handling 12 bit tiffs in EBImage
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Rajarshi Guha ▴ 120
@rajarshi-guha-3531
Last seen 5.5 years ago
Hi, I have a collection of 12 bit tiffs that I would like to analyze using EBImage. However, for the images to show via display() I need to convert them to 8 bit (say by using convert on the command line). Is EBImage capable of handling these types of directly? Or do I always need to sale down to 8 bit outside of R? -- Rajarshi Guha NIH Chemical Genomics Center
convert EBImage convert EBImage • 615 views
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Gregoire Pau ▴ 310
@gregoire-pau-3274
Last seen 7.1 years ago
Hi Rajarshi, In the TIFF format, 12-bit images are stored in 16-bit. EBImage supports these images but they have to be scaled by a factor of 16 (2^4), to adjust the dynamic range. The following commands should work: > library(EBImage) > x = readImage('image.tiff')*16 > display(x) If the signal is too faint, images have to be rescaled before being displayed, e.g. using normalize(), which performs the linear scaling (x - min(x))/ (max(x) - min(x)). > display(normalize(x)) Hope this helps, Best regards, Greg --- Gregoire Pau EMBL Research Officer http://www.embl.de/~gpau/ Rajarshi Guha wrote: > Hi, I have a collection of 12 bit tiffs that I would like to analyze > using EBImage. However, for the images to show via display() I need to > convert them to 8 bit (say by using convert on the command line). Is > EBImage capable of handling these types of directly? Or do I always > need to sale down to 8 bit outside of R? > >
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