32 research outputs found
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
A neuronal network of mitochondrial dynamics regulates metastasis.
The role of mitochondria in cancer is controversial. Using a genome-wide shRNA screen, we now show that tumours reprogram a network of mitochondrial dynamics operative in neurons, including syntaphilin (SNPH), kinesin KIF5B and GTPase Miro1/2 to localize mitochondria to the cortical cytoskeleton and power the membrane machinery of cell movements. When expressed in tumours, SNPH inhibits the speed and distance travelled by individual mitochondria, suppresses organelle dynamics, and blocks chemotaxis and metastasis, in vivo. Tumour progression in humans is associated with downregulation or loss of SNPH, which correlates with shortened patient survival, increased mitochondrial trafficking to the cortical cytoskeleton, greater membrane dynamics and heightened cell invasion. Therefore, a SNPH network regulates metastatic competence and may provide a therapeutic target in cancer
Endothelial junctional membrane protrusions serve as hotspots for neutrophil transmigration
Upon inflammation, leukocytes rapidly transmigrate across the endothelium to enter the inflamed tissue. Evidence accumulates that leukocytes use preferred exit sites, alhough it is not yet clear how these hotspots in the endothelium are defined and how they are recognized by the leukocyte. Using lattice light sheet microscopy, we discovered that leukocytes prefer endothelial membrane protrusions at cell junctions for transmigration. Phenotypically, these junctional membrane protrusions are present in an asymmetric manner, meaning that one endothelial cell shows the protrusion and the adjacent one does not. Consequently, leukocytes cross the junction by migrating underneath the protruding endothelial cell. These protrusions depend on Rac1 activity and by using a photo-activatable Rac1 probe, we could artificially generate local exit-sites for leukocytes. Overall, we have discovered a new mechanism that uses local induced junctional membrane protrusions to facilitate/steer the leukocyte escape/exit from inflamed vessel walls
Myosin VI regulates the spatial organisation of mammalian transcription initiation.
During transcription, RNA Polymerase II (RNAPII) is spatially organised within the nucleus into clusters that correlate with transcription activity. While this is a hallmark of genome regulation in mammalian cells, the mechanisms concerning the assembly, organisation and stability remain unknown. Here, we have used combination of single molecule imaging and genomic approaches to explore the role of nuclear myosin VI (MVI) in the nanoscale organisation of RNAPII. We reveal that MVI in the nucleus acts as the molecular anchor that holds RNAPII in high density clusters. Perturbation of MVI leads to the disruption of RNAPII localisation, chromatin organisation and subsequently a decrease in gene expression. Overall, we uncover the fundamental role of MVI in the spatial regulation of gene expression
Seabird Modulations of Isotopic Nitrogen on Islands
The transport of nutrients by migratory animals across ecosystem boundaries can significantly enrich recipient food webs, thereby shaping the ecosystems’ structure and function. To illustrate the potential role of islands in enabling the transfer of matter across ecosystem boundaries to be gauged, we investigated the influence of seabirds on nitrogen input on islands. Basing our study on four widely differing islands in terms of their biogeography and ecological characteristics, sampled at different spatial and temporal intervals, we analyzed the nitrogen isotopic values of the main terrestrial ecosystem compartments (vascular plants, arthropods, lizards and rodents) and their relationship to seabird values. For each island, the isotopic values of the ecosystem were driven by those of seabirds, which ultimately corresponded to changes in their marine prey. First, terrestrial compartments sampled within seabird colonies were the most enriched in δ15N compared with those collected at various distances outside colonies. Second, isotopic values of the whole terrestrial ecosystems changed over time, reflecting the values of seabirds and their prey, showing a fast turnover throughout the ecosystems. Our results demonstrate that seabird-derived nutrients not only spread across the terrestrial ecosystems and trophic webs, but also modulate their isotopic values locally and temporally on these islands. The wealth of experimental possibilities in insular ecosystems justifies greater use of these model systems to further our understanding of the modalities of trans-boundary nutrient transfers
The Complete Interactome with 5-D GPU Accelerated Analysis, Visualization, and UI for Biological Microscopy Applications
Microscopes now have the ability to collect highly complex data. This thesis presents new algorithms and software packages for analyzing, visualizing, and interacting with biological microscopy image datasets. These new software packages provide functionality not available with existing methods. Along with new functionality, the methods described here are of higher accuracy compared to existing methods. These new software packages provide significant improvements in computational efficiency and usability. Contributions described within this thesis are biologically motivated with examples given throughout. The analysis presented has enabled new biological discoveries along with new mathematical analytic techniques. This thesis is broken into three distinct areas: analysis of interactions between organelles describing the complete interactome, a hardware accelerated image processing library, and software packages providing visualization, validation and analysis. First the complete interactome describes a new method of quantifying the interactions of all of the organelles within a single cell. Where prior methods focus on pairwise interactions, methods described here include a robust quantification method for these high order interactions. Secondly, a hardware accelerated image processing library and framework called Hydra Image Processor (HIP). HIP is capable of swiftly processing arbitrarily large datasets. The HIP framework automatically (without user intervention) distributes data and schedules processing across all available graphic processing units. In addition, HIP processes the edges of images with higher precision than currently available methods. Lastly, visualization, validation, and analysis tools are presented. Visualization of high dimensional datasets captured by modern microscopes is non-trivial. Integrating processing, segmentation, and tracking results embedded is also a challenge. Software packages presented here perform all three of these task within the scripting environment of MATLAB for fast prototyping and swift user interface generation. Validation tools are also described that incorporate user input to inform unsupervised algorithms and reduce underlying segmentation and tracking results significantly. All methods and contributions of this thesis are biologically motivated. Within the three areas described above are biological examples where these methods contributed significantly. They range from describing the high-order interactions within a single cell, to lineaging stem cells in 5D, to the reconstruction of large montage images of the Subventricular Zone. The adoption of these methods will enable future biological findings within highly complex datasets captured by modern and future microscopes.Ph.D., Computer Engineering -- Drexel University, 201