Methods and apparatus for measuring analytes

Patent metadata

Field	Value
Publication number	US-10451585-B2
Application number	US-201514926264-A
Country	US
Kind code	B2
Filing date	Oct 29, 2015
Priority date	May 29, 2009
Publication date	Oct 22, 2019
Grant date	Oct 22, 2019

Abstract

A method is provided to sample a sensor array. The method can include measuring a waveform associated with a chemical event occurring on the sensor array. The waveform can include at least one region associated with expected measured values and at least one region associated with unpredictable measured values. The method can also include applying a first frame averaging to the at least one region associated with the expected measured values. Here, a first number of frames can be included in the first frame averaging. Further, the method can include applying a second frame averaging to the at least one region associated with the unpredictable measured values, where a second number of frames can be included in the second frame averaging. The second number of frames can be less than the first number of frames.

First claim

What is claimed is:

1. A method comprising:
measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values;
applying a first frame averaging to the at least one region associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one region associated with the expected measured values to form first frame-averaged data, wherein the first frame-averaged data have a reduced amount of data for the region associated with the expected measured values;
applying a second frame averaging to the at least one region associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one region associated with the unpredictable measured values, the second number of frames being lower than the first number of frames, to form second frame-averaged data, wherein the second frame-averaged data have a reduced amount of data for the region associated with the unpredictable measured values;
applying a third frame averaging to a second region of the waveform, wherein the second region is associated with another portion of the waveform with expected measured values, and wherein the third frame averaging comprises averaging a third number of frames during the second region, the third number of frames being higher than the second number of frames, wherein the third frame averaging forms third frame-averaged data, wherein the third frame-averaged data have a reduced amount of data for the second region associated with another portion of the waveform with expected measured values; and
applying a keyframe delta compression to the frame-averaged data resulting from the first, second, and third frame averaging, wherein the keyframe delta compression comprises:
storing in a memory an initial value for each pixel in a keyframe of the frame-averaged data,
calculating a difference between a value for each pixel of a second frame of the frame-averaged data and a corresponding initial value for each pixel of the keyframe to form difference values, and
storing in the memory the difference values between the keyframe and the second frame, wherein the keyframe of frame-averaged data and the difference values provide compressed data associated with the waveform for storing in the memory.

2. The method of claim 1 , wherein the measuring the waveform comprises measuring the waveform of a dynamic response of an ion-sensitive field effect transistor (ISFET) array to a change in ionic strength of an analyte solution in fluid contact with the ISFET array.

3. The method of claim 2 , wherein the measuring the waveform of the dynamic response of the ISFET array comprises associating the at least one region with the unpredictable measured values to a stepwise increase in ion concentration in the analyte solution and associating the at least one region with the expected measured values to at least one portion of the dynamic response outside of the stepwise increase in ion concentration.

4. The method of claim 3 , wherein the applying the first frame averaging comprises averaging the first number of frames during the at least one portion of the dynamic response outside of the stepwise increase in ion concentration.

5. The method of claim 3 , wherein the applying the second frame averaging comprises averaging the second number of frames during the stepwise increase in ion concentration in the analyte solution.

6. The method of claim 1 , wherein the keyframe delta compression further comprises:
using a first number of bits to store in the memory the initial value for each pixel in the keyframe; and
using a second number of bits to store in the memory the difference value between the keyframe and the second frame, wherein the second number of bits is less than the first number of bits.

7. A computer program product comprising a computer-usable medium having computer program logic recorded thereon that, when executed by one or more processors, compresses waveform data from a sensor array, the computer program logic comprising:
first computer readable program code that enables a processor to receive measured values of a waveform associated with a chemical event occurring on the sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values;
second computer readable program code that enables the processor to apply a first frame averaging to the at least one region associated with the expected measured values, wherein the first frame averaging comprises averaging a first number of frames during the at least one region associated with the expected measured values to form first frame-averaged data, wherein the first frame-averaged data have a reduced amount of data for the region associated with the expected measured values;
third computer readable program code that enables the processor to apply a second frame averaging to the at least one region associated with the unpredictable measured values, wherein the second frame averaging comprises averaging a second number of frames during the at least one region associated with the unpredictable measured values, the second number of frames being lower than the first number of frames, to form second frame-averaged data, wherein the second frame-averaged data have a reduced amount of data for the region associated with the unpredictable measured values;
fourth computer readable program code that enables the processor to apply a third frame averaging to a second region of the waveform, wherein the second region is associated with a another portion of the waveform with expected measured values, and wherein the third frame averaging comprises averaging a third number of frames during the second region, the third number of frames being higher than the second number of frames, wherein the third frame averaging forms third frame-averaged data, wherein the third frame-averaged data have a reduced amount of data for the second region associated with another portion of the waveform with expected measured values; and
fifth computer readable program code that enables the processor to apply a keyframe delta compression to the frame-averaged data resulting from the first, second, and third frame averaging, wherein the keyframe delta compression comprises:
storing in a memory an initial value for each pixel in a keyframe of the frame-averaged data,
calculating a difference between a value for each pixel of a second frame of the frame-averaged data and a corresponding initial value for each pixel of the keyframe to form difference values, and
storing in the memory the difference values between the keyframe and the second frame, wherein the keyframe of frame-averaged data and the difference values provide compressed data associated with the waveform for storing in the memory.

8. The computer program product of claim 7 , wherein the waveform comprises a dynamic response of an ion-sensitive field effect transistor (ISFET) array to a change in ionic strength of an analyte solution in fluid contact with the ISFET array.

9. The computer program product of claim 8 , wherein the computer program logic further comprises:
sixth computer readable program code that enables the processor to associate the at least one region with the unpredictable measured values to a stepwise increase in ion concentration in the analyte solution and associating the at least one region with the predictable measured values to at least one

Assignees

• Life Technologies Corp

Inventors

• Rearick Todd
• Beauchemin Mark

Classifications

• G01N27/4145 Primary

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• G01N27/27

  Association of two or more measuring systems or cells, each measuring a different parameter, where the measurement results may be either used independently, the systems or cells being physically associated, or combined to produce a value for a further parameter · CPC title

• G01N27/4148

  Integrated circuits therefor, e.g. fabricated by CMOS processing · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title