Methods for encapsulating and assaying cells

A process for encapsulating micro-objects in a microfluidic device, wherein the microfluidic device comprises an enclosure comprising a channel and a first chamber having an opening fluidically connecting the first chamber to the channel, wherein one or both of (i) at least a portion of surfaces forming the channel proximal to the opening of the first chamber and (ii) at least a portion of surfaces forming the first chamber proximal to the channel comprises a first hydrophobic coating, the process comprising:

• filling the channel and the first chamber in the enclosure of the microfluidic device with a first aqueous medium;
• disposing a first micro-object in the first chamber;
• and
• flowing a water immiscible fluidic medium into the channel, displacing substantially all of the first aqueous medium in the channel without substantially displacing the first aqueous medium in the first chamber, thereby reversibly encapsulating the first micro-object in the first chamber.