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BioInstrumatics

By BioInstrumatics, we mean the combination of biomedical instrumentation and computer (informatics) tech­nology.  We both build novel instruments and develop novel control and analysis tools for them.  These novel computer-inte­gra­­ted systems for microscopy and manipulation, which continue to enable research in biomedical engineering and medicine, have long been a primary focus of our resource.  Here are four of our upcoming research foci:

Data Collection and Analysis: The collaborators using our novel Panoptes high-content microscopy system are driving us to develop new unsupervised techniques for data collection, data reduction, and online decision making. We developed and published a scientific loss-less compression algorithm, which targets on videos with beads and can achieve a compression ratio up to 100:1.

PRISM: The collaborators using our novel two-view microscope platform coupled with a 3D interaction probe are driving us to develop a new data fusion system to integrate two orthogonal five-channel 3D fluorescence data sets with live two-plane video in an automatically-calibrated and aligned coordinate system with a 3D force manipulation probe.  This requires bringing together real-time bi-directional deconvolution with interactive 3D manipulation.

Improved Spot Tracking: As our collaborators push to use more and smaller fluorescent beads and shorter exposures, we are pushed to provide accurate and robust automatic detection and tracking of beads in 2D fluores­cence microcopy videos with high bead density and low signal/noise ratios.  As our collaborators increasingly move to 3D tracking, we are expanding our 3D capabilities.

PSF Estimator Program WindowImage (De)Convolution: The PRISM and SketchBio projects and other collaborators require novel bi-directional deconvolution techniques and Point-Spread Function optimization techniques that are better than the state-of-the-art models of either commercial or research systems.  They also require tightly-integrated modeling and convolution to enable scientists to match hypothetical protein assembly solutions to experiment images.