search for: imagej

I am out of my league with this question. The following code starts the java imaging program ImageJ from within R, and displays an image (assuming ImageJ is installed on your computer). library(RImageJ) img <- IJ$openImage( file.choose() ) #pick an available .tif file img$show() # make the image object visible # An image is now displayed # find out about the objects involved > st...

Hi, Maybe this is more a programming questions than a specific R-project question, but maybe there is someone who can point me in the right direction. I have a picture of cirkels which I took with a digital camera. Now I want to use the diameter of the cirkels on the picture for analysis in R. I can use pixmap to import the picture, but how do I find the outside cirkels and calculate the

Hello, I've uploaded the initial release (0.0-142) of the RImageJ package to CRAN. The package allows R to use the facilities of the java based image processing and analysis platform ImageJ. See also the announcement on my blog, with a very simple example showing how to use the package: http://romainfrancois.blog.free.fr/index.php?post/2009/06/22/using-ImageJ-...

Hello, I've uploaded the initial release (0.0-142) of the RImageJ package to CRAN. The package allows R to use the facilities of the java based image processing and analysis platform ImageJ. See also the announcement on my blog, with a very simple example showing how to use the package: http://romainfrancois.blog.free.fr/index.php?post/2009/06/22/using-ImageJ-...

...th many bugs in each image. I want to count the number of bugs and to have an estimate of the area of each one. I've tried searching for an R package to do so with no success. Is this a task that I should pursue doing in R or should I restrict myself to specific image analysis software (e.g. ImageJ)?. The reason I consider R would be a good choice is because then It would probably be possible to use R statistical power to do pattern recognition on each bug's image to try to identify each bug (Family, genus or species). Is anybody working in this direction? Thanks, Angel

Hi I have a string "56 Fe [1]" that I would like to use as a variable name by using "assign" however I think the spaces and brackets might be causing R some trouble. How can I change the string so that it just becomes 56Fe1 and can be used as a variable name. Thank You Kurt _________________________________________________________________ [[elided Hotmail spam]]

Dear all I tried to find some packages (or programs) for image analysis and especially fractal dimension image analysis but so far I had not success. It shall be used for particle surface layer analysis from TEM images. Any suggestions? Best regards Petr

...to further instructions after a package is installed. For example, some packages need to setup environment variables, ... Is there something I have missed ? Romain -- Romain Francois Independent R Consultant +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/qzSl : using ImageJ from R: the RImageJ package |- http://tr.im/qzSJ : with semantics for java objects in rJava `- http://tr.im/qzTs : Better completion popups

...than 0.2 the plot in the .jpg file is blank. If I run the commands from the console (on a Mac) - with the exception of jpeg() and dev.off() then it works even if cex < 0.2. I've tried making .ps files and converting to .jpg but then I run into different problems with the animation software (imageJ). Thanks for any suggestions -- View this message in context: http://www.nabble.com/Problem-with-cex%3D0.1-when-making-jpegs-tp21593744p21593744.html Sent from the R help mailing list archive at Nabble.com.

What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). Thanks, Spencer Graves

...2.4.27 kernel, to the cdrom version of Knoppix. Version 0.7.9.2 ships as one compressed iso file of 2.7gb that is Relative to the previous release 0.7.9.1, several small bugs have been fixed, Sun's Java 1.5.0 SDK has been added along with several Java-based applications (ImageJ, Weka, JGR, Mondrian), several other applications have been added, yet more R packages from CRAN and BioC are included and a few other packages have been updated. Quantian now contains over 2550 Debian packages, over 870 packages for R and a few extra applications. Quantia...

...2.4.27 kernel, to the cdrom version of Knoppix. Version 0.7.9.2 ships as one compressed iso file of 2.7gb that is Relative to the previous release 0.7.9.1, several small bugs have been fixed, Sun's Java 1.5.0 SDK has been added along with several Java-based applications (ImageJ, Weka, JGR, Mondrian), several other applications have been added, yet more R packages from CRAN and BioC are included and a few other packages have been updated. Quantian now contains over 2550 Debian packages, over 870 packages for R and a few extra applications. Quantia...

Hi, I've been looking for Image Processing packages. Thresholding, Edge Filters, Dct, Segmentation, Restoration. I'm aware, that Octave, Matlab etc. would be a good address but then I'm missing the "statistical power" of R. Does anybody know of packages, projects etc. Comments on wether the use of R for such matters is useful are welcome. Greetings Thomas Kaliwe

I have a bunch of jpg files that I need to count cells on. Some cells are green and some cells are red. Is there a function like locator that I could use to manually count the cells? I would like to be able to click on a cell, have it marked so I don't count it again and have a counter keep track. Locator comes close but I would only be able to count one colour at a time. Is there a way I

Hello, I need to do some basic statistics on raster images (tiff or png). I need only an advice where to start, which package is the most appropriate. My search attempts were without success, yet. Many thanks Tomas

Dear R developers, i'm developing a Java application with a very efficient image transfer api between ImageJ and R. In my next release i can transfer bytes to R very fast with the help of the Rserve application. Furthermore i added an easy to use interface to the clustering algorithm "clara" in the cluster package. At the moment i can cluster an R,G,B image with size 4000*4000 without any proble...

Folks, In brief -- how many of you have found the 'operators' package to be valuable in their work? Not that I lack respect for the amount of work involved in creating and maintaining a package, but I am unsure about the utility of these new operators. Several of the operators appear to offer different ways of accomplishing tasks that are already relatively easy in base R -- regular

Is there an specific function to eliminate blank space within strings? Thanks -- Dr. Agustin Lobo Institut de Ciencies de la Terra "Jaume Almera" (CSIC) LLuis Sole Sabaris s/n 08028 Barcelona Spain Tel. 34 934095410 Fax. 34 934110012 email: Agustin.Lobo at ija.csic.es http://www.ija.csic.es/gt/obster

Hi, I am looking for a R package which is capable to process and analysis pictures of tissues (stained) in an automatic way. I had a look on biops and EBImage (Bioconductor) but they are not automatic... Did you already use/know a such package ? Thanks, - Martial _________________________________________________________________ Tchattez en direct en en vidéo avec vos amis !

Hi, on a lattice, I have binary 0/1 data. 1s are rare and may form clusters. I would like to know the size/length of largest cluster. Any help warmly welcome, Sylvain.