Method for detecting particles using structured illumination

1. A method for detecting particles on a target, the method comprising the steps of:

for a region of the target, illuminating the target with a plurality of structured illumination patterns to generate a first series of raw intensity values for the region of the target, each structured illumination pattern characterized by a spatial frequency and an illumination phase, wherein each raw intensity value in the first series of raw intensity values is obtained by measuring a corresponding optical signal from the region of the target illuminated with a corresponding structured illumination pattern;

generating a first estimate that indicates whether a particle is present at the region of the target from the first series of raw intensity values;

for another region of the target, illuminating the target with the plurality of structured illumination patterns to generate a second series of raw intensity values for the another region of the target, wherein each raw intensity value in the second series of raw intensity values is obtained by measuring a corresponding optical signal from the another region of the target illuminated with a corresponding structured illumination pattern; and

generating a second estimate that indicates whether the particle or another particle is present at the another region of the target from the second series of raw intensity values.

2. The method of claim 1 , further comprising:

after generating the first estimate, for the region of the target, illuminating the target with the plurality of structured illumination patterns to generate a third series of raw intensity values for the region of the target, wherein each raw intensity value in the third series of raw intensity values is obtained by measuring a corresponding optical signal from the region of the target illuminated with a corresponding structured illumination pattern; and

generating a third estimate that indicates whether the particle is present at the region of the target from the third series of raw intensity values.

3. The method of claim 1 , wherein generating the first estimate comprises:

determining a first modulation score indicating a degree of variation in the first series of raw intensity values; and

generating the first estimate for the region of the target by comparing the first modulation score to a predetermined threshold.

4. The method of claim 3 , wherein determining the first modulation score comprises calculating a variance of two or more of the first series of raw intensity values, calculating a range of two or more of the first series of raw intensity values, calculating the variance of two or more of the first series of raw intensity values normalized by a mean of the two or more of the first series of raw intensity values, or a goodness-of-fit metric to a reference curve of two or more of the first series of raw intensity values.

5. The method of claim 3 , wherein determining the first modulation score comprises:

determining a set of sub-modulation scores, each sub-modulation score determined by combining a respective subset of the first series of raw intensity values; and

combining the set of sub-modulation scores to determine the first modulation score.

6. The method of claim 5 , wherein the respective subset of the first series of raw intensity values are obtained by illuminating the region of the target with a corresponding subset of the plurality of structured illumination patterns having a same spatial frequency.

7. The method of claim 1 , wherein the plurality of structured illumination patterns are selective excitation patterns.

8. The method of claim 1 , wherein the particle is a biological molecule including at least one of DNA segments, mRNA segments, or lncRNA.

9. The method of claim 1 , further comprising:

generating a reconstructed image by processing at least the first series of raw intensity values, the reconstructed image including a set of reconstructed intensity values obtained from processing the at least the first series of raw intensity values;

for the region of the target, determining a third estimate that indicates whether the particle is present at the region of the target based on one or more reconstructed intensity values corresponding to the region of the target; and

generating a combined estimate for the region of the target by comparing the first estimate to the third estimate.

10. The method of claim 1 , further comprising responsive to determining that the particle is present at the region of the target based on the first estimate, determining that the same particle is present at the another region of the target based on the second estimate.

11. The method of claim 1 , wherein the detection module is further configured to:

responsive to determining that the particle is present at the region of the target based on the first estimate, determine that the same particle is present at the another region of the target based on the second estimate.

12. A system for detecting particles on a target, the system comprising:

a plurality of illumination modules configured to illuminate a region of the target with a plurality of structured illumination patterns that are each characterized by a spatial frequency and an illumination phase, and at a later time, illuminate another region of the target with the plurality of structured illumination patterns,

an optical imaging module configured to generate a first series of raw intensity values for the region of the target, wherein each raw intensity value in the first series of raw intensity values is obtained by measuring a corresponding optical signal from the region of the target illuminated with a corresponding structured illumination pattern, and generate a second series of raw intensity values for the another region of the target, wherein each raw intensity value in the second series of raw intensity values is obtained by measuring a corresponding optical signal from the another region of the target illuminated with a corresponding structured illumination pattern; and

a detection module configured to generate, for the region of the target, a first estimate that indicates whether a particle is present at the region of the target from the first series of raw intensity values, and generate, for the another region of the target, a second estimate that indicates whether the particle or another particle is present at the another region of the target from the second series of raw intensity values.

13. The system of claim 12 ,

wherein the plurality of illumination modules is further configured to:

after generating the first estimate, for the region of the target, illuminate the target with the plurality of structured illumination patterns to generate a third series of raw intensity values for the region of the target, wherein each raw intensity value in the third series of raw intensity values is obtained by measuring a corresponding optical signal from the region of the target illuminated with a corresponding structured illumination pattern, and

wherein the detection module is further configured to:

generate a third estimate that indicates whether the particle is present at the region of the target from the third series of raw intensity values.

14. The system of claim 12 , wherein the detection module is further configured to:

determine a first modulation score indicating a degree of variation in the first series of raw intensity values; and

generate the first estimate for the region of the target by comparing the first modulation score to a predetermined threshold.

15. The system of claim 14 , wherein the first modulation score is determined by calculating a variance of two or more of the first series of raw intensity values, calculating a range of two or more of the first series of raw intensity values, calculating the variance of two or more of the first series of raw intensity values normalized by a mean of the two or more of the first series of raw intensity values, or a goodness-of-fit metric to a reference curve of two or more of the first series of raw intensity values.

16. The system of claim 14 , wherein the detection module is further configured to:

determine a set of sub-modulation scores, each sub-modulation score determined by combining a respective subset of the first series of raw intensity values; and

combine the set of sub-modulation scores to determine the first modulation score.

17. The system of claim 16 , wherein the respective subset of the first series of raw intensity values are obtained by illuminating the region of the target with a corresponding subset of the plurality of structured illumination patterns having a same spatial frequency.

18. The system of claim 12 , wherein the plurality of structured illumination patterns are selective excitation patterns.

19. The system of claim 12 , wherein the particle is a biological molecule including at least one of DNA segments, mRNA segments, or lncRNA.

20. The system of claim 12 , further comprising:

a reconstruction module configured to generate a reconstructed image by processing at least the first series of raw intensity values, the reconstructed image including a set of reconstructed intensity values obtained from processing the at least the first series of raw intensity values, and

wherein the detection module is further configured to:

for the region of the target, determine a third estimate that indicates whether the particle is present at the region of the target based on one or more reconstructed intensity values corresponding to the region of the target; and

generate a combined estimate for the region of the target by comparing the first estimate to the third estimate.