A particle processing system comprising: a microfluidic chip having: a plurality of microfluidic channels, an input region in which a sample containing particles is input into the microfluidic chip via the plurality of microfluidic channels, a plurality of interrogation regions downstream of the input region, each of the plurality of interrogation regions associated with a respective one of the plurality of microfluidic channels, and each of the plurality of interrogation regions positioned relative to an electromagnetic radiation source to receive an emitted output therefrom to interrogate the particles flowing therethrough via the plurality of microchannels, and a plurality of sorting mechanisms associated with a respective one of the plurality of microfluidic channels, downstream of the plurality of interrogation regions, for directing particles flowing within the respective channel into various downstream channels of the plurality of microfluidic channels; a detector system including one or more detector subsystems associated with the plurality of interrogation regions, at least one of the detector subsystems including a micro-lens array having a plurality of micro-lens systems (250, 250', 250", 250"', 250"", 250a, 250b, 250c, 250d), each micro-lens system having a first lens (252, 252', 252", 352, 452, 552) and a second lens (254, 254', 254", 354, 454, 554) arranged along a common optical axis; and wherein each of the plurality of micro-lens systems in the micro-lens array is configured and adapted to collect light emitted from one or more of the plurality of interrogation regions. a microfluidic chip having: a plurality of microfluidic channels, an input region in which a sample containing particles is input into the microfluidic chip via the plurality of microfluidic channels, a plurality of interrogation regions downstream of the input region, each of the plurality of interrogation regions associated with a respective one of the plurality of microfluidic channels, and each of the plurality of interrogation regions positioned relative to an electromagnetic radiation source to receive an emitted output therefrom to interrogate the particles flowing therethrough via the plurality of microchannels, and a plurality of sorting mechanisms associated with a respective one of the plurality of microfluidic channels, downstream of the plurality of interrogation regions, for directing particles flowing within the respective channel into various downstream channels of the plurality of microfluidic channels; a plurality of microfluidic channels, an input region in which a sample containing particles is input into the microfluidic chip via the plurality of microfluidic channels, a plurality of interrogation regions downstream of the input region, each of the plurality of interrogation regions associated with a respective one of the plurality of microfluidic channels, and each of the plurality of interrogation regions positioned relative to an electromagnetic radiation source to receive an emitted output therefrom to interrogate the particles flowing therethrough via the plurality of microchannels, and a plurality of sorting mechanisms associated with a respective one of the plurality of microfluidic channels, downstream of the plurality of interrogation regions, for directing particles flowing within the respective channel into various downstream channels of the plurality of microfluidic channels; a detector system including one or more detector subsystems associated with the plurality of interrogation regions, at least one of the detector subsystems including a micro-lens array having a plurality of micro-lens systems (250, 250', 250", 250"', 250"", 250a, 250b, 250c, 250d), each micro-lens system having a first lens (252, 252', 252", 352, 452, 552) and a second lens (254, 254', 254", 354, 454, 554) arranged along a common optical axis; and wherein each of the plurality of micro-lens systems in the micro-lens array is configured and adapted to collect light emitted from one or more of the plurality of interrogation regions.