Shawndouglas: Completely updated content.

2014-06-18T02:07:54Z

Completely updated content.

← Older revision		Revision as of 02:07, 18 June 2014
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	''~~(This article was taken from Wikipedia)~~''		[[File:Keck Bioimaging Lab.jpg\|thumb\|500px\|right\|The Keck Bioimaging Lab and other labs like it depend on bioimage informatics tools ever day.]]
			'''Bioimage informatics''' is a multidisciplinary sub-field of [[bioinformatics]] and computational biology that involves the development and use of computational techniques to analyze bioimages, especially cellular and molecular images, on a large scale fashion, with the goal of mining useful knowledge out of complicated and heterogeneous images and related metadata.<ref name="BlaschkeLink">{{cite book \|url=http://books.google.com/books?id=YsAIwLlBZosC&pg=PA8 \|chapter=Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns \|title=Linking, Literature, Information, and Knowledge for Biology: Workshop of the BioLINK Special Interest Group, ISBM/ECCB 2009, Stockholm, June 28-29, 2009, Revised Selected Paper \|author=Coelho, Luis P.; Glory-Afshar, Estelle; Kangas, Joshua; Quinn, Shannon; Shariff, Aabid; Murphy, Robert F. \|publisher=Springer \|year=2010 \|pages=8–18 \|isbn=9783642131301 \|accessdate=17 June 2014}}</ref>

	~~'''Bioimage~~ informatics~~'''~~ is ~~a subfield of~~ [[~~bioinformatics~~]] ~~and computational biology. It is most related to using computational techniques to analyze bioimages~~, ~~especially cellular and molecular images, at large scale and high throughput, with~~ the ~~goal~~ to ~~mine useful knowledge out~~ of ~~complicated and heterogeneous image and related metadata~~. ~~There has been an increasing focus on developing novel~~ image ~~processing, [[data mining]], database and visualization techniques~~ to ~~extract, compare, search and manage the biological knowledge in these data-intensive~~ problems.<ref name="~~pmid18603566~~">{{cite journal \|~~author~~=~~Peng H~~ \|title=Bioimage informatics: a new area of engineering biology \|~~journal~~=~~Bioinformatics~~ \|volume=24 \|issue=17 \|pages=1827–36 \|year=2008 \|month=September \|pmid=18603566 \|pmc=2519164 \|doi=10.1093/bioinformatics/btn346 \|~~url~~=}}</ref>		The field of bioimage informatics is somewhat related to [[imaging informatics\|medical imaging informatics]], in so much as some of the advances in that field have found their way to the technology of analyzing bioimages. However, "it is very challenging to directly apply existing medical image analysis methods to ... bioimage informatics problems."<ref name="PengBI">{{cite journal \|url=http://bioinformatics.oxfordjournals.org/content/24/17/1827.full \|journal=Bioinformatics \|title=Bioimage informatics: a new area of engineering biology \|author=Peng, Hanchuan \|volume=24 \|issue=17 \|pages=1827–36 \|year=2008 \|month=September \|pmid=18603566 \|pmc=2519164 \|doi=10.1093/bioinformatics/btn346 \|accessdate=17 June 2014}}</ref> Some of the challenges bioimages pose to researchers include:

	~~This field is in quick growth in recent years~~, ~~apparently due~~ to the ~~flood~~ of ~~complicated molecular~~ and cellular ~~microscopic images produced~~ in ~~a series~~ of ~~projects~~ that ~~create compelling challenges~~ for the image ~~computing community~~.		* special techniques are required to analyze images on the cellular and molecular scales.
			* the file size of some bioimages can be hundreds of megabytes or reach even several gigabytes.
			* many days would be required to manually analyze the thousands of images generated from today's optical microscopy techniques and labeling methods.

			These challenges require automatic high-throughput analysis techniques, novel algorithms, and advanced systems to deal with the tasks of processing, storing, visualizing, and mining bioimages.<ref name="PengBI" />

			==Application==
			Imaging informatics can help tackle problems and tasks such as the following<ref name="BlaschkeLink" /><ref name="PengBI" />:

			* the measurement of the effects of pharmaceuticals on cells and their structure
			* the localization of cellular proteomes
			* the analysis of cellular phenotypes
			* the tracking of cellular activity and other dynamic processes
			* the mapping of gene expression in embryos
			* the creation of an "atlas" for modelling an organism
			* the three-dimensional reconstruction of neuronal structures of body and brain
			* the prediction of sequence motifs that may have regulatory functions in an organism

			==Informatics==
			Bioimage informatics features five "top-level stages" in its use of computational techniques: image acquisition and screening; image processing; information management; data modeling and statistical analysis; and system-biology integration.<ref name="LodhiElements">{{cite book \|url=http://books.google.com/books?id=UO3VM58KLrkC&pg=PA381 \|chapter=Chapter 17: Computational Imaging and Modeling for Systems Biology \|title=Elements of Computational Systems Biology \|author=Wu, Ling-Yun; Zhou, Xiaobo; Wong, Stephen T. C. \|publisher=John Wiley & Sons \|year=2010 \|pages=381–401 \|isbn=9780470556740 \|accessdate=17 June 2014}}</ref> In the acquisition phase, informatics tools "must be capable of capturing the raw data (the individual pixels) and the metadata around the acquisition methodology itself, including instrument settings, exposure details etc."<ref name="SwedlowOS">{{cite journal \|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789254/ \|journal=Trends in Cell Biology \|title=Open source bioimage informatics for cell biology \|author=Swedlow, Jason R.; Eliceiri, Kevin W. \|volume=19 \|issue=11-3 \|pages=656–660 \|year=2009 \|month=November \|doi=10.1016/j.tcb.2009.08.007 \|accessdate=17 June 2014}}</ref> During image processing, the informatics tools must be able to read well over 80 proprietary file formats for optical microscopy and other imaging techniques. The information management stage requires roomy databases capable of organizing and holding terabytes of data.<ref name="SwedlowOS" /> Modeling and statistical analysis tools must be extensible and capable of being applied in different combinations to different images.<ref name="SwedlowInfo">{{cite journal \|url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522889/ \|journal=Science \|title=Informatics and Quantitative Analysis in Biological Imaging \|author=Swedlow, Jason R.; Goldberg, Ilya; Brauner, Erik; Sorger, Peter K. \|volume=300 \|issue=5616 \|pages=100–102 \|date=04 April 2003 \|doi=10.1126/science.1082602 \|accessdate=17 June 2014}}</ref> Finally, an integrated approach towards various biological tools and informatics systems is required to ensure the other four stages take place optimally.

			Open-source bioimage informatics tools are helping to expand the scope of biomolecular researchers' work.<ref name="SwedlowOS" /> Examples include OMERO — software for visualizing, managing, and analyzing biological microscope images — and FARSIGHT, a toolkit for associative image analysis.

			==External links==

			* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789254/table/tbl2/ A list of open-source bioimage tools as of 2009]
			* [http://www.vibconferences.be/event/bioimage-informatics BioImage Informatics International Conference]
			* [http://www.biomedcentral.com/bmcbioinformatics/series/BioimageInfo Bioimage Informatics at BMC Bioinformatics]

	==References==		==References==
	<references/>		<references />

			<!---Place all category tags here-->
	[[Category:Informatics]]		[[Category:Informatics]]

Shawndouglas: Updated cat.

2011-11-22T21:55:41Z

Updated cat.

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	<references/>		<references/>

	~~{{DEFAULTSORT:Bioimage Informatics}}~~		[[Category:Informatics]]
	[[Category:~~Bioimage informatics~~]]

Mikelong88888 at 14:26, 21 July 2011

2011-07-21T14:26:10Z

← Older revision		Revision as of 14:26, 21 July 2011
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	{{DEFAULTSORT:Bioimage Informatics}}		{{DEFAULTSORT:Bioimage Informatics}}
	[[Category:~~Bioinformatics~~]]		[[Category:Bioimage informatics]]

Mikelong88888 at 18:56, 20 July 2011

2011-07-20T18:56:36Z

← Older revision		Revision as of 18:56, 20 July 2011
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	==References==		==References==
	~~{{reflist}}~~		<references/>

	{{DEFAULTSORT:Bioimage Informatics}}		{{DEFAULTSORT:Bioimage Informatics}}
	[[Category:Bioinformatics]]		[[Category:Bioinformatics]]

Mikelong88888: Creation of Article

2011-07-20T18:56:06Z

Creation of Article

New page

''(This article was taken from Wikipedia)''

'''Bioimage informatics''' is a subfield of [[bioinformatics]] and computational biology. It is most related to using computational techniques to analyze bioimages, especially cellular and molecular images, at large scale and high throughput, with the goal to mine useful knowledge out of complicated and heterogeneous image and related metadata. There has been an increasing focus on developing novel image processing, [[data mining]], database and visualization techniques to extract, compare, search and manage the biological knowledge in these data-intensive problems.<ref name="pmid18603566">{{cite journal |author=Peng H |title=Bioimage informatics: a new area of engineering biology |journal=Bioinformatics |volume=24 |issue=17 |pages=1827–36 |year=2008 |month=September |pmid=18603566 |pmc=2519164 |doi=10.1093/bioinformatics/btn346 |url=}}</ref>

This field is in quick growth in recent years, apparently due to the flood of complicated molecular and cellular microscopic images produced in a series of projects that create compelling challenges for the image computing community.

==References==
{{reflist}}

{{DEFAULTSORT:Bioimage Informatics}}
[[Category:Bioinformatics]]

Bioimage informatics - Revision history

Shawndouglas: Completely updated content.

Shawndouglas: Updated cat.

Mikelong88888 at 14:26, 21 July 2011

Mikelong88888 at 18:56, 20 July 2011

Mikelong88888: Creation of Article