similar to: cell counting in R

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

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 >

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.

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

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 !

I'm trying to automate making a bunch of figures and I need a way to automate legend position. As I understand it the legend is placed based on coordinates. I don't know before hand what the coordinates are going to be. On one graph my y axis might go from -50 to -10. On another it might go from 0 to 180. Is there any way to query where the origin is? Or is there another way to

Hello everyone,  I'm working in a project to create an special analysis about visualization in some animals and its behaviour, through checking eye movement. The point is this is very important to get data from the image as a resume of what this animal sees. I think an RGB histogram like photoshop does, but I need to get the data from this histogram analysis and I was wondering about using R

I need to refresh my memory on Probability Theory, especially on conditional probability. In particular, I want to solve the following two problems. Can somebody point me some good books on Probability Theory? Thank you! 1. Z=X+Y, where X and Y are independent random variables and their distributions are known. Now, I want to compute E(X | Z = z). 2.Suppose that I have $I \times J$ random number

Dear all I need to run an anova from a factorial model y_{ijk}=\alpha_i+\beta_j+(\alpha\beta)_{ij}+e_{ijk} and calculate type II and III sums of square, but I have an empty cells, so anova function from package car fail. (I believe) y<-c(7,13,6,10,8,11,8,3,7,5,65) a<-as.factor(c(1,1,2,2,3,3,3,1,1,1,2)) b<-as.factor( c(rep(1,7),rep(2,4)) ) table(b,a) # cell (2,3) is empty

Hi everyone! This is a ridiculously simple problem, I just can't seem to find the solution! All I need is something equivalent to sum(is.na(x)) but instead of counting missing values, to count empty cells (with a value of 0). A naive attempt with is.empty didn't work :) Thanks! Maja Oh, and if the proposed solution would be to make all the empty cells into missing cells, that is

Hallo, I didn´t found any facilities for Halbergs cosinor analysis in R. This analysis is well known in the Chronobiology as the least square approximation of time series using cosine function of known period (in my case of 24hours-period). I tried to write a script but crashed... Can you give me some advices, please!? Thanks Anne Berger Institute of Zoo- and Wildlife Research, Berlin, Germany

Hi, I have a set of x,y data points and each data point lies between (0,0) and (1,1). Of this set I have selected all those that lie in the lower triangle (of the plot of these points). What I would like to do is to divide the region (0,0) to (1,1) into cells of say, side = 0.01 and then count the number of cells that contain a point. My first approach is to generate the coordinates of these

Dear all, As our previous email did not get any response, we try again with a reformulated question! We are trying to do something which needs an efficient loop over a huge array, possibly functions such as apply and related (tapply, lapply...?), but can't really understand syntax and examples in practice...i.e. cant' make it work. to be more specific: we are trying to apply a mask

As far as I can tell, there are no facilities in the "base" R for image analysis. Is there any extension or package for R that implements image analysis? I'm thinking of features such as o Reading and writing image files, o displaying indexed or "true color" images, o resizing, cropping, etc, of images, o filters for manipulating images (smoothing, edge detection, etc) o

Dear R developers, I was looking for a function analogous to base::diag() for getting and setting bands of a matrix. The closest I could find was Matrix::band(), but this was not exactly what I wanted for two reasons. Firstly, Matrix::band() returns a matrix rather than just the specified band. Secondly, Matrix::band() cannot be used for setting the values for a matrix band. Setting or

Dear all I would like to ask you if an assignment can be done inside a lapply statement. For example I would like to covert a double nested for loop for (i in c(1:dimx)){ for (j in c(1:dimy)){ Powermap[i,j] <- Pr(c(i,j),c(PRX,PRY),f) } } to something like that: ij<-expand.grid(i=seq(1:dimx),j=(1:dimy)) unlist(lapply(1:nrow(ij),function(rowId) { return

Hi R, Wanted to check if there are any packages available for getting the (x,y) data points of a graph or a plot, which is in the image format. Say, the plot could be a published report, and I want to get the points of the curve plotted. (I am speaking something related the subject discussed in http://www.uniphiz.com/digitizing.htm) Thanks, Shubha This e-mail may contain

Hi, I am trying to parameterize the following mixed model (following Piepho and Ogutu 2002), to test for a trend over time, using multiple sites: y[ij]=mu+b[j]+a[i]+w[j]*(beta +t[i])+c[ij] where: y[ij]= a response variable at site i and year j mu = fixed intercept Beta=fixed slope w[j]=constant representing the jth year (covariate) b[j]=random effect of jth year, iid N(0,sigma2[b]) a[i]=random

Dear all, Does anybody have an idea or suggestion how to construct (plot) 4-dimensional hypercube in R. Thanks in advance for any pointers. Regards, Andrej

I'm trying to: Resample with replacement pairs of distinct rows from a 120 x 65,000 matrix H of 0's and 1's. For each resampled pair sum the resulting 2 x 65,000 matrix by column: 0 1 0 1 ... + 0 0 1 1 ... _______ = 0 1 1 2 ... For each column accumulate the number of 0's, 1's and 2's over the resamples to obtain a 3 x 65,000 matrix G. For those