System, method, and product for scanning of biological materials

• US 8,208,710 B2
• Filed: 06/09/2011
• Issued: 06/26/2012
• Est. Priority Date: 03/15/2002
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Weiner, Nathan K., Odoy, Patrick J., Schultz, Eric, Jones, Mark, Overbeck, James T., DeWeerd, Herman, Stura, David A., Bukys, Albert K., Woolaver, Tim J., Regan, Thomas P., Bradbury, David, McKenzie, Eric E., DiPaolo, Roger, Miles, Christopher, Katz, Joel M., Oleinik-Ovod, Ksenia
• Primary Examiner(s): Johns, Andrew W
• Application Number:
  US13/156,928
• Publication Number:
  US 20110243411A1
• Time in Patent Office: 383 Days
• Field of Search: 382/128, 382/129, 382/133, 382/291, 382/294, 356/614, 356/620
• US Class Current: 382/133
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 21/253 for batch operation, i.e. multisample apparatus analytical automats G01N35/00
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates

Abstract

An embodiment of a scanning system is described including optical elements that direct an excitation beam at a probe array, detectors that receive reflected intensity data responsive to the excitation beam, where the reflected intensity data is responsive to a focusing distance between an optical element and the probe array, a transport frame that adjusts the focusing distance in a direction with respect to the probe array, an auto-focuser that determines a best plane of focus based upon characteristics of the reflected intensity data of at least two focusing distances where the detectors further receive pixel intensity values based upon detected emissions from a plurality of probe features disposed on the probe array at the best plane of focus, and an image generator that associates each of the pixel intensity values with at least one image pixel position of a probe array based upon one or more position correction values.

Claims

1. A method of generating an error correction table, which comprises:

scanning a probe array by irradiating the probe array with an illumination beam,

wherein the probe array comprises one or more calibration features;

detecting one or more signal intensity values responsive to the illumination beam;

generating one or more error correction values, wherein each of the one or more error correction values is based, at least in part, on a difference between the detected signal intensity value position and a corresponding known probe array position obtained from stored calibration feature data comprised of one or more probe array positions; and

generating an error correction table, wherein the error correction table comprises the one or more error correction values.

2. The method of claim 1, wherein each of the one or more calibration features is represented by one or more pixels in a displayed image.

3. The method of claim 1, wherein the one or more detected signal intensity values is assigned to a preliminary probe array position.

4. The method of claim 3, wherein the preliminary probe array position is assigned to one or more preliminary pixel positions.

5. The method of claim 4, wherein the one or more preliminary pixel positions is determined by a pixel position determiner, wherein the pixel position determiner compares a first pixel position located at a leading edge of the calibration feature relative to a second pixel position located at the center of the array.

6. The method of claim 4, wherein each of the one or more preliminary pixel positions is assigned a pixel offset position by a pixel offset determiner, wherein the pixel offset position is based on the position of each of the one or more preliminary pixel positions in the error correction table relative to a preliminary pixel position located at the center of the error correction table.

7. The method of claim 6, wherein the pixel offset position is a negative value, wherein the negative value signifies a direction toward an edge of the probe array which corresponds to a start position of the probe array scan.

8. The method of claim 4, wherein each of the one or more preliminary pixel positions is assigned to a corrected pixel position by a corrected image generator, wherein the corrected pixel position is obtained, at least in part, from the error correction values in the error correction table.

9. The method of claim 1, wherein the one or more detected signal intensity values is generated, at least in part, from one or more emissions from the one or more calibration features on the probe array.

10. The method of claim 9, wherein the one or more calibration features are probe features.

11. The method of claim 1, wherein the one or more detected signal intensity values corresponds to one or more reflections of the illumination beam from the one or more calibration features on the array.

12. The method of claim 1, wherein the one or more calibration features are chrome features.

13. The method of claim 1, wherein the one or more calibration features are present on the probe array in a horizontal pattern.

14. The method of claim 1, wherein the illumination beam comprises a laser beam.

15. The method of claim 1, which further comprises:

providing a computer;

providing calibration feature data comprising one or more known probe array positions; and

uploading the calibration feature data into a calibration executable stored on the computer.

16. A method of generating an error correction table, which comprises:

irradiating a probe array comprising one or more calibration features with an illumination beam;

detecting one or more signal intensity values responsive to the illumination beam;

measuring a galvo arm position at each instance of detection of the one or more signal intensity values;

generating one or more error correction values, wherein each of the one or more error correction values is based, at least in part, on the difference between the galvo arm position and a reference probe array position obtained position obtained from stored calibration feature data comprised of one or more probe array positions; and

generating an error correction table, wherein the error correction table comprises the one or more error correction values.

17. The method of claim 16, wherein each galvo arm position corresponds to a detected signal intensity value position.

18. The method of claim 16, wherein the one or more detected signal intensity values is assigned to a preliminary probe position.

19. The method of claim 18, wherein the preliminary probe position is assigned to one or more preliminary pixel positions.

20. The method of claim 19, wherein each of the one or more preliminary pixel positions is based, at least in part, on the galvo arm position corresponding to the pixel position located at a leading edge of the calibration feature.