System, method, and product for imaging probe arrays with small feature size

1. A method for resolving features on a probe array, comprising:

acquiring images of a region of a probe array with an image acquisition device comprising an objective lens and a sensing element;

shifting the images by less than one half a size of a pixel of the sensing element while maintaining a fixed spatial relationship between the probe array and the objective lens to produce micro-shifted images;

reconstructing pixels of the micro-shifted images by unboxing the micro-shifted images, wherein unboxing comprises deconvolving the micro-shifted images using the Richardson-Lucy algorithm, wherein the Richardson-Lucy algorithm is controlled by at least three independent parameters, and wherein the at least three independent parameters comprise over-relaxation or acceleration, momentum, and total variation control; and

deriving intensity values for one or more features from the reconstructed pixels of the micro-shifted images, thereby resolving features on the probe array.

2. The method of claim 1 , wherein the reconstructing step further comprises:

tiling a single pixel from a common location within each of the micro-shifted images to preserve spatial orientation of the micro-shifted images.

3. The method of claim 1 , wherein the image is shifted in increments of (1/N) multiplied by a pixel size, wherein N is any integer greater than 3, and wherein the pixel size is the size of each of the pixels of the sensing element.

4. The method of claim 1 , wherein each of the one or more probe features on the probe array has a feature size from 1 μm to 8 μm in a dimension, and wherein each of the pixels of the sensing element comprises a size of 1.0 μm, 1.5 μm, or 2.5 μm.

5. The method of claim 1 , wherein the unboxing step further comprises deconvolving the micro-shifted images with an optical point spread function value.

6. The method of claim 1 , wherein the unboxing step further comprises employing SIR3, algebraic reconstruction technique (ART), or simultaneous algebraic reconstruction technique (SART).

7. A method of deriving signal intensity values in a probe array experiment, which comprises:

hybridizing a labeled sample to a probe array;

acquiring images of the labeled sample on the probe array with an image acquisition device comprising an objective lens and a sensing element;

shifting the images by less than one half a size of a pixel while maintaining a fixed spatial relationship between the probe array and the objective lens to create micro-shifted images;

tiling a single pixel from a common location within each of the micro-shifted images to provide a reconstructed image;

unboxing the reconstructed image by applying a set of linear equations to determine subpixel values, thereby providing a final image, wherein unboxing comprises using the Richardson-Lucy algorithm, wherein the Richardson-Lucy algorithm is controlled by at least three independent parameters, wherein the at least three independent parameters comprise over-relaxation or acceleration, momentum, and total variation control; and

deriving intensity values for one of more probe features disposed on the probe array from the final image.

8. The method of claim 1 , wherein the shifting step comprises shifting an element of the objective lens relative to the positions of the objective lens and the sensing element.

9. The method of claim 1 , wherein the shifting step comprises shifting an element of the sensing element.

10. The method of claim 7 , wherein the shifting step comprises shifting an element of the objective lens relative to the positions of the objective lens and the sensing element.

11. The method of claim 7 , wherein the shifting step comprises shifting an element of the sensing element.