Denoising of Fluorescence Confocal Microscopy Images with Photobleaching compensation in a Bayesian framework [chapter]

Isabel Rodrigues, Joao Sanches
2009 Recent Advances in Biomedical Engineering  
+PVTQFWEVKQP )OXRUHVFHQFH FRQIRFDO PLFURVFRS\ LPDJLQJ LV WRGD\ RQH RI WKH PRVW LPSRUWDQW WRROV LQ ELRPHGLFDO UHVHDUFK ,Q WKLV PRGDOLW\ WKH LPDJH LQWHQVLW\ LQIRUPDWLRQ LV REWDLQHG IURP VSHFLILF WDJJLQJ SURWHLQV WKDW IOXRUHVFH QDQRVHFRQGV DIWHU WKH DEVRUSWLRQ RI SKRWRQV DVVRFLDWHG ZLWK D VSHFLILF ZDYHOHQJWK UDGLDWLRQ $GGLWLRQDOO\ WKH FRQIRFDO WHFKQRORJ\ UHMHFWV DOO WKH RXWIRFXV UDGLDWLRQ WKHUHE\ DOORZLQJ ' LPDJLQJ DOPRVW ZLWKRXW EOXU 7KHUHIRUH WKLV WHFKQLTXH LV KLJKO\ VHOHFWLYH DOORZLQJ WKH
more »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www.intechopen.com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Ċ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p 'XSp HW DO ZKHUH D GHFRQYROXWLRQ DOJRULWKP XVHV D IDVW SUR[LPDO EDFNZDUGIRUZDUG VSLWWLQJ LWHUDWLRQ ZKLFK
doi:10.5772/7477 fatcat:ywvdzynvv5ejhpgsyvynsd7mha