System and method for automated single cell processing

A system for automatically processing a sample, the system comprising:

• a deck configured to support and position:
• a reagent cartridge at a first region of a first side of the deck;
• a sample processing cartridge at a second region of the first side;
• and
• a tool container at a third region of the first side;
• a fluid level detection subsystem coupled to the deck and aligned with an inlet reservoir of the sample processing cartridge upon positioning the sample processing cartridge at the deck, the fluid level detection subsystem configured to detect light transmitted across the inlet reservoir;
• a gantry coupled to the deck and comprising:
• a set of tracks defining paths of movement along a set of axes, within a three dimensional volume bound by the first side of the deck, for a pipette interface;
• and
• a base opposite the first side of the deck and supporting:
• a heating and cooling subsystem comprising a set of thermal bodies for transferring heat to the reagent cartridge and the sample processing cartridge;
• a separation subsystem comprising a set of magnets coupled to a magnet actuator configured to transition the set of magnets between a retracted state and an extended state, wherein in the extended state, the set of magnets passes into the first region of the deck;
• a pumping subsystem comprising a vacuum port extending into the second region.