25,926 research outputs found
Geometry Processing of Conventionally Produced Mouse Brain Slice Images
Brain mapping research in most neuroanatomical laboratories relies on
conventional processing techniques, which often introduce histological
artifacts such as tissue tears and tissue loss. In this paper we present
techniques and algorithms for automatic registration and 3D reconstruction of
conventionally produced mouse brain slices in a standardized atlas space. This
is achieved first by constructing a virtual 3D mouse brain model from annotated
slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed
model generates ARA-based slice images corresponding to the microscopic images
of histological brain sections. These image pairs are aligned using a geometric
approach through contour images. Histological artifacts in the microscopic
images are detected and removed using Constrained Delaunay Triangulation before
performing global alignment. Finally, non-linear registration is performed by
solving Laplace's equation with Dirichlet boundary conditions. Our methods
provide significant improvements over previously reported registration
techniques for the tested slices in 3D space, especially on slices with
significant histological artifacts. Further, as an application we count the
number of neurons in various anatomical regions using a dataset of 51
microscopic slices from a single mouse brain. This work represents a
significant contribution to this subfield of neuroscience as it provides tools
to neuroanatomist for analyzing and processing histological data.Comment: 14 pages, 11 figure
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries
Recent advances in electron microscopy have enabled the imaging of single
cells in 3D at nanometer length scale resolutions. An uncharted frontier for in
silico biology is the ability to simulate cellular processes using these
observed geometries. Enabling such simulations requires watertight meshing of
electron micrograph images into 3D volume meshes, which can then form the basis
of computer simulations of such processes using numerical techniques such as
the Finite Element Method. In this paper, we describe the use of our recently
rewritten mesh processing software, GAMer 2, to bridge the gap between poorly
conditioned meshes generated from segmented micrographs and boundary marked
tetrahedral meshes which are compatible with simulation. We demonstrate the
application of a workflow using GAMer 2 to a series of electron micrographs of
neuronal dendrite morphology explored at three different length scales and show
that the resulting meshes are suitable for finite element simulations. This
work is an important step towards making physical simulations of biological
processes in realistic geometries routine. Innovations in algorithms to
reconstruct and simulate cellular length scale phenomena based on emerging
structural data will enable realistic physical models and advance discovery at
the interface of geometry and cellular processes. We posit that a new frontier
at the intersection of computational technologies and single cell biology is
now open.Comment: 39 pages, 14 figures. High resolution figures and supplemental movies
available upon reques
Ultrastructural Localization of Rhodopsin in the Vertebrate Retina
Early work by Dewey and collaborators has shown the distribution of rhodopsin in the frog retina. We have repeated these experiments on cow and mouse eyes using antibodies specific to rhodopsin alone. Bovine rhodopsin in emulphogene was purified on an hydroxyapatite column. The purity of this reagent was established by spectrophotometric criteria, by sodium dodecyl sulfate (SDS) gel electrophoresis, and by isoelectric focusing. This rhodopsin was used as an immunoadsorbent to isolate specific antibodies from the antisera of rabbits immunized with bovine rod outer segments solubilized in 2% digitonin. The antibody so prepared was shown by immunoelectrophoresis to be in the IgG class and did not cross-react with lipid extracts of bovine rod outer segments. Papain-digested univalent antibodies (Fab) coupled with peroxidase were used to label rhodopsin in formaldehyde-fixed bovine and murine retinas. In addition to the disk membranes, the plasma membrane of the outer segment, the connecting cilium, and part of the rod inner segment membrane were labeled. We observed staining on both sides of the rod outer segment plasma membrane and the disk membrane. Discrepancies were observed between results of immunolabeling experiments and observations of membrane particles seen in freeze-cleaved specimens. Our experiments indicate that the distribution of membrane particles in freeze cleaving experiments reflects the distribution of membrane proteins. Immunolabeling, on the other hand, can introduce several different types of artifact, unless controlled with extreme care
Optimizing intermittent water supply in urban pipe distribution networks
In many urban areas of the developing world, piped water is supplied only
intermittently, as valves direct water to different parts of the water
distribution system at different times. The flow is transient, and may
transition between free-surface and pressurized, resulting in complex dynamical
features with important consequences for water suppliers and users. Here, we
develop a computational model of transition, transient pipe flow in a network,
accounting for a wide variety of realistic boundary conditions. We validate the
model against several published data sets, and demonstrate its use on a real
pipe network. The model is extended to consider several optimization problems
motivated by realistic scenarios. We demonstrate how to infer water flow in a
small pipe network from a single pressure sensor, and show how to control water
inflow to minimize damaging pressure gradients
Real-time edge tracking using a tactile sensor
Object recognition through the use of input from multiple sensors is an important aspect of an autonomous manipulation system. In tactile object recognition, it is necessary to determine the location and orientation of object edges and surfaces. A controller is proposed that utilizes a tactile sensor in the feedback loop of a manipulator to track along edges. In the control system, the data from the tactile sensor is first processed to find edges. The parameters of these edges are then used to generate a control signal to a hybrid controller. Theory is presented for tactile edge detection and an edge tracking controller. In addition, experimental verification of the edge tracking controller is presented
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