uu.seUppsala University Publications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Detection of cell aggregation and altered cell viability by automated label-free video microscopy: A promising alternative to endpoint viability assays in high throughput screening
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine.
Show others and affiliations
2015 (English)In: Journal of Biomolecular Screening, ISSN 1087-0571, E-ISSN 1552-454X, Vol. 20, no 3, 372-381 p.Article in journal (Refereed) Published
Abstract [en]

Automated phase-contrast video microscopy now makes it feasible to monitor a high-throughput (HT) screening experiment in a 384-well microtiter plate format by collecting one time-lapse video per well. Being a very cost-effective and label-free monitoring method, its potential as an alternative to cell viability assays was evaluated. Three simple morphology feature extraction and comparison algorithms were developed and implemented for analysis of differentially time-evolving morphologies (DTEMs) monitored in phase-contrast microscopy videos. The most promising layout, pixel histogram hierarchy comparison (PHHC), was able to detect several compounds that did not induce any significant change in cell viability, but made the cell population appear as spheroidal cell aggregates. According to recent reports, all these compounds seem to be involved in inhibition of platelet-derived growth factor receptor (PDGFR) signaling. Thus, automated quantification of DTEM (AQDTEM) holds strong promise as an alternative or complement to viability assays in HT in vitro screening of chemical compounds.

Place, publisher, year, edition, pages
2015. Vol. 20, no 3, 372-381 p.
Keyword [en]
time-lapse microscopy, video microscopy, phase contrast microscopy, differentially time evolving morphologies, high throughput screening (HTS), cell aggregation, PDGFR signalling.
National Category
Bioinformatics (Computational Biology) Social and Clinical Pharmacy
Research subject
Bioinformatics; Clinical Pharmacology
Identifiers
URN: urn:nbn:se:uu:diva-234561DOI: 10.1177/1087057114562158ISI: 000350310000007PubMedID: 25520371OAI: oai:DiVA.org:uu-234561DiVA: diva2:757066
Available from: 2014-10-21 Created: 2014-10-21 Last updated: 2017-12-05Bibliographically approved
In thesis
1. Towards High-Throughput Phenotypic and Systemic Profiling of in vitro Growing Cell Populations using Label-Free Microscopy and Spectroscopy: Applications in Cancer Pharmacology
Open this publication in new window or tab >>Towards High-Throughput Phenotypic and Systemic Profiling of in vitro Growing Cell Populations using Label-Free Microscopy and Spectroscopy: Applications in Cancer Pharmacology
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Modern techniques like automated microscopy and spectroscopy now make it possible to study quantitatively, across multiple phenotypic and molecular parameters, how cell populations are affected by different treatments and/or environmental disturbances. As the technology development at the instrument level often is ahead of the data analytical tools and the scientific questions, there is a large and growing need for computational algorithms enabling desired data analysis. These algorithms must have capacity to extract and process quantitative dynamic information about how the cell population is affected by different stimuli with the final goal to transform this information into development of new powerful therapeutic strategies. In particular, there is a great need for automated systems that can facilitate the analysis of massive data streams for label-free methods such as phase contrast microscopy (PCM) imaging and spectroscopy (NMR). Therefore, in this thesis, algorithms for quantitative high-throughput phenotypic and systemic profiling of in vitro growing cell populations via label-free microscopy and spectroscopy are developed and evaluated. First a two-dimensional filter approach for high-throughput screening for drugs inducing autophagy and apoptosis from phase contrast time-lapse microscopy images is studied. Then new methods and applications are presented for label-free extraction and comparison of time-evolving morphological features in phase-contrast time-lapse microscopy images recorded from in vitro growing cell populations. Finally, the use of dynamic morphology and NMR/MS spectra for implementation of a reference database of drug induced changes, analogous to the outstanding mRNA gene expression based Connectivity Map database, is explored. In conclusion, relatively simple computational methods are useful for extraction of very valuable biological and pharmacological information from time-lapse microscopy images and NMR spectroscopy data offering great potential for biomedical applications in general and cancer pharmacology in particular.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2014. 50 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1045
Keyword
label free vesicle detector, high-throughput, phase contrast microscopy, Library of Pharmacologically Active Compounds, High Content Screening, fluorometric microculture cytotoxicity assay, nuclear magnetic resonance, mass spectrometry
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-234565 (URN)978-91-554-9082-9 (ISBN)
Public defence
2014-11-25, Robergsalen, entrance 40, 4th floor, Akademiska Sjukhuset, Uppsala, 09:30 (English)
Opponent
Supervisors
Available from: 2014-11-04 Created: 2014-10-21 Last updated: 2015-02-03

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Authority records BETA

Aftab, ObaidFryknäs, MårtenHammerling, UlfLarsson, RolfGustafsson, Mats

Search in DiVA

By author/editor
Aftab, ObaidFryknäs, MårtenHammerling, UlfLarsson, RolfGustafsson, Mats
By organisation
Cancer Pharmacology and Computational Medicine
In the same journal
Journal of Biomolecular Screening
Bioinformatics (Computational Biology)Social and Clinical Pharmacy

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 520 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf