Methods and apparatus for measuring analytes using chemfet arrays
Methods and apparatus relating to FET arrays including large FET arrays for monitoring chemical and/or biological reactions such as nucleic acid sequencing-by-synthesis reactions. Some methods provided herein relate to improving signal (and also signal to noise ratio) from released hydrogen ions during nucleic acid sequencing reactions.
1. A method of determining pixel values comprising:
selecting at least one row of pixels to be read out of an array of pixels, wherein the array of pixels is arranged in a plurality of rows and columns; each pixel including a reaction chamber and a chemically-sensitive sensor;
outputting pixel data for the selected at least one row of pixels at a first rate, wherein a first sampling period of the first rate is a time period that is insufficient for an output signal to settle to a final value;
converting the pixel data at a second rate that is multiple times the first rate such that an oversampled pixel data set is made for each pixel in the at least one row of pixels;
determining an estimated pixel value from the oversampled pixel data set for each pixel in the at least one row of pixels by implementing a settling correction that compensates for the incomplete settling of the output signal;
generating a frame of data from an estimated pixel value for each pixel in the array of pixels, and
averaging a series of frames; each frame comprising an estimated value for each pixel in the array, thereby creating a final frame of data.
2. The method of claim 1 , wherein the second rate is less than 5 times the first rate.
3. The method of claim 1 , wherein the second rate is 5 times the first rate.
4. The method of claim 1 , wherein the second rate is greater than 5 times the first rate.
5. The method of claim 1 , wherein implementing the settling correction includes employing an application specific integrated circuit (ASIC).
6. The method of claim 1 , wherein implementing the settling correction includes employing a gate array.
7. The method of claim 1 , wherein implementing the settling correction includes employing a field programable gate array (FPGA).
8. The method of claim 1 , wherein converting the pixel data to provide the oversampled pixel data set comprises oversampling the pixel data using analog-to-digital converters (ADCs).
9. The method of claim 1 , wherein each pixel in the array of pixels includes an ion-sensitive field effect (ISFET) transistor.
10. The method of claim 9 , wherein outputting the pixel data comprises outputting pixel data indicative of a reaction in the reaction chamber.
11. The method of claim 10 , wherein outputting the pixel data comprises outputting the pixel data in response to formation of a byproduct of a sequencing reaction.
12. The method of claim 11 , wherein the byproduct of the sequencing reaction is hydrogen ions.
13. The method of claim 11 , wherein the byproduct of the sequencing reaction is pyrophosphate ions.
14. The method of claim 11 , wherein the byproduct of the sequencing reaction is inorganic phosphate ions.
15. The method of claim 1 , wherein selecting at least one row of pixels comprises selecting at least one row from an array of at least 10 6 pixels.