     
         90 . The method of  claim 89 , wherein the first applied fiducial is one of a stamp, a sticker, a drawing, or a laser etching located on a substrate on which the array and the array fiducial are located. 
     
     
         91 . The method of  claim 90 , wherein the first array fiducial is formed from a material including a dye, a chemical, a contrast agent, or a nanoparticle. 
     
     
         92 . The method of  claim 91 , wherein the material forming the first array fiducial improves a visible contrast of the first array fiducial. 
     
     
         93 . The method of  claim 83 , wherein the first array image is acquired from a substrate comprising the array, the array fiducial, and at least one spacer, the method further comprising
 receiving, by the data processor, the second array image data further comprising the at least one spacer in the overlay in the second array image, wherein a location of the sample is associated with the second coordinate system;   registering, by the data processor, the first array image to the second array image by aligning the location of the array fiducial and the location of the sample in a common coordinate system comprising the first coordinate system and the second coordinate system, the common coordinate system further comprising the location of the array fiducial and the location of the sample;   determining, by the data processor, the location of the array fiducial in the first array image based on the common coordinate system;   determining, by the data processor, the location of the sample in the second array image based on the common coordinate system; and   comparing, by the data processor, the location of the array fiducial in the first array image and the location of the sample in the second array image using the common coordinate system.   
     
     
         94 . The method  claim 83 , wherein the second array image is acquired at the first illumination and includes the sample overlaid atop the substrate comprising the array, the array fiducial, and at least one spacer visible in the second array image acquired at the first illumination, the method further comprising
 receiving, by the data processor, second array image data comprising a second array image acquired at the second illumination, the second array image acquired at the second illumination comprising the sample overlaid atop the substrate comprising the array, the array fiducial, and the at least one spacer, wherein the at least one spacer is visible in the second array image acquired at the second illumination;   determining, by the data processor, the location of the array fiducial in the second array image acquired at the first illumination based on a first coordinate system;   determining, by the data processor, the location of the sample in the second array image acquired at the second illumination based on the a second coordinate system;   registering, by the data processor, the second array image acquired at the first illumination to the second array image acquired at the second illumination by aligning the location of the array fiducial and the location of the sample in a common coordinate system comprising the first coordinate system and the second coordinate system, the common coordinate system further comprising the location of the array fiducial and the location of the sample;   determining, by the data processor, the location of the array fiducial in the second array image acquired at the first illumination based on the common coordinate system;   determining, by the data processor, the location of the sample in the second array image acquired at the second illumination based on the common coordinate system; and   comparing, by the data processor, the location of the array fiducial in the second array image acquired at the first illumination and the location of the sample in the second array image acquired at the second illumination using the common coordinate system.   
     
     
         95 . A system for detecting fiducials associated with an array, the system comprising:
 a sample holder comprising
 a first retaining mechanism configured to retain a first substrate received within the first retaining mechanism, the first substrate comprising a sample, and 
 a second retaining mechanism configured to retain a second substrate received within the second retaining mechanism, the second substrate comprising an array and an array fiducial, the sample holder configured to adjust a location of the first substrate relative to the second substrate to cause all or a portion of the sample to be aligned with the array; 
   a microscope operatively coupled to the sample holder, the microscope configured to view the first substrate and the second substrate within the sample holder and to acquire image data associated with the sample and/or the array; and   a first computing device communicatively coupled to the microscope and to the sample holder, the computing device comprising a display, a data processor, and a non-transitory computer readable storage medium storing computer readable and executable instructions, which when executed cause the data processor to perform operations comprising   receiving first array image data comprising a first array image of the second substrate, the first array image comprising the array and the array fiducial;   receiving second array image data comprising a second array image comprising an overlay of the sample of the first substrate and the array of the second substrate, and the array fiducial of the second substrate, wherein the sample obscures the array fiducial in the overlay;   determining the location of the array fiducial in the first array image based on a first coordinate system;   determining the location of the sample in the second array image based on the first coordinate system;   comparing the location of the array fiducial in the first array image and the location of the sample in the second array image; and   providing the location of the array fiducial relative to the location of the sample based on the comparing.   
     
     
         96 . The system of  claim 95 , wherein the first array image and the second array image are taken when the sample is in contact with the array. 
     
     
         97 . The system of  claim 96 , wherein the first array image is acquired at a first focal depth so as to exclude the sample from the first array image, and wherein the second array image is acquired at a second focal depth as to include the sample overlaid with the array. 
     
     
         98 . The system of  claim 96 , wherein the first array image is acquired at a first illumination causing a contrast of the sample to be lower than a contrast of the array fiducial and wherein the second array image is acquired at a second illumination causing a contrast of the sample to be higher than a contrast of the array fiducial. 
     
     
         99 . The system of  claim 95 , wherein the first array image further comprises a first applied fiducial, the instructions further cause the data processor to perform operations comprising
 receiving the second array image data further comprising the first applied fiducial in the second array image, wherein the sample obscures the array fiducial and the first applied fiducial in the overlay;   determining the location of the array fiducial relative to the first applied fiducial in the first array image;   determining, by the data processor, the location of the sample relative to the first applied fiducial in the first array image based on the first coordinate system; and   comparing the location of the array fiducial in the first array image and the location of the sample in the second array image.   
     
     
         100 . The system of  claim 99 , wherein the first applied fiducial is one of a stamp, a sticker, a drawing, or a laser etching located on the second substrate. 
     
     
         101 . The system of  claim 100 , wherein the first array fiducial is formed from a material including a dye, a chemical, a contrast agent, or a nanoparticle. 
     
     
         102 . The system of  claim 101 , wherein the material forming the first array fiducial improves a visible contrast of the first array fiducial.