Hello Gregoire, Good news, you got the answer. Thanks a lot, Samuel Gregoire Pau wrote: > Hello Samuel, > > Running the following code on my system: > > library("EBImage") > > a = matrix(runif(20*20), 20, 20) > > writeImage(a, "a.tiff") > > system("tiffinfo a.tiff") > > Gives me: > Image Width: 20 Image Length: 20 > Resolution: 72, 72 pixels/inch > Bits/Sample: 16 > Compression Scheme: None > Photometric Interpretation: min-is-black > FillOrder: msb-to-lsb > Orientation: row 0 top, col 0 lhs > Samples/Pixel: 1 > Rows/Strip: 204 > Planar Configuration: single image plane > Page Number: 0-1 > DocumentName: a.tiff > Software: ImageMagick 6.5.7-8 2010-12-02 Q16 > > Only one sample per pixel is present here. I am using EBImage 3.7.1 > and ImageMagick 6.5.7. It seems that your version of ImageMagick is > very old and is likely the cause of the extra alpha layer. I guess > updating it will solve your problem. > > Hope this helps, > > Best, > > Greg > --- > Gregoire Pau > EMBL Research Officer > http://www.embl.de/~gpau/ > > On 28/02/11 14:35, Samuel GRANJEAUD - IR/ICIM wrote: >> Hello, >> >> Sometimes we build examples that do not reflect our minds. Sorry I was >> wrong in putting the same value in the matrix. Nevertheless, the runif >> matrix leads to the same result in respect to my point. As tiffinfo >> enlights it, there is an extra plane (aka ExtraSamples) in the tiff, >> that leads to a SamplePerPixel value of 2. Now BitsPerSample are 16 of >> course. >> >> Best regards. >> >> > library(EBImage) >> Loading required package: abind >> > a = matrix(runif(20*20), 20, 20) >> > writeImage(a, "a.tiff") >> > system("tiffinfo a.tiff") >> TIFF Directory at offset 0x648 (1608) >> Image Width: 20 Image Length: 20 >> Resolution: 72, 72 pixels/inch >> Bits/Sample: 16 >> Compression Scheme: None >> Photometric Interpretation: min-is-black >> Extra Samples: 1<unassoc-alpha> >> FillOrder: msb-to-lsb >> Orientation: row 0 top, col 0 lhs >> Samples/Pixel: 2 >> Rows/Strip: 102 >> Planar Configuration: single image plane >> DocumentName: a.tiff >> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >> >> >> Gregoire Pau wrote: >>> Hello Samuel, >>> >>> EBImage uses ImageMagick's WriteImage() to write images and doesn't do >>> anything more. Image format is guessed by ImageMagick from the file >>> name and the dynamic range of the image. As an example, the following >>> code creates a random uniform 16-bit grayscale TIFF 20x20 image: >>> > library("EBImage") >>> > a = matrix(runif(20*20), 20, 20) >>> > display(a) >>> > writeImage(a, "a.tiff") >>> >>> Your example uses an image with only one color and ImageMagick (and >>> therefore EBImage) uses the 1-bit mode of the TIFF image format to >>> write it. The bug you are facing seems to come from the fact that >>> ImageJ does not support the 1-bit TIFF image format. >>> >>> In the future, it would be nice to have more control in the output >>> image format. But, in the meanwhile, just use more colors to force >>> EBImage to use the 16-bit format. >>> >>> Hope this helps, >>> Best regards, >>> >>> Greg >>> --- >>> Gregoire Pau >>> EMBL Research officer >>> http://www.embl.de/~gpau/ >>> >>> On 25/02/2011 19:37, Samuel GRANJEAUD - IR/ICIM wrote: >>>> Hello, >>>> >>>> I am using EBImage to convert matrix to tiff grey scale. And I would >>>> like to read them directly in ImageJ. Unfortunately such image >>>> contains >>>> an extra plane that is not needed and not supported by ImageJ. This >>>> alpha plane seems to be automatically added at the creation of the >>>> image >>>> in the C code (I guess). In ImageMagick API, this is referred as >>>> "matte" >>>> http://www.imagemagick.org/api/magick- image.php#MagickSetImageMatte >>>> >>>> If I am not wrong, it would be nice if this alpha plane could be >>>> removed >>>> in next release. >>>> >>>> Regards, >>>> Samuel >>>> >>>> ~$ R --vanilla >>>> >>>> R version 2.12.1 (2010-12-16) >>>> Copyright (C) 2010 The R Foundation for Statistical Computing >>>> ISBN 3-900051-07-0 >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>>> You are welcome to redistribute it under certain conditions. >>>> Type 'license()' or 'licence()' for distribution details. >>>> >>>> Natural language support but running in an English locale >>>> >>>> R is a collaborative project with many contributors. >>>> Type 'contributors()' for more information and >>>> 'citation()' on how to cite R or R packages in publications. >>>> >>>> Type 'demo()' for some demos, 'help()' for on-line help, or >>>> 'help.start()' for an HTML browser interface to help. >>>> Type 'q()' to quit R. >>>> >>>> > library(EBImage) >>>> Loading required package: abind >>>> > a <- matrix(10,20,20) >>>> > b <- Image(a) >>>> > b >>>> Image >>>> colormode: Grayscale >>>> storage.mode: double >>>> dim: 20 20 >>>> nb.total.frames: 1 >>>> nb.render.frames: 1 >>>> >>>> imageData(object)[1:5,1:6]: >>>> [,1] [,2] [,3] [,4] [,5] [,6] >>>> [1,] 10 10 10 10 10 10 >>>> [2,] 10 10 10 10 10 10 >>>> [3,] 10 10 10 10 10 10 >>>> [4,] 10 10 10 10 10 10 >>>> [5,] 10 10 10 10 10 10 >>>> >>>> > writeImage(b,"b.tif") >>>> > system("tiffinfo b.tif") >>>> TIFF Directory at offset 0x6c (108) >>>> Image Width: 20 Image Length: 20 >>>> Resolution: 72, 72 pixels/inch >>>> Bits/Sample: 1 >>>> Compression Scheme: None >>>> Photometric Interpretation: min-is-black >>>> Extra Samples: 1<unassoc-alpha> >>>> FillOrder: msb-to-lsb >>>> Orientation: row 0 top, col 0 lhs >>>> Samples/Pixel: 2 >>>> Rows/Strip: 1638 >>>> Planar Configuration: single image plane >>>> DocumentName: b.tif >>>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >>>> > system("convert b.tif +matte c.tif") >>>> > system("tiffinfo c.tif") >>>> TIFF Directory at offset 0x44 (68) >>>> Image Width: 20 Image Length: 20 >>>> Resolution: 72, 72 pixels/inch >>>> Bits/Sample: 1 >>>> Compression Scheme: None >>>> Photometric Interpretation: min-is-black >>>> FillOrder: msb-to-lsb >>>> Orientation: row 0 top, col 0 lhs >>>> Samples/Pixel: 1 >>>> Rows/Strip: 2730 >>>> Planar Configuration: single image plane >>>> DocumentName: c.tif >>>> Software: ImageMagick 6.3.7 12/02/10 Q16 http://www.imagemagick.org >>>> > sessionInfo() >>>> R version 2.12.1 (2010-12-16) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 >>>> LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8 [7] >>>> LC_PAPER=en_GB.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] >>>> LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> other attached packages: >>>> [1] EBImage_3.6.0 abind_1.1-0 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >