Systems and methods for optically processing samples

1. A mixture comprising:

an encapsulation reagent;

one or more first particles suspended in aqueous media, each first particle comprising a first binding partner; and

a population of cells, comprising at least one cell of interest that secretes a protein of interest having a second binding partner, wherein the first binding partner is specific to the second binding partner.

2. A method of preparing a sample for a clustering assay system, the method comprising:

providing a population of cells, the population of cells comprising at least one cell of interest;

combining the population of cells, a first plurality of particles, and an encapsulation reagent to create a mixture, wherein each particle of the first plurality of particles is suspended in aqueous media and comprises a first binding partner that is specific to a second binding partner secreted by the at least one cell of interest; and

agitating the mixture to create an emulsion, thereby encapsulating the population of cells into a plurality of polydisperse sample entities.

3. A method of selecting at least one cell of interest from a population of cells, the method comprising:

providing an emulsion comprising the population of cells and a first plurality of particles, wherein the population of cells and the first plurality of particles are encapsulated into a plurality of polydisperse sample entities, and wherein each particle of the first plurality of particles is suspended in aqueous media and comprises a first binding partner that is specific to a second binding partner secreted by the at least one cell of interest;

measuring a signal for at least one sample entity, wherein the signal is at least partially associated with binding of the first and second binding partners; and

identifying the at least one cell of interest based at least in part on the measured signal.

4. The method of claim 3 , wherein the second binding partner is coupled to a first component of a protein of interest secreted by the at least one cell of interest, and wherein the measured signal quantifies the protein of interest in the at least one sample entity.

5. The method of claim 4 , wherein identifying the at least one cell of interest comprises identifying at least a portion of the sample entities that has a measured signal greater than a predetermined threshold.

6. The method of claim 3 , wherein measuring the signal for the at least one sample entity comprises receiving at least one shadow image of the at least one sample entity, and determining a size score of at least one object in the sample entity based on the at least one shadow image, wherein the measured signal is based at least in part on the size score.

7. The method of claim 3 , the emulsion further comprising a second plurality of particles encapsulated into the plurality of polydisperse sample entities, wherein each particle of the second plurality of particles comprises a third binding partner that is specific to a fourth binding partner secreted by the at least one cell of interest, and wherein the signal is at least partially associated with a binding of the first and second binding partners, and at least partially associated with a binding of the third and fourth binding partners.

8. The method of claim 7 , wherein the second binding partner and the fourth binding partner are associated with a protein of interest secreted by the at least one cell of interest, and wherein the measured signal quantifies binding affinity of the protein of interest to the first binding partner or the third binding partner.

9. The method of claim 3 , further comprising the step of removing the at least one cell of interest from the polydisperse sample entities.

10. The method of claim 3 , wherein the first plurality of particles comprise a second population of cells, and the first binding partner comprises antigens expressed on the second population of cells.