Center for Bio-Image Informatics

Engineering, Biology and Computer Science, working together.

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Project Meetings

Fall 2011 NSF projects

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October 12, 2011HFH 3164 330PM - 5PM

330: Geoff: update on the imaging side, progress with regard to confocal imaging.

345: Brian: update (summer progress and fall plans)

4:00: Min-Chi: update (summer progress and fall plans)

4:15: Rahul: update (summer progress and fall plans)

4:30: Vignesh: Fall'11 plan

4:40: Aruna:  Fall'11 plan

4:50: James:  Fall'11 plan

More info

Register to

Whole Cell Tomography and Analysis

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Andrew Noske will be presenting November 5th,
Friday at Noon in HFH 4164
Whole Cell Tomography and Analysis

This talk is an overview of my recently finished PhD project with Dr. Brad Marsh in Australia entitled "Multi-Scale, Spatio-Temporal Analysis of Mammalian Cell Tomograms". In this project we developed a simplified, efficient approach for the 3D reconstruction and analyses of mammalian cells in toto by electron microscope tomography (ET), in order to provide quantitative information regarding 'global' cellular organization at ~15-20 nm resolution and thus analyze the cell as a complex unitary system (see attached picture). By reconstructing insulin-secreting pancreatic beta cells, isolated intact from mouse pancreas, we were able to afford several unique insights into fundamental structure-function relationships among key organelles involved in the biosynthesis and release of insulin that could not be provided by other methods. To allow us to create these whole cell models with greater speed and accuracy we also developed several novel methods and interactive tools to facilitate faster segmentation and correct for deformation of serially aligned sections. (more info here)


====================================================================================================== Andrew Noske is currently a postdoctoral fellow in image processing and neuroscience at the National Center for Microscopy and Imaging Research (NCMIR) at the University of California, San Diego (UCSD). He completed his PhD in computer science, electron tomography and cellular biology at the Institute for Molecular Bioscience (IMB), University of Queensland (UQ) in Brisbane, Australia, and subsequently received an Australian Postgraduate Award (APA) scholarship. He received a computer science/IT degree with honours at James Cook University (JCU) in Cairns, Australia. You can find a variety of image processing tools, a list of publications, and his resume on his website:

2009-03-06 - Alphan Altinok

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Alphan Altinok - Research updates

Location: CS conference room.
Time: 10AM, March 6


04/23/2008 - Erkan Kiris

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Effects of tau protein phosphorylation upon microtubule dynamic instability in cells.

In this talk, I will present how we determine microtubule (MT) dynamic instability in GFP-Tubulin expressing MCF7 cells with new MT tracking and analysis software developed in ITR project.


03/25/2008 - Kris Kvilekval

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A taste of bisque: Recent development in the bisque platform

In this talk, we present new functionality that has been added to bisque, including support for nested datasets and new analysis functionality.

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Weekly Meeting

These are the details for the meeting of this week.

DATE:  Wed. April 30th
TIME 11.45 a.m.
LOCATION: Eng I room 4164

Luca will give research updates.