Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis
Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2015
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| Online Access: | http://hdl.handle.net/1721.1/97824 |
| _version_ | 1811069168697475072 |
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| author | Gorman, Bryan Robert |
| author2 | Paul H. Lerou. |
| author_facet | Paul H. Lerou. Gorman, Bryan Robert |
| author_sort | Gorman, Bryan Robert |
| collection | MIT |
| description | Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015. |
| first_indexed | 2024-09-23T08:06:47Z |
| format | Thesis |
| id | mit-1721.1/97824 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T08:06:47Z |
| publishDate | 2015 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/978242019-04-09T16:42:26Z Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis Gorman, Bryan Robert Paul H. Lerou. Harvard--MIT Program in Health Sciences and Technology. Harvard--MIT Program in Health Sciences and Technology. Harvard--MIT Program in Health Sciences and Technology. Thesis: Ph. D., Harvard-MIT Program in Health Sciences and Technology, 2015. Cataloged from PDF version of thesis. Includes bibliographical references (pages 86-97). Human pluripotent stem (hPS) cells have the ability to reproduce indefinitely and differentiate into any cell type of the body, making them a potential source of cells for medical therapy and an ideal system to study fate decisions in early development. However, hPS cells exhibit a high degree of heterogeneity, which may be an obstacle to their clinical translation. Heterogeneity is at least partially induced as an artifact of removing the cells from the embryo and culturing them on a plastic dish. hPS cells grow in spatially patterned colony structures, which necessitates in situ quantitative single-cell image analysis. This dissertation offers a tool for analyzing the spatial population context of hPS cells that integrates automated fluorescent microscopy with an analysis pipeline. It enables high-throughput detection of colonies at low resolution, with single-cellular and sub-cellular analysis at high resolutions, generating seamless in situ maps of single-cellular data organized by colony. We demonstrate the tool's utility by analyzing inter- and intra-colony heterogeneity of hPS cell cycle regulation and pluripotency marker expression. We measured the heterogeneity within individual colonies by analyzing cell cycle as a function of distance. Cells loosely associated with the outside of the colony are more likely to be in G1, reflecting a less pluripotent state, while cells within the first pluripotent layer are more likely to be in G2, possibly reflecting a G2/M block. Our analysis tool can group colony regions into density classes, and cells belonging to those classes have distinct distributions of pluripotency markers and respond differently to DNA damage induction. Our platform also enabled noninvasive texture analysis of live hPS colonies, which was applied to monitoring subtle changes in differentiation state. Lastly, we demonstrate that our pipeline can robustly handle high-content, high-resolution single molecular mRNA FISH data by using novel image processing techniques. Overall, the imaging informatics pipeline presented offers a novel approach to the analysis of hPS cells, which includes not only single cell features but also spatial configuration across multiple length scales. by Bryan Robert Gorman. Ph. D. 2015-07-17T19:50:20Z 2015-07-17T19:50:20Z 2015 2015 Thesis http://hdl.handle.net/1721.1/97824 913225900 eng 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. http://dspace.mit.edu/handle/1721.1/7582 113 pages application/pdf Massachusetts Institute of Technology |
| spellingShingle | Harvard--MIT Program in Health Sciences and Technology. Gorman, Bryan Robert Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| title | Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| title_full | Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| title_fullStr | Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| title_full_unstemmed | Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| title_short | Multi-scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| title_sort | multi scale imaging and informatics pipeline for in situ pluripotent stem cell analysis |
| topic | Harvard--MIT Program in Health Sciences and Technology. |
| url | http://hdl.handle.net/1721.1/97824 |
| work_keys_str_mv | AT gormanbryanrobert multiscaleimagingandinformaticspipelineforinsitupluripotentstemcellanalysis |