CellVisualizer : exploring hierarchical, multi-dimensional data with applications to high-throughput microscopy

In this thesis, we present a system for visualizing hierarchical, multi-dimensional, memory-intensive datasets. Specifically, we designed an interactive system to visualize data collected by high-throughput microscopy and processed by CellProfiler, an open-source system jointly developed by researchers at MIT CSAIL and the White-head Institute. A typical high-throughput microscopy experiment produces thousands of images, with thousands of objects in each image. CellProfiler then measures hundreds of features for each cell, nuclei, and cytoplasm. In contrast to previously demonstrated visualization software, our system visualizes datasets that are on the order of hundreds of gigabytes, datasets too large to store in physical memory. We also implement tools to link the dataset to available resources such as online genetic databases and the actual images acquired by the microscope. Finally, we demonstrate how the system was used to highlight interesting genes for more detailed analysis in real biological studies.

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2006

Author dc:creator

• Kang, InHan

Advisor dc:contributor.advisor

• Polina Golland.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/41605

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/41605