Sample processing system and methods

1. 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.

2. The system according to claim 1 , configured so that light from a light source can at least partially penetrate through at least a part of a sample that is being separated in the centrifuge chamber through the detection window, and light passing through at least part of the sample can be detected by a light detector.

3. The system according to claim 1 , wherein the detector is positioned such that it can monitor separation of the components in the centrifuge chamber through the detection window from an area adjacent to the rotation axis of the centrifuge chamber to an area adjacent to the perimeter of the container.

4. The system according to claim 1 , wherein a prism or a mirror is positioned radially along the detection window.

5. The system according to claim 4 , wherein the prism or mirror is positioned to cover a channel that is positioned in or near a lid of the centrifuge chamber, wherein the channel is configured such that at least a part of the sample can flow into it during centrifugation.

6. The system according to claim 1 , wherein the centrifuge chamber comprises a plurality of layered surfaces between the top and the bottom and perpendicular to the rotational axis upon which cells may be cultured.

7. The system according to claim 6 , wherein the centrifuge chamber comprises at least one layer of growing cells thereon.

8. The system according to claim 7 wherein the centrifuge chamber is disposable and/or can be sterilized.

9. The system according to claim 1 , wherein the centrifuge chamber comprises a material chosen from the group consisting of: plastics, polystyrol (PS), polystyrene, polyvinylchloride, polycarbonate, glass, polyacrylate, polyacrylamide, polymethylmethacrylate (PMMA), polyethylene terephthalate (PET), polytetrafluoroethylene (PTFE), thermoplastic polyurethane (TPU), silicone, polyethylene (PE), collagen, chitin, alginate, hyaluronic acid derivatives, polylactide (PLA), polyglycolide (PGA) and their copolymers, polystyrol (PS), polycarbonate, polyacrylate, ceramics, hydroxyapatite (HA), calcium phosphate, and combinations thereof.

10. The system according to claim 1 , wherein the inlet port of the sample processing unit is connected to the internal compartment of the centrifuge chamber by way of a central line that passes through rotational seals and along the rotational axis.

11. The system according to claim 1 , wherein both the inlet port and the outlet port of the sample processing unit are connected to the internal compartment of the centrifuge chamber by way of an inner line and an outer line that both pass through rotational seals and along the rotational axis.