Sandeep Bhat
Research
Research Interests
Since
my undergrad days, I have been interested in Signal Processing. As an
engineer developing multimedia systems for personal video players, I
was fascinated by the how video and audio were processed for different
applications.
After coming to UCSB, I became particularly
interested in Image Processing thanks to courses I did under Prof.
Manjunath, Prof. Lee and Prof. Turk. The course on Computational
BioMicroscopy under Prof. Liebling introduced me to an exciting
application of image processing....biology.
I have been
working with Prof. Liebling since Summer 2008. I am interested in all
facets of Biological imaging: novel ways to prepare biological samples
for in vivo imaging, improved techniques for acquiring images
automatically over long periods of time, algorithms to process these
images and make "sense" out of them.
Past Research
Please visit my Publications page for more information.MULTIPLE-CARDIAC-CYCLE NOISE REDUCTION IN DYNAMIC OPTICAL COHERENCE TOMOGRAPHY OF THE EMBRYONIC HEART AND VASCULATURE
Recent progress in optical coherence tomography (OCT)
allows imaging dynamic structures and fluid flow within scattering
tissue, such as the beating heart and blood flow in mouse embryos.
Accurate representation and analysis of these dynamic behaviors require
reducing the noise of the acquired data. Although noise can be reduced
by averaging multiple neighboring pixels in space or time, such
operations reduce the effective spatial or temporal resolution that can
be achieved.
Click on the above image to play the movie
We
have developed a computational postprocessing technique to restore
image sequences of cyclically moving structures that preserves frame
rate and spatial resolution. The signal-to-noise ratio (SNR) is
improved by combining images from multiple cycles that have been
synchronized with a temporally elastic registration procedure. Here we
show how this technique can be applied to OCT images of the circulatory
system in cultured mouse embryos. Our technique significantly improves
the SNR while preserving temporal and spatial resolution.
CARDIAC TISSUE AND ERYTHROCYTE SEPARATION IN BRIGHT-FIELD MICROSCOPY IMAGES OF THE EMBRYONIC ZEBRAFISH HEART FOR MOTION ESTIMATION
This is what I have been working on since Summer 2008. I presented this work at the IEEE ISBI'09 conference. You can download the paper from the publications page. A variation of this work was presented as a poster in the BioImage Informatics Conference in 2009. It was also part of a talk by Prof. Michael Liebling in the same conference.
Bright-field
(BF) microscopy enables imaging the beating embryonic zebrafish
heart at high frame rates, thereby revealing motion of both tissues
that form the heart and red blood cells (RBCs). 
However,
single-channel BF images lack the specificity seen in multi-color fluorescence
microscopy since all structures in the field of view
contribute similarly to image contrast (top row, left image).
We have developed an algorithm that overcomes this limitation by
separating a
BF sequence of the beating heart into two distinct image sequences: one
showing only the heart and surrounding tissues (top row,middle image)
and the other showing only the transient structures such as RBCs (top
row, right image).These sequences can be analyzed separately to
characterize heart wall and RBCs motion using common optical
flow techniques (bottom row).
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In the above figure the flow analysis was done using FlowJ plugin in ImageJ. The flow is visualized as a dynamic color map where the hue indicates the direction of flow and the saturation indicates the flow velocity. This technique has potential for facilitating quantitative characterization of heart function during cardiac morphogenesis. |
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Current Research
THESIS TOPICI am currently investigating techniques for reconstructing and analysing multi-dimensional images of the embryonic heart. I hope this work to feed into a bigger goal of ours; to build a complete functional and morphological heart atlas. Here is my thesis proposal abstract.
CARDIAC TISSUE AND ERYTHROCYTE SEPARATION IN 3D
Blood flow and motion of cardiac structures is a 3D+time phoenomenon. So we need to analyze flow in 3D to quantify tissue deformation and blood flow in the heart. So we are currently extending the above technique to 3D image stacks of the zebrafish heart.
site info
Tools and resources I used for creating this website.
© 2009-2010 Sandeep
Bhat | Original design by Andreas Viklund
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