Analysis-aware microscopy video compression.

This article introduces an analysis-aware microscopy video compression method designed for microscopy videos that are consumed by analysis algorithms rather than by the human visual system. We define the quality of a microscopy video based on the level of preservation of analysis results. We evaluated our method with a bead tracking analysis program. For the same error level in the analysis result, our method can achieve 1,000× compression on certain test microscopy videos. Compared with a previous technique that yields exactly the exact same results by analysis algorithms, our method gives more flexibility for a user to control the quality. A modification to the new method also provides faster compression speed.

The Virtual Pediatric Airways Workbench.

The Virtual Pediatric Airways Workbench (VPAW) is a patient-centered surgical planning software system targeted to pediatric patients with airway obstruction. VPAW provides an intuitive surgical planning interface for clinicians and supports quantitative analysis regarding prospective surgeries to aid clinicians deciding on potential surgical intervention. VPAW enables a full surgical planning pipeline, including importing DICOM images, segmenting the airway, interactive 3D editing of airway geometries to express potential surgical treatment planning options, and creating input files for offline geometric analysis and computational fluid dynamics simulations for evaluation of surgical outcomes. In this paper, we describe the VPAW system and its use in one case study with a clinician to successfully describe an intended surgery outcome.

ChromoShake: a chromosome dynamics simulator reveals that chromatin loops stiffen centromeric chromatin.

ChromoShake is a three-dimensional simulator designed to find the thermodynamically favored states for given chromosome geometries. The simulator has been applied to a geometric model based on experimentally determined positions and fluctuations of DNA and the distribution of cohesin and condensin in the budding yeast centromere. Simulations of chromatin in differing initial configurations reveal novel principles for understanding the structure and function of a eukaryotic centromere. The entropic position of DNA loops mirrors their experimental position, consistent with their radial displacement from the spindle axis. The barrel-like distribution of cohesin complexes surrounding the central spindle in metaphase is a consequence of the size of the DNA loops within the pericentromere to which cohesin is bound. Linkage between DNA loops of different centromeres is requisite to recapitulate experimentally determined correlations in DNA motion. The consequences of radial loops and cohesin and condensin binding are to stiffen the DNA along the spindle axis, imparting an active function to the centromere in mitosis.

Analysis-preserving video microscopy compression via correlation and mathematical morphology.

The large amount video data produced by multi-channel, high-resolution microscopy system drives the need for a new high-performance domain-specific video compression technique. We describe a novel compression method for video microscopy data. The method is based on Pearson's correlation and mathematical morphology. The method makes use of the point-spread function (PSF) in the microscopy video acquisition phase. We compare our method to other lossless compression methods and to lossy JPEG, JPEG2000, and H.264 compression for various kinds of video microscopy data including fluorescence video and brightfield video. We find that for certain data sets, the new method compresses much better than lossless compression with no impact on analysis results. It achieved a best compressed size of 0.77% of the original size, 25× smaller than the best lossless technique (which yields 20% for the same video). The compressed size scales with the video's scientific data content. Further testing showed that existing lossy algorithms greatly impacted data analysis at similar compression sizes.

DNA loops generate intracentromere tension in mitosis.

The centromere is the DNA locus that dictates kinetochore formation and is visibly apparent as heterochromatin that bridges sister kinetochores in metaphase. Sister centromeres are compacted and held together by cohesin, condensin, and topoisomerase-mediated entanglements until all sister chromosomes bi-orient along the spindle apparatus. The establishment of tension between sister chromatids is essential for quenching a checkpoint kinase signal generated from kinetochores lacking microtubule attachment or tension. How the centromere chromatin spring is organized and functions as a tensiometer is largely unexplored. We have discovered that centromere chromatin loops generate an extensional/poleward force sufficient to release nucleosomes proximal to the spindle axis. This study describes how the physical consequences of DNA looping directly underlie the biological mechanism for sister centromere separation and the spring-like properties of the centromere in mitosis.

Inverse-power-law behavior of cellular motility reveals stromal-epithelial cell interactions in 3D co-culture by OCT fluctuation spectroscopy.

The progression of breast cancer is known to be affected by stromal cells within the local microenvironment. Here we study the effect of stromal fibroblasts on the in-place motions (motility) of mammary epithelial cells within organoids in 3D co-culture, inferred from the speckle fluctuation spectrum using optical coherence tomography (OCT). In contrast to Brownian motion, mammary cell motions exhibit an inverse power-law fluctuation spectrum. We introduce two complementary metrics for quantifying fluctuation spectra: the power-law exponent and a novel definition of the motility amplitude, both of which are signal- and position-independent. We find that the power-law exponent and motility amplitude are positively (p<0.001) and negatively (p<0.01) correlated with the density of stromal cells in 3D co-culture, respectively. We also show how the hyperspectral data can be visualized using these metrics to observe heterogeneity within organoids. This constitutes a simple and powerful tool for detecting and imaging cellular functional changes with OCT.

Random per-element luminance modulation for improved visual tracking.

Using random per-element luminance modulation can increase the visual salience of details in a range of visualizations (2D, 3D, and ND scalar, vector, and tensor fields). Although random luminance has been used in specific designs, its wide applicability isn't reflected in visualizations, perhaps because it hasn't yet been presented as a cross-cutting technique. Adding random-luminance contrast can benefit both static and animated visualizations. The article presents perceptual reasons for this technique's effectiveness. This article has two accompanying videos, at http://youtu.be/TTaSFMvBgvg and http://youtu.be/Rx1oPMTpPA4, showing animations of cones moving through a weather simulation, with and without random luminance modulation.

Does topology drive fiber polymerization?

We have developed new procedures to examine the early steps in fibrin polymerization. First, we isolated fibrinogen monomers from plasma fibrinogen by gel filtration. Polymerization of fibrinogen monomers differed from that of plasma fibrinogen. The formation of protofibrils was slower and the transformation of protofibrils to fibers faster for the fibrinogen monomers. Second, we used formaldehyde to terminate the polymerization reactions. The formaldehyde-fixed products obtained at each time point were examined by dynamic light scattering and transmission electron microscopy (TEM). The data showed the formaldehyde-fixed products were stable and representative of the reaction intermediates. TEM images showed monomers, short oligomers, protofibrils, and thin fibers. The amount and length of these species varied with time. Short oligomers were less than 5% of the molecules at all times. Third, we developed models that recapitulate the TEM images. Fibrin monomer models were assembled into protofibrils, and protofibrils were assembled into two-strand fibers using Chimera software. Monomers were based on fibrinogen crystal structures, and the end-to-end interactions between monomers were based on D-dimer crystal structures. Protofibrils assembled from S-shaped monomers through asymmetric D:D interactions were ordered helical structures. Fibers were modeled by duplicating a protofibril and rotating the duplicate 120° around its long axis. No specific interactions were presumed. The two protofibrils simply twisted around one another to form a fiber. This model suggests that the conformation of the protofibril per se promotes the assembly into fibers. These findings introduce a novel mechanism for fibrin assembly that may be relevant to other biopolymers.

SketchBio: a scientist's 3D interface for molecular modeling and animation.

BACKGROUND: Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. RESULTS: SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. CONCLUSIONS: The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.

A 3D map of the yeast kinetochore reveals the presence of core and accessory centromere-specific histone.

The budding yeast kinetochore is ~68 nm in length with a diameter slightly larger than a 25 nm microtubule. The kinetochores from the 16 chromosomes are organized in a stereotypic cluster encircling central spindle microtubules. Quantitative analysis of the inner kinetochore cluster (Cse4, COMA) reveals structural features not apparent in singly attached kinetochores. The cluster of Cse4-containing kinetochores is physically larger perpendicular to the spindle axis relative to the cluster of Ndc80 molecules. If there was a single Cse4 (molecule or nucleosome) at the kinetochore attached to each microtubule plus end, the cluster of Cse4 would appear geometrically identical to Ndc80. Thus, the structure of the inner kinetochore at the surface of the chromosomes remains unsolved. We have used point fluorescence microscopy and statistical probability maps to deduce the two-dimensional mean position of representative components of the yeast kinetochore relative to the mitotic spindle in metaphase. Comparison of the experimental images to three-dimensional architectures from convolution of mathematical models reveals a pool of Cse4 radially displaced from Cse4 at the kinetochore and kinetochore microtubule plus ends. The pool of displaced Cse4 can be experimentally depleted in mRNA processing pat1Δ or xrn1Δ mutants. The peripheral Cse4 molecules do not template outer kinetochore components. This study suggests an inner kinetochore plate at the centromere-microtubule interface in budding yeast and yields information on the number of Ndc80 molecules at the microtubule attachment site.

The spatial segregation of pericentric cohesin and condensin in the mitotic spindle.

In mitosis, the pericentromere is organized into a spring composed of cohesin, condensin, and a rosette of intramolecular chromatin loops. Cohesin and condensin are enriched in the pericentromere, with spatially distinct patterns of localization. Using model convolution of computer simulations, we deduce the mechanistic consequences of their spatial segregation. Condensin lies proximal to the spindle axis, whereas cohesin is radially displaced from condensin and the interpolar microtubules. The histone deacetylase Sir2 is responsible for the axial position of condensin, while the radial displacement of chromatin loops dictates the position of cohesin. The heterogeneity in distribution of condensin is most accurately modeled by clusters along the spindle axis. In contrast, cohesin is evenly distributed (barrel of 500-nm width × 550-nm length). Models of cohesin gradients that decay from the centromere or sister cohesin axis, as previously suggested, do not match experimental images. The fine structures of cohesin and condensin deduced with subpixel localization accuracy reveal critical features of how these complexes mold pericentric chromatin into a functional spring.

Pericentric chromatin loops function as a nonlinear spring in mitotic force balance.

The mechanisms by which sister chromatids maintain biorientation on the metaphase spindle are critical to the fidelity of chromosome segregation. Active force interplay exists between predominantly extensional microtubule-based spindle forces and restoring forces from chromatin. These forces regulate tension at the kinetochore that silences the spindle assembly checkpoint to ensure faithful chromosome segregation. Depletion of pericentric cohesin or condensin has been shown to increase the mean and variance of spindle length, which have been attributed to a softening of the linear chromatin spring. Models of the spindle apparatus with linear chromatin springs that match spindle dynamics fail to predict the behavior of pericentromeric chromatin in wild-type and mutant spindles. We demonstrate that a nonlinear spring with a threshold extension to switch between spring states predicts asymmetric chromatin stretching observed in vivo. The addition of cross-links between adjacent springs recapitulates coordination between pericentromeres of neighboring chromosomes.

Increasing the perceptual salience of relationships in parallel coordinate plots.

We present three extensions to parallel coordinates that increase the perceptual salience of relationships between axes in multivariate data sets: (1) luminance modulation maintains the ability to preattentively detect patterns in the presence of overplotting, (2) adding a one-vs.-all variable display highlights relationships between one variable and all others, and (3) adding a scatter plot within the parallel-coordinates display preattentively highlights clusters and spatial layouts without strongly interfering with the parallel-coordinates display. These techniques can be combined with one another and with existing extensions to parallel coordinates, and two of them generalize beyond cases with known-important axes. We applied these techniques to two real-world data sets (relativistic heavy-ion collision hydrodynamics and weather observations with statistical principal component analysis) as well as the popular car data set. We present relationships discovered in the data sets using these methods.

Exploring Ensemble Visualization.

An ensemble is a collection of related datasets. Each dataset, or member, of an ensemble is normally large, multidimensional, and spatio-temporal. Ensembles are used extensively by scientists and mathematicians, for example, by executing a simulation repeatedly with slightly different input parameters and saving the results in an ensemble to see how parameter choices affect the simulation. To draw inferences from an ensemble, scientists need to compare data both within and between ensemble members. We propose two techniques to support ensemble exploration and comparison: a pairwise sequential animation method that visualizes locally neighboring members simultaneously, and a screen door tinting method that visualizes subsets of members using screen space subdivision. We demonstrate the capabilities of both techniques, first using synthetic data, then with simulation data of heavy ion collisions in high-energy physics. Results show that both techniques are capable of supporting meaningful comparisons of ensemble data.

Comparative Visualization of Ensembles Using Ensemble Surface Slicing.

By definition, an ensemble is a set of surfaces or volumes derived from a series of simulations or experiments. Sometimes the series is run with different initial conditions for one parameter to determine parameter sensitivity. The understanding and identification of visual similarities and differences among the shapes of members of an ensemble is an acute and growing challenge for researchers across the physical sciences. More specifically, the task of gaining spatial understanding and identifying similarities and differences between multiple complex geometric data sets simultaneously has proved challenging. This paper proposes a comparison and visualization technique to support the visual study of parameter sensitivity. We present a novel single-image view and sampling technique which we call Ensemble Surface Slicing (ESS). ESS produces a single image that is useful for determining differences and similarities between surfaces simultaneously from several data sets. We demonstrate the usefulness of ESS on two real-world data sets from our collaborators.

Nanoparticle diffusion measures bulk clot permeability.

A clot's function is to achieve hemostasis by resisting fluid flow. Permeability is the measurement of a clot's hemostatic potential. It is sensitive to a wide range of biochemical parameters and pathologies. In this work, we consider the hydrodynamic phenomenon that reduces the mobility of fluid near the fiber surfaces. This no-slip boundary condition both defines the gel's permeability and suppresses nanoparticle diffusion in gel interstices. Here we report that, unlike previous work where steric effects also hindered diffusion, our system-nanoparticles in fibrin gel-was subject exclusively to hydrodynamic diffusion suppression. This result enabled an automated, high-throughput permeability assay that used small clot volumes. Permeability was derived from nanoparticle diffusion using the effective medium theory, and showed one-to-one correlation with measured permeability. This technique measured permeability without quantifying gel structure, and may therefore prove useful for characterizing similar materials (e.g., extracellular matrix) where structure is uncontrolled during polymerization and difficult to measure subsequently. We also report that PEGylation reduced, but did not eliminate, the population of immobile particles. We studied the forces required to pull stuck PEG particles free to confirm that the attachment is a result of neither covalent nor strong electrostatic binding, and discuss the relevance of this force scale to particle transport through physiological clots.

The power of correlative microscopy: multi-modal, multi-scale, multi-dimensional.

Correlative microscopy is a sophisticated approach that combines the capabilities of typically separate, but powerful microscopy platforms: often including, but not limited, to conventional light, confocal and super-resolution microscopy, atomic force microscopy, transmission and scanning electron microscopy, magnetic resonance imaging and micro/nano CT (computed tomography). When targeting rare or specific events within large populations or tissues, correlative microscopy is increasingly being recognized as the method of choice. Furthermore, this multi-modal assimilation of technologies provides complementary and often unique information, such as internal and external spatial, structural, biochemical and biophysical details from the same targeted sample. The development of a continuous stream of cutting-edge applications, probes, preparation methodologies, hardware and software developments will enable realization of the full potential of correlative microscopy.

Cohesin, condensin, and the intramolecular centromere loop together generate the mitotic chromatin spring.

Sister chromatid cohesion provides the mechanistic basis, together with spindle microtubules, for generating tension between bioriented chromosomes in metaphase. Pericentric chromatin forms an intramolecular loop that protrudes bidirectionally from the sister chromatid axis. The centromere lies on the surface of the chromosome at the apex of each loop. The cohesin and condensin structural maintenance of chromosomes (SMC) protein complexes are concentrated within the pericentric chromatin, but whether they contribute to tension-generating mechanisms is not known. To understand how pericentric chromatin is packaged and resists tension, we map the position of cohesin (SMC3), condensin (SMC4), and pericentric LacO arrays within the spindle. Condensin lies proximal to the spindle axis and is responsible for axial compaction of pericentric chromatin. Cohesin is radially displaced from the spindle axis and confines pericentric chromatin. Pericentric cohesin and condensin contribute to spindle length regulation and dynamics in metaphase. Together with the intramolecular centromere loop, these SMC complexes constitute a molecular spring that balances spindle microtubule force in metaphase.

Linked Exploratory Visualizations for Uncertain MR Spectroscopy Data.

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations.

Matching visual saliency to confidence in plots of uncertain data.

Conveying data uncertainty in visualizations is crucial for preventing viewers from drawing conclusions based on untrustworthy data points. This paper proposes a methodology for efficiently generating density plots of uncertain multivariate data sets that draws viewers to preattentively identify values of high certainty while not calling attention to uncertain values. We demonstrate how to augment scatter plots and parallel coordinates plots to incorporate statistically modeled uncertainty and show how to integrate them with existing multivariate analysis techniques, including outlier detection and interactive brushing. Computing high quality density plots can be expensive for large data sets, so we also describe a probabilistic plotting technique that summarizes the data without requiring explicit density plot computation. These techniques have been useful for identifying brain tumors in multivariate magnetic resonance spectroscopy data and we describe how to extend them to visualize ensemble data sets.