System and method for determining an immune activation state

A system for diagnosing a probability of sepsis in a patient comprising:

• a sample preparation subsystem comprising:
• a sample holder configured to retain a test tube comprising a blood sample from the patient;
• a spindle configured to attach to the test tube via a seal, wherein the spindle comprises one or more reagent ports fluidly connected to a reagent reservoir, and to a vacuum pump, wherein the spindle is configured to centrifuge the blood sample within the test tube to generate a prepared blood sample;
• a cytometry module comprising:
• a microfluidic cartridge configured to receive the prepared blood sample from the sample preparation subsystem, wherein the microfluidic cartridge comprises a microfluidic channel with a deformation region wherein a stress is applied to cells within the deformation region;
• a heating element configured to maintain a temperature of the microfluidic cartridge at a target temperature;
• an imaging system comprising an image sensor and a microscope;
• and
• a pressure system connected to the microfluidic channel, wherein the pressure system displaces the prepared blood sample through the microfluidic cartridge;
• and
• an image analysis system configured to:
• analyze images of the prepared blood sample acquired using the imaging system;
• and
• determine the probability that the patient has sepsis.