EBImage: Minimum and Maximum intensity on the edge of an object
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Kevin ▴ 40
@kevin-5879
Last seen 6.9 years ago
Hello, I have recently started to test out EBImage to see if it is suitable to analyze some biological image data I have. I need to measure the relative intensity of fluorescent data on lipid membranes of a cell- like structure (the edge of an object, almost perfectly round). One problem I am having is that I can only find some predefined functions that will give me the average intensity of an object that is found after segmentation. Instead I want to be able to find the minimum and maximum intensity levels in that object and in some number of pixels around the max and min. I would also like to know which pixels these are. I could possibly write my own function to do this if there is nothing available in EBImage to do this. I was thinking of doing a search on the bitmap image after segmentation to find the pixels where 0 is next to a non 0 value and then from that identify the max and min intensity values in the grayscale image. Thank you. Kevin [[alternative HTML version deleted]]
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Bernd Fischer ▴ 540
@bernd-fischer-5348
Last seen 4.6 years ago
Germany / Heidelberg / DKFZ
Dear Kevin! You can easily implement a function yourself that searches for minimum and maximum value: >library(EBImage) >Img = readImage(system.file(file.path("images","nuclei.tif"),package= "EBImage")) >bwl = bwlabel(thresh(Img,w=20,offset=0.1)) >tapply(Img,bwl,min) >tapply(Img,bwl,max) Best, Bernd -- Bernd Fischer EMBL Heidelberg Meyerhofstra├če 1 69117 Heidelberg Tel: +49 [0] 6221 387-8131 E-Mail: bernd.fischer@embl.de Homepage: http://www-huber.embl.de/users/befische/ On 09.04.2013, at 22:19, Kevin <kevinjspring@gmail.com> wrote: > Hello, > > I have recently started to test out EBImage to see if it is suitable to analyze some biological image data I have. I need to measure the relative intensity of fluorescent data on lipid membranes of a cell- like structure (the edge of an object, almost perfectly round). One problem I am having is that I can only find some predefined functions that will give me the average intensity of an object that is found after segmentation. Instead I want to be able to find the minimum and maximum intensity levels in that object and in some number of pixels around the max and min. I would also like to know which pixels these are. > > I could possibly write my own function to do this if there is nothing available in EBImage to do this. I was thinking of doing a search on the bitmap image after segmentation to find the pixels where 0 is next to a non 0 value and then from that identify the max and min intensity values in the grayscale image. > > Thank you. > > Kevin > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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