A system, comprising: a) a sample processing unit (104, 332), comprising a rotating container having at least one sample chamber for holding and processing of a sample, wherein the rotating container comprises a means for detecting the progress of separation (188; 237; 810) of at least a first component and a second component of a deposited sample in the rotating container, and an input port and an output port coupled to the rotating container, wherein the sample processing unit (104, 332) is configured - to rotate the container so as to apply a centrifugal force to the sample deposited in the chamber and separate at least the first component and the second component of the deposited sample; and b) a magnetic sample separation unit coupled to the output port of the sample processing unit (104, 332), the sample separation unit comprising - a separation column holder, - a pump, and - a plurality of valves (1-11; 12, 14, 15, 16; 17; 18; 19; 110; 310, 311; 424, 425; 427, 428, 429) configured to at least partially control fluid flow through a fluid circuitry, and - a separation column (2; 40; 322) positioned in the holder, wherein the separation column (2; 40; 322) is configured to separate magnetically labeled and unlabeled components of sample flowed through the column (2; 40; 322). a) a sample processing unit (104, 332), comprising a rotating container having at least one sample chamber for holding and processing of a sample, wherein the rotating container comprises a means for detecting the progress of separation (188; 237; 810) of at least a first component and a second component of a deposited sample in the rotating container, and an input port and an output port coupled to the rotating container, wherein the sample processing unit (104, 332) is configured - to rotate the container so as to apply a centrifugal force to the sample deposited in the chamber and separate at least the first component and the second component of the deposited sample; and a rotating container having at least one sample chamber for holding and processing of a sample, wherein the rotating container comprises a means for detecting the progress of separation (188; 237; 810) of at least a first component and a second component of a deposited sample in the rotating container, and an input port and an output port coupled to the rotating container, wherein the sample processing unit (104, 332) is configured - to rotate the container so as to apply a centrifugal force to the sample deposited in the chamber and separate at least the first component and the second component of the deposited sample; and - to rotate the container so as to apply a centrifugal force to the sample deposited in the chamber and separate at least the first component and the second component of the deposited sample; and b) a magnetic sample separation unit coupled to the output port of the sample processing unit (104, 332), the sample separation unit comprising - a separation column holder, - a pump, and - a plurality of valves (1-11; 12, 14, 15, 16; 17; 18; 19; 110; 310, 311; 424, 425; 427, 428, 429) configured to at least partially control fluid flow through a fluid circuitry, and - a separation column (2; 40; 322) positioned in the holder, wherein the separation column (2; 40; 322) is configured to separate magnetically labeled and unlabeled components of sample flowed through the column (2; 40; 322). - a separation column holder, - a pump, and - a plurality of valves (1-11; 12, 14, 15, 16; 17; 18; 19; 110; 310, 311; 424, 425; 427, 428, 429) configured to at least partially control fluid flow through a fluid circuitry, and - a separation column (2; 40; 322) positioned in the holder,