METHODS AND SYSTEMS FOR OBTAINING AND PROCESSING SEQUENCING DATA

1 .- 123 . (canceled)

124 . A method of determining nucleic acid sequences of a plurality of sequencing colonies, comprising:

obtaining an input image of a surface, wherein the plurality of sequencing colonies are attached to the surface;

detecting a set of sequencing colonies of the plurality of sequencing colonies in the input image;

executing in parallel, using a graphics processor, a plurality of iterative processes to obtain signal amplitudes for the detected set of sequencing colonies,

wherein each iterative process in the plurality of iterative processes corresponds to a respective sequencing colony in the detected set of sequencing colonies, and

wherein each iterative process comprises:

(a) obtaining amplitude, location, and profile estimates of one or more neighboring sequencing colonies that are adjacent to the respective sequencing colony;

(b) calculating, using the graphics processor, a crosstalk value for the respective sequencing colony based on the amplitude, location, and profile estimates of the one or more neighboring sequencing colonies;

(c) subtracting, using the graphics processor, the crosstalk value and a colony-specific background to obtain a current signal amplitude estimate of the respective sequencing colony;

(d) performing a next iteration of (a)-(c) for a predetermined number of times or until a condition is met; and

determining, at least partially based on the signal amplitudes for the detected set of sequencing colonies, portions of nucleic acid sequences of the plurality of sequencing colonies.

125 . The method of claim 124 , wherein each iterative process further comprises: determining, using the graphics processor, a current location estimate of the respective sequencing colony.

126 . The method of claim 124 , wherein each iterative process further comprises: determining, using the graphics processor, one or more current profile properties of the respective sequencing colony.

127 . The method of claim 126 , wherein the one or more current profile properties include a current full width at half maximum (“FWHM”) estimate, a pseudo-Voigt Lorentzian weight (tail) parameter, or parameters of an elliptic model.

128 . The method of claim 124 ,

wherein the input image is a first input image corresponding to a first flow step,

wherein the obtained signal amplitudes correspond to the first flow step, and

wherein the method further comprises:

obtaining a second input image corresponding to a second flow step; and

obtaining signal amplitudes corresponding to the second flow step.

129 . The method of claim 128 , further comprising: identifying, based on the signal amplitudes corresponding to the first flow step and the second flow step, the nucleic acid sequences of the plurality of sequencing colonies.

130 . The method of claim 124 , further comprising:

a. capturing the input image of the surface; and

b. combining the plurality of sequencing colonies with nucleotides before capturing the input image, wherein at least a portion of the nucleotides are labeled.

131 . The method of claim 124 , wherein detecting the set of sequencing colonies comprises: applying one or more filters to the input image.

132 . The method of claim 131 , wherein the one or more filters comprise a Gaussian filter.

133 . The method of claim 131 , further comprising: obtaining, based on a global background value, a binary image having a plurality of pixel values.

134 . The method of claim 133 , further comprising: grouping, based on the plurality of pixel values, pixels of the binary image into the detected set of sequencing colonies.

135 . The method of claim 124 , further comprising determining an initial location for each of the detected set of sequencing colonies.

136 . The method of claim 135 , wherein the initial location is a sub-pixel location.

137 . The method of claim 135 , wherein the determination comprises a center of mass estimation.

138 . The method of claim 124 , further comprising:

dividing the input image into a plurality of sub-images;

identifying, for each sub-image of the plurality of sub-images, a respective group of pixels in the respective sub-image based on pixel-specific amplitude information;

extending, for each sub-image, the respective group of pixels;

calculating, for each sub-image, a local background value based on the extended respective group of pixels; and

generating a background map based on local background values of the plurality of sub-images.

139 . The method of claim 138 , further comprising: deriving a colony-specific background for each detected sequencing colony of the detected set of sequencing colonies by bi-linear interpolation of the background map.

140 . The method of claim 138 , further comprising: deriving a global background value based on a median of all extended groups of pixels for the plurality of sub-images.

141 . The method of claim 124 , further comprising: capturing an arc-shaped or ring-shaped image of the surface.

142 . The method of claim 141 , further comprising: dividing the captured image into a plurality of image tiles, wherein the input image is one image tile of the plurality of image tiles.

143 . The method of claim 124 , further comprising:

detecting a plurality of sequencing colonies in a reference image;

generating a simulated image based on the plurality of detected sequencing colonies in the reference image;

subtracting the simulated image from the reference image to obtain a residual image; and

detecting one or more additional sequencing colonies based on the residual image.