Sample processing system and methods

A system for separating cells, comprising:

• a) a sample processing unit, comprising an input port, an output port, and a centrifuge chamber,
• wherein the centrifuge chamber comprises a circular bottom, a circular top, and a wall passing therebetween, thus forming an internal compartment that is configured to contain and process a biological sample comprising cells;
• wherein the sample processing unit is configured to rotate the centrifuge chamber about an axis that passes through the circular bottom and the circular top so as to apply a centrifugal force to a sample deposited in the chamber and thereby to separate at least a first component and a second component of the deposited sample;
• wherein the input port and the output port are configured and positioned to deliver a sample to and from the internal compartment while the centrifuge chamber is rotating;
• wherein the centrifuge chamber comprises a detection window that extends radially in the bottom or top of the chamber from a position adjacent to the rotation axis to a position near the perimeter of the chamber;
• and
• wherein the sample processing unit further comprises a detector that is constructed and aligned to receive light passing through a sample in the detection window of the centrifuge chamber so as to assess a characteristic of the deposited sample radially through and along the detection window, thereby monitoring separation of the first component from the second component in the chamber;
• the system further comprising:
• b) a sample separation unit coupled to the output port of the sample processing unit, the sample separation unit comprising:
• a separation column holder,
• a pump,
• a plurality of valves configured to at least partially control fluid flow through a fluid circuitry, and
• a separation column positioned in the holder, wherein the separation column is configured to separate labeled and unlabeled components of a sample flowed through the column.