Rapid and specific detection of intact viral particles using functionalized microslit silicon membranes as a fouling-based sensor.

The COVID-19 pandemic demonstrated the public health benefits of reliable and accessible point-of-care (POC) diagnostic tests for viral infections. Despite the rapid development of gold-standard reverse transcription polymerase chain reaction (RT-PCR) assays for SARS-CoV-2 only weeks into the pandemic, global demand created logistical challenges that delayed access to testing for months and helped fuel the spread of COVID-19. Additionally, the extreme sensitivity of RT-PCR had a costly downside as the tests could not differentiate between patients with active infection and those who were no longer infectious but still shedding viral genomes. To address these issues for the future, we propose a novel membrane-based sensor that only detects intact virions. The sensor combines affinity and size based detection on a membrane-based sensor and does not require external power to operate or read. Specifically, the presence of intact virions, but not viral debris, fouls the membrane and triggers a macroscopically visible hydraulic switch after injection of a 40 µL sample with a pipette. The device, which we call the µSiM-DX (microfluidic device featuring a silicon membrane for diagnostics), features a biotin-coated microslit membrane with pores ∼2-3× larger than the intact virus. Streptavidin-conjugated antibody recognizing viral surface proteins are incubated with the sample for ∼1 hour prior to injection into the device, and positive/negative results are obtained within ten seconds of sample injection. Proof-of-principle tests have been performed using preparations of vaccinia virus. After optimizing slit pore sizes and porous membrane area, the fouling-based sensor exhibits 100% specificity and 97% sensitivity for vaccinia virus (n = 62). Moreover, the dynamic range of the sensor extends at least from 105.9 virions per mL to 1010.4 virions per mL covering the range of mean viral loads in symptomatic COVID-19 patients (105.6-107 RNA copies per mL). Forthcoming work will test the ability of our sensor to perform similarly in biological fluids and with SARS-CoV-2, to fully test the potential of a membrane fouling-based sensor to serve as a PCR-free alternative for POC containment efforts in the spread of infectious disease.

Compressed Sensing Structured Illumination Microscopy.

We propose a new framework for super-resolution structured illumination microscopy (SR-SIM) based on compressed sensing (CS). Our framework addresses several key problems in SIM, including long readout time and photobleaching. CS has the potential to eliminate these problems because it allows the reduction of the number of measurements, can record an image faster, and excites fluorochromes with less excitation light. Key contribution of our proposed method is that sampling and down-modulation of an object scene are simultaneously performed. The impact of our contribution is demonstrated by simulation-based experiments involving computer-generated super-resolution microscopy images, considering reductions in both data quality and quantity.

Three-dimensional image reconstruction of macroscopic objects from a single digital hologram using stereo disparity.

We present depth extraction of macroscopic three-dimensional (3D) objects from a single digital hologram using stereo disparity. The method does not require the phase information of the hologram but two perspectives of the scene, which are easily obtained by dividing the hologram into two parts (two apertures) before the reconstruction. Variation of the hologram division is countless since each piece of a single hologram contains all the information regarding the scene; therefore, stereo disparity can be calculated along any arbitrary direction. We investigated the effects of gradual and sharp divisions of the holograms for the disparity map calculations, specifically for divisions in the vertical, horizontal, and diagonal directions. After obtaining the depth map from the stereo images, a regular two-dimensional image of the object is merged with the depth information to form 3D visualization of the object. Holograms were recorded with a rigid endoscope, and experimentally obtained depth profiles of the objects are in very good agreement with the actual profiles.