4,892 research outputs found
Particle detection and tracking in fluorescence time-lapse imaging: a contrario approach
This paper proposes a probabilistic approach for the detection and the
tracking of particles in fluorescent time-lapse imaging. In the presence of a
very noised and poor-quality data, particles and trajectories can be
characterized by an a contrario model, that estimates the probability of
observing the structures of interest in random data. This approach, first
introduced in the modeling of human visual perception and then successfully
applied in many image processing tasks, leads to algorithms that neither
require a previous learning stage, nor a tedious parameter tuning and are very
robust to noise. Comparative evaluations against a well-established baseline
show that the proposed approach outperforms the state of the art.Comment: Published in Journal of Machine Vision and Application
Interferometric scattering enables fluorescence-free electrokinetic trapping of single nanoparticles in free solution
Anti-Brownian traps confine single particles in free solution by closed-loop
feedback forces that directly counteract Brownian motion. The extended-duration
measurement of trapped objects allows detailed characterization of
photophysical and transport properties, as well as observation of infrequent or
rare dynamics. However, this approach has been generally limited to particles
that can be tracked by fluorescent emission. Here we present the
Interferometric Scattering Anti-Brownian ELectrokinetic trap (ISABEL trap),
which uses interferometric scattering rather than fluorescence to monitor
particle position. By decoupling the ability to track (and therefore trap) a
particle from collection of its spectroscopic data, the ISABEL trap enables
confinement and extended study of single particles that do not fluoresce, that
only weakly fluoresce, or which exhibit intermittent fluorescence or
photobleaching. This new technique significantly expands the range of nanoscale
objects that may be investigated at the single-particle level in free solution.Comment: Manuscript and SI; videos available upon reques
Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences
Results: We present an application that enables the quantitative analysis of
multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence
microscopy images. The image sequences show stem cells together with blood
vessels, enabling quantification of the dynamic behaviors of stem cells in
relation to their vascular niche, with applications in developmental and cancer
biology. Our application automatically segments, tracks, and lineages the image
sequence data and then allows the user to view and edit the results of
automated algorithms in a stereoscopic 3-D window while simultaneously viewing
the stem cell lineage tree in a 2-D window. Using the GPU to store and render
the image sequence data enables a hybrid computational approach. An
inference-based approach utilizing user-provided edits to automatically correct
related mistakes executes interactively on the system CPU while the GPU handles
3-D visualization tasks. Conclusions: By exploiting commodity computer gaming
hardware, we have developed an application that can be run in the laboratory to
facilitate rapid iteration through biological experiments. There is a pressing
need for visualization and analysis tools for 5-D live cell image data. We
combine accurate unsupervised processes with an intuitive visualization of the
results. Our validation interface allows for each data set to be corrected to
100% accuracy, ensuring that downstream data analysis is accurate and
verifiable. Our tool is the first to combine all of these aspects, leveraging
the synergies obtained by utilizing validation information from stereo
visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc
Super-Resolution Microscopy: A Virus’ Eye View of the Cell
It is difficult to observe the molecular choreography between viruses and host cell components, as they exist on a spatial scale beyond the reach of conventional microscopy. However, novel super-resolution microscopy techniques have cast aside technical limitations to reveal a nanoscale view of virus replication and cell biology. This article provides an introduction to super-resolution imaging; in particular, localisation microscopy, and explores the application of such technologies to the study of viruses and tetraspanins, the topic of this special issue
A multi-object spectral imaging instrument
We have developed a snapshot spectral imaging system which fits onto the side camera port of a commercial inverted microscope. The system provides spectra, in real time, from multiple points randomly selected on the microscope image. Light from the selected points in the sample is directed from the side port imaging arm using a digital micromirror device to a spectrometer arm based on a dispersing prism and CCD camera. A multi-line laser source is used to calibrate the pixel positions on the CCD for wavelength. A CMOS camera on the front port of the microscope allows the full image of the sample to be displayed and can also be used for particle tracking, providing spectra of multiple particles moving in the sample. We demonstrate the system by recording the spectra of multiple fluorescent beads in aqueous solution and from multiple points along a microscope sample channel containing a mixture of red and blue dye
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