Fast and selective isolation of single cells with unique spatial and morphological traits remains a technical challenge. Here, we address this by establishing high-speed image-enabled cell sorting (ICS), which records multicolor fluorescence images and sorts cells based on measurements from image data at speeds up to 15,000 events per second. We show that ICS quantifies cell morphology and localization of labeled proteins and increases the resolution of cell cycle analyses by separating mitotic stages. We combine ICS with CRISPR-pooled screens to identify regulators of the nuclear factor κB (NF-κB) pathway, enabling the completion of genome-wide image-based screens in about 9 hours of run time. By assessing complex cellular phenotypes, ICS substantially expands the phenotypic space accessible to cell-sorting applications and pooled genetic screening.

The ability to control the shape of a flow in a passive microfluidic device enables potential applications in chemical reaction control, particle separation, and complex material fabrication. Recent work has demonstrated the concept of sculpting fluid streams in a microchannel using a set of pillars or other structures that individually deform a flow in a predictable pre-computed manner. These individual pillars are then placed in a defined sequence within the channel to yield the composition of the individual flow deformations -and ultimately complex user-defined flow shapes. In this way, an elegant mathematical operation can yield the final flow shape for a sequence without an experiment or additional numerical simulation. Although these approaches allow for programming complex flow shapes without understanding the detailed fluid mechanics, the design of an arbitrary flow shape of interest remains difficult, requiring significant design iteration. The development of intuitive basic operations (i.e. higher-level functions that consist of combinations of obstacles) that act on the flow field to create a basis for more complex transformations would be useful in systematically achieving a desired flow shape. Here, we show eight transformations that could serve as a partial basis for more complex transformations. We initially used inhouse, freely available custom software (uFlow), which allowed us to arrive at these transformations that include making a fluid stream concave and convex, tilting, stretching, splitting, adding a vertex, shifting, and encapsulating another flow stream. The pillar sequences corresponding to these transformations were subsequently fabricated and optically analyzed using confocal imaging -yielding close agreement with uFlowpredicted shapes. We performed topological analysis on each transformation, characterizing potential sequences leading to these outputs and trends associated with changing diameter and placement of the pillars. We classify operations into four sets of sequence-building concatenations: stacking, recursion, mirroring, and shaping. The developed basis should help in the design of microfluidic systems that have a phenomenal variety of applications, such as optofluidic lensing, enhanced heat transfer, or new polymer fiber design.

Microparticles with complex 3D shape and composition are produced using a novel fabrication method, optical transient liquid molding, in which a 2D light pattern exposes a photopolymer precursor stream shaped along the flow axis by software-aided inertial flow engineering.

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Standard tissue culture of adherent cells is known to poorly replicate physiology and often entails suspending cells in solution for analysis and sorting, which modulates protein expression and eliminates intercellular connections. To allow adherent culture and processing in flow, we present 3D-shaped hydrogel cell microcarriers, which are designed with a recessed nook in a first dimension to provide a tunable shear-stress shelter for cell growth, and a dumbbell shape in an orthogonal direction to allow for self-alignment in a confined flow, important for processing in flow and imaging flow cytometry. We designed a method to rapidly design, using the genetic algorithm, and manufacture the microcarriers at scale using a transient liquid molding optofluidic approach. The ability to precisely engineer the microcarriers solves fundamental challenges with shear-stress-induced cell damage during liquid-handling, and is poised to enable adherent cell culture, in-flow analysis, and sorting in a single format.

of structures, we use software that numerically predicts the total deformation function for any pillar sequence. Using this program, we engineer the cross-stream translation of a fluid stream to achieve solution exchange around particles, where both the particles and fluid stream remain focused and can be extracted at high purity. An extraction device, called a pillar separation device, is then designed and validated with suspensions of rigid particles to identify optimal operating parameters. At a flow rate of 250 µL/min, up to 96 % beads and 70.5 % of an initial buffer stream inputted into the system can be collected downstream in separate outlets, respectively, with 10.9 % buffer and 0.3 % bead contamination. This device was further applied to a functionalized bead bioassay, achieving high-yield and continuous separation of 98 % of biotin-coated beads from 72.2 % of extra FITC-biotin. In a last study, we performed the extraction of 80 % of leukocytes from lysed blood, which validates our platform can be applied on living cells and used for various functions of cellular sample preparation.

Vesicle transport is a major underlying mechanism of cell communication. Inhibiting vesicle transport in brain cells results in blockage of neuronal signals, even in intact neuronal networks. Modulating intracellular vesicle transport can have a huge impact on the development of new neurotherapeutic concepts, but only if we can specifically interfere with intracellular transport patterns. Here, we propose to modulate motion of intracellular lipid vesicles in rat cortical neurons based on exogenously bioconjugated and cell internalized superparamagnetic iron oxide nanoparticles (SPIONs) within microengineered magnetic gradients on-chip. Upon application of 6–126 pN on intracellular vesicles in neuronal cells, we explored how the magnetic force stimulus impacts the motion pattern of vesicles at various intracellular locations without modulating the entire cell morphology. Altering vesicle dynamics was quantified using, mean square displacement, a caging diameter and the total traveled distance. We observed a de-acceleration of intercellular vesicle motility, while applying nanomagnetic forces to cultured neurons with SPIONs, which can be explained by a decrease in motility due to opposing magnetic force direction. Ultimately, using nanomagnetic forces inside neurons may permit us to stop the mis-sorting of intracellular organelles, proteins and cell signals, which have been associated with cellular dysfunction. Furthermore, nanomagnetic force applications will allow us to wirelessly guide axons and dendrites by exogenously using permanent magnetic field gradients.

We develop a process to surface pattern PDMS with ferromagnetic structures of varying sizes (micron to mm) and thicknesses (> 70 micron). We utilize their flexibility and magnetic reach to confer dynamic, additive properties to a variety of substrates such as coverslips and eppendorf tubes. We find these substrates can generate additional modes of magnetic droplet manipulation, and can tunably steer magnetic-cell organization.