Instrument systems for integrated sample processing

Abstract

An integrated system for processing and preparing samples for analysis may include a microfluidic device including a plurality of parallel channel networks for partitioning the samples including various fluids, and connected to a plurality of inlet and outlet reservoirs, at least a portion of the fluids comprising reagents, a holder including a closeable lid hingedly coupled thereto, in which in a closed configuration, the lid secures the microfluidic device in the holder, and in an open configuration, the lid is a stand orienting the microfluidic device at a desired angle to facilitate recovery of partitions or droplets from the partitioned samples generated within the microfluidic device, and an instrument configured to receive the holder and apply a pressure differential between the plurality of inlet and outlet reservoirs to drive fluid movement within the channel networks.

1 - 20 . (canceled) 
     
     
         21 . A method for measurement of parameters of fluid in samples for analysis in a microfluidic device, the method comprising:
 positioning an optical detector in optical communication with a channel segment of at least one fluid channel of the microfluidic device;   imaging, by the optical detector, in a detection line across the channel segment; and   processing images of particulate or droplet based materials of the samples as the materials pass through the detection line to determine parameters of the fluid.   
     
     
         22 . The method of  claim 21 , wherein the optical detector and the detection line are angled from an axis perpendicular to the channel segment. 
     
     
         23 . The method of  claim 22 , wherein the optical detector is angled from 5-80 degrees from an axis perpendicular to the channel segment. 
     
     
         24 . The method of  claim 21 , wherein the optical detector comprises at least one line scan sensor. 
     
     
         25 . The method of  claim 21 , further comprising determining the shape or size of the materials in the fluid. 
     
     
         26 . The method of  claim 21 , wherein the channel segment is downstream of a partitioning segment of the fluid channel of the microfluidic device. 
     
     
         27 . The method of  claim 21 , wherein the channel segment is upstream of a partitioning segment of the fluid channel of the microfluidic device. 
     
     
         28 . An optical detection system for measurement of parameters of fluid in samples for analysis in a microfluidic device, the system comprising an optical detector configured to image a fluid in a detection line across a channel segment of a first channel of the microfluidic device and to measure at least a parameter of the fluid in the channel segment; and a stage for holding the microfluidic device. 
     
     
         29 . The system of  claim 28 , further comprising the microfluidic device. 
     
     
         30 . The system of  claim 29 , wherein the first channel comprises a partitioning segment, a pre-partitioning segment, and a post partitioning segment. 
     
     
         31 . The system of  claim 30 , wherein the channel segment is the post-partitioning segment. 
     
     
         32 . The system of  claim 30 , wherein the channel segment is the pre-partitioning segment. 
     
     
         33 . The system of  claim 28 , wherein the optical detector comprises at least one line scan sensor. 
     
     
         34 . The system of  claim 28 , further comprising one or more light sources to direct illumination at the channel segment. 
     
     
         35 . The system of  claim 28 , wherein the optical detector comprises an objective lens. 
     
     
         36 . The system of  claim 28 , wherein the optical detector comprises a spectral filter. 
     
     
         37 . The system of  claim 28 , wherein the optical detector comprises a dichroic mirror. 
     
     
         38 . The system of  claim 28 , wherein the optical detector comprises a light microscope. 
     
     
         39 . The system of  claim 28 , wherein the optical detector detects fluorescence. 
     
     
         40 . The system of  claim 28 , wherein the optical detector is angled from an axis perpendicular to the channel segment.