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Model organisms play an important role in our understanding of basic life science.In recent years,microfluidics as an emerging platform has been dedicated to manipulating and imaging small model organisms.Thus far,precisely controlling dynamic microenvironments,high-efficient trapping,separating and real-time tracking of live model organisms in microfluidics are still the bottleneck has to be addressed.We have developed two microfluidic systems for high-efficient separation and real-time detection of small model organisms in Caenorhabditis elegans and Chlamydomonas reinhardtii.A microfluidic system of real-time monitoring of flagellar length in living Chlamydomonas at the single cell level was developed.Sequential flow of gas-liquid plugs combined with optimum microwells allowed complete,automated and fast media exchange with good time resolution.Applying this technique,Chlamydomonas were trapped into the microwells for real-time monitoring of the instantaneous and long-term dynamics of flagellar lengths in response to extracellular stimuli.Our microfluidic system is easy to set up and operate,which reduces the early costs to biology labs interested in adopting microfluidics to study flagellar length in Chlamydomonas.A simple microfluidic platform for the separation of all stages of C.elegans with high efficiency and high throughput was developed.The separation was achieved via micropillars filtration for size restriction and reversible bonding for recovery of the trapped worms.At a low pressure,the younger worms passed through the sorting chamber while preventing the older ones; while,at a high pressure,the micropillars inside of sorting chamber were deformed and detached from the substrate for releasing all trapped worms at the old stage.Using this system,all stages of worms were sorted in a high-efficiency/throughput manner without affecting their viability.The mechanism of size-based restriction is a general methodology that could be used for separation of other mobile organisms.