Self-contained slide processing unit for biological specimens

A biological specimen processing system comprising:

• a fluidic handling unit comprising:
• a baseplate;
• a fluidic inlet block;
• a fluidic outlet block;
• a first pump in fluidic communication with the fluidic inlet block;
• a second pump in fluidic communication with the fluidic outlet block;
• a carrier control board in electrical communication with the first pump and the second pump;
• and
• a rotary encoder system arranged to monitor an angular motion of a rotating portion of the first pump and the second pump, wherein the carrier control board is in electrical communication with the rotary encoder system, and wherein the rotary encoder system comprises:
• a first optical encoder wheel attached to the rotating portion of the first pump;
• a first reflectance sensor arranged to capture infrared reflection off of the first optical encoder wheel;
• a second optical encoder wheel attached to the rotating portion of the second pump;
• and
• a second reflectance sensor arranged to capture infrared reflection off of the second optical encoder wheel.

A method for processing a biological specimen comprising:

• disposing a microfluidic flow cell in a microfluidic flow cell receiving area of a flow cell carrier;
• attaching the flow cell carrier to a fluidic handling unit, the fluidic handling unit comprising:
• a baseplate,
• a fluidic inlet block,
• a fluidic outlet block,
• a pump in fluidic communication with the fluidic inlet block and the fluidic outlet block,
• a carrier control board in electrical communication with the pump, and
• a rotary encoder system arranged to monitor an angular motion of a rotating portion of the pump, and wherein the carrier control board is in electrical communication with the rotary encoder system;
• adding fluid to the fluidic inlet block;
• and
• pumping fluid through the microfluidic flow cell.

A biological specimen processing system comprising:

• a fluidic handling unit comprising:
• a baseplate;
• a fluidic inlet block;
• a fluidic outlet block;
• a pump in fluidic communication with the fluidic inlet block and the fluidic outlet block;
• a carrier control board in electrical communication with the pump;
• a flow cell carrier comprising a microfluidic flow cell receiving area, wherein the flow cell carrier is configured to receive and retain the fluidic handling unit, wherein the fluidic inlet block and the fluidic outlet block are each arranged to form a fluidic connection with a microfluidic flow cell when the microfluidic flow cell is disposed in the microfluidic flow cell receiving area and when the fluidic handling unit is disposed in the flow cell carrier;
• and
• a rotary encoder system arranged to monitor an angular motion of a rotating portion of the pump, wherein the carrier control board is in electrical communication with the rotary encoder system.

A biological specimen processing system comprising:

• a fluidic handling unit comprising:
• a baseplate;
• a fluidic inlet block;
• a fluidic outlet block;
• a pump in fluidic communication with the fluidic inlet block and the fluidic outlet block;
• a carrier control board in electrical communication with the pump;
• a flow cell carrier comprising a microfluidic flow cell receiving area and a microfluidic flow cell disposed in the microfluidic flow cell receiving area, wherein the flow cell carrier is configured to receive and retain the fluidic handling unit;
• and
• a rotary encoder system arranged to monitor an angular motion of a rotating portion of the pump, wherein the carrier control board is in electrical communication with the rotary encoder system.