154 research outputs found
Prediction of Cellular Identities from Trajectory and Cell Fate Information
Determining cell identities in imaging sequences is an important yet
challenging task. The conventional method for cell identification is via cell
tracking, which is complex and can be time-consuming. In this study, we propose
an innovative approach to cell identification during early embryogenesis using machine learning. Cell identification during
embryogenesis would provide insights into neural
development with implications for higher organisms including humans. We
employed random forest, MLP, and LSTM models, and tested cell classification
accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of
embryogenesis. By leveraging a small number of spatial-temporal features of
individual cells, including cell trajectory and cell fate information, our
models achieve an accuracy of over 91%, even with limited data. We also
determine the most important feature contributions and can interpret these
features in the context of biological knowledge. Our research demonstrates the
success of predicting cell identities in time-lapse imaging sequences directly
from simple spatio-temporal features
Spatio-angular fluorescence microscopy III. Constrained angular diffusion, polarized excitation, and high-NA imaging
We investigate rotational diffusion of fluorescent molecules in angular
potential wells, the excitation and subsequent emissions from these diffusing
molecules, and the imaging of these emissions with high-NA aplanatic optical
microscopes. Although dipole emissions only transmit six low-frequency angular
components, we show that angular structured illumination can alias higher
frequency angular components into the passband of the imaging system. We show
that the number of measurable angular components is limited by the
relationships between three time scales: the rotational diffusion time, the
fluorescence decay time, and the acquisition time. We demonstrate our model by
simulating a numerical phantom in the limits of fast angular diffusion, slow
angular diffusion, and weak potentials.Comment: 22 pages, 5 figure
Phase Diverse Phase Retrieval for Microscopy: Comparison of Gaussian and Poisson Approaches
Phase diversity is a widefield aberration correction method that uses
multiple images to estimate the phase aberration at the pupil plane of an
imaging system by solving an optimization problem. This estimated aberration
can then be used to deconvolve the aberrated image or to reacquire it with
aberration corrections applied to a deformable mirror. The optimization problem
for aberration estimation has been formulated for both Gaussian and Poisson
noise models but the Poisson model has never been studied in microscopy nor
compared with the Gaussian model. Here, the Gaussian- and Poisson-based
estimation algorithms are implemented and compared for widefield microscopy in
simulation. The Poisson algorithm is found to match or outperform the Gaussian
algorithm in a variety of situations, and converges in a similar or decreased
amount of time. The Gaussian algorithm does perform better in low-light regimes
when image noise is dominated by additive Gaussian noise. The Poisson algorithm
is also found to be more robust to the effects of spatially variant aberration
and phase noise. Finally, the relative advantages of re-acquisition with
aberration correction and deconvolution with aberrated point spread functions
are compared.Comment: 13 pages, 9 figure
Single-fluorophore orientation determination with multiview polarized illumination : modeling and microscope design
Author Posting. © Optical Society of America, 2017. This article is posted here by permission of Optical Society of America for personal use, not for redistribution. The definitive version was published in Optics Express 25 (2017): 31309-31325, doi:10.1364/OE.25.031309.We investigate the use of polarized illumination in multiview microscopes for determining the orientation of single-molecule fluorescence transition dipoles. First, we relate the orientation of single dipoles to measurable intensities in multiview microscopes and develop an information-theoretic metric—the solid-angle uncertainty—to compare the ability of multiview microscopes to estimate the orientation of single dipoles. Next, we compare a broad class of microscopes using this metric—single- and dual-view microscopes with varying illumination polarization, illumination numerical aperture (NA), detection NA, obliquity, asymmetry, and exposure. We find that multi-view microscopes can measure all dipole orientations, while the orientations measurable with single-view microscopes is halved because of symmetries in the detection process. We also find that choosing a small illumination NA and a large detection NA are good design choices, that multiview microscopes can benefit from oblique illumination and detection, and that asymmetric NA microscopes can benefit from exposure asymmetry.National Institute of Health (NIH) (R01GM114274, R01EB017293)
Three-Level Parallel J-Jacobi Algorithms for Hermitian Matrices
The paper describes several efficient parallel implementations of the
one-sided hyperbolic Jacobi-type algorithm for computing eigenvalues and
eigenvectors of Hermitian matrices. By appropriate blocking of the algorithms
an almost ideal load balancing between all available processors/cores is
obtained. A similar blocking technique can be used to exploit local cache
memory of each processor to further speed up the process. Due to diversity of
modern computer architectures, each of the algorithms described here may be the
method of choice for a particular hardware and a given matrix size. All
proposed block algorithms compute the eigenvalues with relative accuracy
similar to the original non-blocked Jacobi algorithm.Comment: Submitted for publicatio
Clustered nuclei maintain autonomy and nucleocytoplasmic ratio control in a syncytium
© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology of the Cell 27 (2016): 2000-2007, doi:10.1091/mbc.E16-02-0129.Nuclei in syncytia found in fungi, muscles, and tumors can behave independently despite cytoplasmic translation and the homogenizing potential of diffusion. We use a dynactin mutant strain of the multinucleate fungus Ashbya gossypii with highly clustered nuclei to assess the relative contributions of nucleus and cytoplasm to nuclear autonomy. Remarkably, clustered nuclei maintain cell cycle and transcriptional autonomy; therefore some sources of nuclear independence function even with minimal cytosol insulating nuclei. In both nuclear clusters and among evenly spaced nuclei, a nucleus’ transcriptional activity dictates local cytoplasmic contents, as assessed by the localization of several cyclin mRNAs. Thus nuclear activity is a central determinant of the local cytoplasm in syncytia. Of note, we found that the number of nuclei per unit cytoplasm was identical in the mutant to that in wild-type cells, despite clustered nuclei. This work demonstrates that nuclei maintain autonomy at a submicrometer scale and simultaneously maintain a normal nucleocytoplasmic ratio across a syncytium up to the centimeter scale.his work was supported by National Institutes of Health R01-GM081506 (A.S.G., S.E.R., and P.O.), the National Science Foundation GK-12 Program and the Neukom Institute at Dartmouth College (S.E.R.), the Alfred P. Sloan Foundation and National Science Foundation DMS-1351860 (M.R. and S.-S.C.), a National Institutes of Health Ruth L. Kirschstein National Research Service Award (T32-GM008185; S.-S.C.), and the Intramural Research Programs of the National Institutes of Health National Institute of Biomedical Imaging and Bioengineering Whitman Investigator and Grass Foundation Programs at the Marine Biological Laboratory at Woods Hole (A.K. and H.S.
Visualizing calcium flux in freely moving nematode embryos
Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here by permission of Cell Press for personal use, not for redistribution. The definitive version was published in Biophysical Journal 112 (2017): 1975-1983, doi:10.1016/j.bpj.2017.02.035.The lack of physiological recordings from Caenorhabditis elegans
embryos stands in stark contrast to the comprehensive anatomical and gene
expression datasets already available. Using light-sheet fluorescence
microscopy (LSFM) to address the challenges associated with functional
imaging at this developmental stage, we recorded calcium dynamics in
muscles and neurons and developed analysis strategies to relate activity and
movement. In muscles, we found that the initiation of twitching was
associated with a spreading calcium wave in a dorsal muscle bundle.
Correlated activity in muscle bundles was linked with early twitching and
eventual coordinated movement. To identify neuronal correlates of behavior,
we monitored brain-wide activity with subcellular resolution and identified a
particularly active cell associated with muscle contractions. Finally, imaging
neurons of a well-defined adult motor circuit, we found that reversals in the
eggshell correlated with calcium transients in AVA interneurons.E.A. and A.K. acknowledge
support from the Grass Fellowship Program and D. C-R. and H.S. acknowledge the
Whitman Fellowship program at MBL. This work was supported by the intramural research
program of the National Institute of Biomedical Imaging and Bioengineering and
NIH grants U01 HD075602 and R24OD016474 to D.C-R and A.K.2018-05-0
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