A system for deforming and analyzing a plurality of particles carried in a sample flow, the system comprising: a substrate defining an inlet, configured to receive the sample, and an outlet; a fluidic pathway fluidly coupled to the inlet and the outlet and comprising: a delivery region coupled to the inlet and configured to inertially focus the particles within the sample flow to a common streamline; a plurality of branch channels coupled to the delivery region; a deformation region formed by an intersection of the plurality of branch channels, wherein fluid flow within the deformation region induces deformation forces on the particles; an imaging subsystem comprising a first light source, an objective lens and a sensor, the first light source configured to transmit light through a portion of the fluidic pathway that includes the deformation region and into the objective lens, the objective lens configured to magnify light from the deformation region onto the sensor for generating a morphology dataset of one or more particles in the plurality of particles, the system being characterised in that at least one of the plurality of branch channels carries substantially all of the particles and in that the system further comprises a fluorescence subsystem comprising a second light source and a photomultiplier tube, the second light source configured to focus light onto a portion of the fluidic pathway, in which the focused light produces emitted light from fluorescent labels on the plurality of particles that is collected by the objective lens and focused onto the PMT for generating the fluorescence dataset characterizing fluorescence of one or more particles in the plurality of particles; and a processor configured to output a phenotype analysis of the plurality of particles based at least in part on the morphology dataset and the fluorescent dataset for the plurality of particles. a substrate defining an inlet, configured to receive the sample, and an outlet; a fluidic pathway fluidly coupled to the inlet and the outlet and comprising: a delivery region coupled to the inlet and configured to inertially focus the particles within the sample flow to a common streamline; a plurality of branch channels coupled to the delivery region; a deformation region formed by an intersection of the plurality of branch channels, wherein fluid flow within the deformation region induces deformation forces on the particles; an imaging subsystem comprising a first light source, an objective lens and a sensor, the first light source configured to transmit light through a portion of the fluidic pathway that includes the deformation region and into the objective lens, the objective lens configured to magnify light from the deformation region onto the sensor for generating a morphology dataset of one or more particles in the plurality of particles, the system being characterised in that at least one of the plurality of branch channels carries substantially all of the particles and in that the system further comprises a fluorescence subsystem comprising a second light source and a photomultiplier tube, the second light source configured to focus light onto a portion of the fluidic pathway, in which the focused light produces emitted light from fluorescent labels on the plurality of particles that is collected by the objective lens and focused onto the PMT for generating the fluorescence dataset characterizing fluorescence of one or more particles in the plurality of particles; and a processor configured to output a phenotype analysis of the plurality of particles based at least in part on the morphology dataset and the fluorescent dataset for the plurality of particles. a delivery region coupled to the inlet and configured to inertially focus the particles within the sample flow to a common streamline; a plurality of branch channels coupled to the delivery region; a deformation region formed by an intersection of the plurality of branch channels, wherein fluid flow within the deformation region induces deformation forces on the particles; an imaging subsystem comprising a first light source, an objective lens and a sensor, the first light source configured to transmit light through a portion of the fluidic pathway that includes the deformation region and into the objective lens, the objective lens configured to magnify light from the deformation region onto the sensor for generating a morphology dataset of one or more particles in the plurality of particles, the system being characterised in that at least one of the plurality of branch channels carries substantially all of the particles and in that the system further comprises a fluorescence subsystem comprising a second light source and a photomultiplier tube, the second light source configured to focus light onto a portion of the fluidic pathway, in which the focused light produces emitted light from fluorescent labels on the plurality of particles that is collected by the objective lens and focused onto the PMT for generating the fluorescence dataset characterizing fluorescence of one or more particles in the plurality of particles; and a processor configured to output a phenotype analysis of the plurality of particles based at least in part on the morphology dataset and the fluorescent dataset for the plurality of particles.