Current research in Retinal Studies
12 Noon, CS Conference Room (Harold Frank Hall, Room 1132).
To be decided
Organization of the Vertebrate Retina (Part 2)
12 Noon, CS Conference Room (Harold Frank Hall, Room 1132).
Professor Dowling will giving a general overview of the vertebrate retina, focusing especially on its functional organization. This is intended to be an informal presentation so that the audience can ask questions, raise issues, and participate in the discussions.
About the speaker:
Dr. John E. Dowling received his Ph.D. degree in Biology from Harvard University in 1961. He is presently Llura & Gordon Gund Professor of Neuroscience at Harvard, and Professor of Ophthalmology (Neuroscience), Harvard Medical School.
Early in his career, Dowling worked as a researcher under Nobel Prize winner George Wald. During this time, Dowling mapped the exchange of retinoids between the retinal photoreceptors where they are used in photoreception and the pigment epithelial cell where the retinoids are stored. Because of Dowling's work, this process is now described in
all biology textbooks. In addition, Dowling's groundbreaking work on the functional organization of the retina laid the foundation for understanding how the retina begins to integrate and analyze visual information. Dowling has received numerous awards including the Friedenwald Medal, the highest scientific award from the Association for Research in Vision and Ophthalmology. He is an elected member of the National Academy of Science.
Dr. Dowling has published many books, including the classic "The Retina: An Approachable Part of the Brain," Harvard University Press, Cambridge, MA (1987); "Neurons and Networks: An Introduction to Neuroscience, " Harvard University Press, Cambridge, MA (1992); and "Creating Mind: How the Brain Works," W. W. Norton & Co., New York, NY (1998).
Presentation slides from John Dowling for "Organization of the Vertebrate Retina"
PDF: Dowling_Retina.pdf
PPT: Dowling_Retina.ppt
Organization of the Vertebrate Retina
12 Noon, CS Conference Room (Harold Frank Hall, Room 1132).
Professor Dowling will giving a general overview of the vertebrate retina, focusing especially on its functional organization. This is intended to be an informal presentation so that the audience can ask questions, raise issues, and participate in the discussions.
About the speaker:
Dr. John E. Dowling received his Ph.D. degree in Biology from Harvard University in 1961. He is presently Llura & Gordon Gund Professor of Neuroscience at Harvard, and Professor of Ophthalmology (Neuroscience), Harvard Medical School.
Early in his career, Dowling worked as a researcher under Nobel Prize winner George Wald. During this time, Dowling mapped the exchange of retinoids between the retinal photoreceptors where they are used in photoreception and the pigment epithelial cell where the retinoids are stored. Because of Dowling's work, this process is now described in
all biology textbooks. In addition, Dowling's groundbreaking work on the functional organization of the retina laid the foundation for understanding how the retina begins to integrate and analyze visual information. Dowling has received numerous awards including the Friedenwald Medal, the highest scientific award from the Association for Research in Vision and Ophthalmology. He is an elected member of the National Academy of Science.
Dr. Dowling has published many books, including the classic "The Retina: An Approachable Part of the Brain," Harvard University Press, Cambridge, MA (1987); "Neurons and Networks: An Introduction to Neuroscience, " Harvard University Press, Cambridge, MA (1992); and "Creating Mind: How the Brain Works," W. W. Norton & Co., New York, NY (1998).
Presentation slides from John Dowling for "Organization of the Vertebrate Retina"
PDF: Dowling_Retina.pdf
PPT: Dowling_Retina.ppt
Determinants of Dendritic Morphology, Connectivity, Spacing and Functional Coverage of Retinal Nerve Cells
Prof. Benjamin Reese
July 23, 2007
Abstract:
My lab has been exploring the determinants of dendritic morphology, connectivity and intercellular spacing that underlie the functional coverage of retinal nerve cell mosaics.Recent studies have focused on the horizontal cells of the retina, being inhibitory interneurons with dendritic fields that overlap one another, contacting the pedicles of cone photoreceptors.Because of their regular spacing, their dendrites provide a uniform coverage of the retinal surface.The developmental mechanisms establishing their intercellular spacing and morphological properties are undefined, but fate-determination events and cell-intrinsic instructions have been suggested to underlie these features. I will consider an alternative hypothesis, that interactions with neighboring cells drive the intercellular spacing and dendritic differentiation of these cells. Using a variety of natural and genetically-modified strains of mice, we have modulated the relationship between horizontal and cone cell number to study the role of homotypic and afferent density upon mosaic patterning and differentiation. A number of spatial statistics for analyzing the patterning of retinal mosaics in 2D will be discussed. Variation in horizontal cell density is shown to produce a corresponding change in the average spacing between horizontal cells and in the size of the dendritic field, while altering cone density leaves dendritic field size unaffected and does not perturb mosaic patterning, but drives higher order dendritic branching and terminal clustering. Afferent and homotypic interactions therefore generate the network properties of horizontal cells that underlie their functional coverage. Such issues have not been addressed within networks of nerve cells within the brain for a variety of reasons, partly because determining such spatial statistics in 3D is computationally demanding, and because of the difficulty in visualizing nerve cell patterning in 3D. At the end of the talk, I will describe the creation of new software tools permitting the analysis and modeling of such nerve cell patterning in three dimensions.
Imaging Solutions for Problems in Anatomic Pathology
Dr. David Rimm
Department of Pathology at the Yale University School of Medicine
April 18th, 2007
Professor Rimm will talk about using spectral imaging and fluorescence-based automated quantitative analysis to address current medical problems in anatomic pathology. The problems addressed will be the problem of atypical cells and pre-malignancy in cytopathology and the problem of accurate protein measurement as a mechanism to predict response to targeted therapies or to predict metastasis in breast cancer and melanoma.
Model-Based Biomedical Image Analysis
Prof James S. Duncan
Biomedical Engineering, Diagnostic Radiology and Electrical Engineering, Yale University
Mar. 12, 2007
Abstract:
The development of methods to accurately and reproducibly recover useful quantitative information from medical images is often hampered by uncertainties in handling the data related to: image acquisition parameters, the variability of normal human anatomy and physiology, the presence of disease or other abnormal conditions, and a variety of other factors. This talk will review image analysis strategies that make use of models based on geometrical and physical/biomechanical information to help constrain the range of possible solutions in the presence of such uncertainty. The discussion will be focused by looking primarily at several problem areas in the realms of neuroanatomical structure analysis and cardiac function analysis, with an emphasis on image segmentation and motion/deformation tracking. The presentation will include a description of the problem areas and visual examples of the image datasets being used, an overview of the mathematical techniques involved and a presentation of results obtained when analyzing actual patient image data using these methods. Emphasis will be placed on how image-derived information and appropriate modeling can be used together to address the image analysis and processing problems noted above.
Challenges for Intelligent Image Processing in Cryo-Electron Microscopy
Christoph Best
Dept. of Molecular Structural Biology, Max Planck Institut fuer Biochemie, Martinsried, Germany
Nov 9, 2006
Abstract:
Cryo-electron microscopy enable the imaging of macromolecular complexes and cellular structures in a near-natural state at molecular resolution. Recent developments in preparation, instrumentation, and automation carry the promise of imaging molecular structures at sub-nanometer resolutions in their native environment, as well as creating molecular maps of the macromolecular complexes in the living cell. These advancements pose unique new informatics problems in image processing. In particular, methods from machine learning and probabilistic modeling will play a large role in classifying images, combining them into three-dimensional structures, and extracting information from them. I will discuss several examples where modern informatics methods may improve electron microscopy such as model-free maximum-likelihood classification of projection images, particle picking through support vector machines, and 3D reconstruction from random projections using the Baum-Welch algorithm and Level Set methods.
Multi-dimensional Image Analysis Methods for Modern Optical Microscopy
Professor Badri Roysam
ECSE Department, Rensselaer Polytechnic Institute
Jan 26, 2006
Abstract:
Modern optical microscopes, aided by a family of support technologies, have matured into a truly multi-dimensional imaging tool for conducting diverse biological investigations at the sub- cellular, cellular, and tissue levels. The widespread availability of confocal and multi-photon microscopes and high-NA objectives, have made high-resolution (axial and lateral) three-dimensional (3-D) imaging of multiple structures and functional markers routine. From a systems biology perspective, modern microscopy is valuable for its ability to record processes in the spatial context of intact tissue, unlike biochemical assays, gene arrays and flow cytometry, in which spatial information is unavoidably disrupted. A variety of complementary advances in biochemistry (e.g., conjugated quantum dots, fluorescent proteins), image pre-processing software, and high- throughput specimen preparation serve to magnify the capabilities of optical microscopy.
There is a compelling need for technologies to translate this wealth of imaging data into quantitative insight. Specifically, two types of needs exist: (i) analysis of complex data sets involving interactions among multiple structures and functional markers, and multiple imaging dimensions; and (ii) analysis of large batches of such images. Quantitative measurements are needed in contexts ranging from hypothesis testing, drug discovery, assay development, high- throughput assays, quantitative tissue engineering, cytomic mapping.
In this talk, Dr. Roysam will describe the FARSIGHT project at Rensselaer that is producing software technologies that address the above needs in a systematic manner. This project is specifically designed for the multi-dimensional imaging capabilities of modern optical microscopy, and the complex image analysis needs of contemporary cell/tissue biology.
Micro and Nanostructured Materials and Devices for Biomolecular Analysis
Arun Majumdar
Department of Mechanical Engineering, University of California, Berkeley
Nov. 12, 2004
Abstract:
Over the last decade, we have witnessed an exponential growth in genomic information, which was highlighted by the Human Genome Project.Accompanying that was an exponential decrease in cost per sequenced gene. While these trends are expected to continue in genomics, they also provoke the question of whether there would be similar increases in information for other biomolecules, such as proteins, which are more complex in their structure and function. As part of this talk, I will present some of our and others’ work in developing technologies that could lead to rapid biomolecular analysis. In particular, I will focus on analysis based on cantilever mechanics, electrical capacitance, nanofluidics, and nanoparticle imaging. One of the goals of this talk is to catalyze discussion on how such technologies could address important biological questions that are difficult to address otherwise.
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