System and method for leakage control in a particle capture system

A method comprising:

• receiving, in single-cell format, a set of target cells into an array of wells defined at a surface plane of a substrate;
• receiving a set of particles into the array of wells, thereby co-capturing the set of target cells and the set of particles across the array of wells;
• achieving a state of specific capture for the array of wells, wherein a well of the array of wells in the state of specific capture has a target cell of the set of target cells and a particle of the set of particles and wherein the well has a width configured to prevent positioning of the target cell laterally next to the particle in the state of specific capture, upon receiving a washing fluid into a cavity in communication with the array of wells and transmitting excess particles of the set of particles away from the array of wells;
• providing the array of microwells at a temperature below 15° C.;
• receiving a lysis buffer into the array of microwells in laminar flow;
• receiving a partitioning fluid into the cavity, thereby displacing the lysis buffer from the cavity in laminar flow and partitioning each of the array of wells from adjacent wells of the array of wells, at the surface plane;
• transitioning the array of microwells to a temperature of above 25° C., thereby lysing the set of target cells;
• and
• retaining intercellular material of the set of target cells, individually with the set of particles within the array of wells, thereby mitigating leakage of intracellular material of a first well to a second well of the array of wells.