FAQ Database Discussion Community


ImageJ package for R [closed]

r,image-processing,imagej
I'm looking for an integration of ImageJ and R. There was a package called RImageJ as referenced in [1][2] for previous versions of R (I'm using R 3.1.2 (2014-10-31) -- "Pumpkin Helmet" ) but it isn't available anymore. Basically what I'd like to try is a region growing algorithm over...

ImageJ, roiManager(“add”)

java,macros,imagej
It's my first question in StackOverflow. I have a doubt about roiManager("add") macro command. I'm trying to insert a macro content inside a plugin but im trying to understand what is adding to the roi manager. Here is the code: run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Masks display clear record"); for (i=0;...

ImageJ overlay get removed when rotating

rotation,overlay,imagej
I'm learning ImageJ now but I got a problem. First, I added an overlay to an image (using Image-Overlay-AddImage in menu). Now I want to rotate the image and keep the upper overlay remained as a reference. But when I use the rotate command(Image-Transform-rotate), the overlay is removed. However, this...

Displaying a 32-bit image with NaN values (ImageJ)

python,image-processing,imagej
I wrote a multilanguage 3-D image denoising ImageJ plugin that does some operations on an image and returns the denoised image as a 1-D array. The 1-D array contains NaN values (around the edges). The 1-D array is converted back into an image stack and displayed. It is simply black....

How to convert an image from 8-Bit to RGB in ImageJ2 using Java

java,imagej
I'm trying to use ImageJ2 directly from Java to create a binarised image coming from an input image. A somewhat working version of my code looks like this: final File file = new File("input.png"); try { DefaultDataTypeService dataTypeService = new DefaultDataTypeService(); Dataset dataset = imageJ.dataset().open(file.getAbsolutePath()); Img inputImg = dataset.getImgPlus(); PluginInfo...

Convert tiff to dicom using Matlab

matlab,tiff,dicom,imagej
I have a series of dicom images and did change the HUs in the images using MATLAB scripts, then I imported them in ImageJ for display. Then I realised I can modify the images using ImageJ gui (which much easier, just moving the mouse). However, when I saved the modified...

Implementing ImageJ macro commands into an existing Plugin

java,plugins,imagej
I'm trying to change the existing plugin OpenComet for ImageJ. I'm not into Java, so perhaps it's an easy task. What I'm trying to implement are the following things run("Bio-Formats Windowless Importer", "open=path autoscale color_mode=Default view=Hyperstack stack_order=XYCZT"); opening my files with the help of the Bioformat Importer plugin run("Flip Horizontally");...

[Solved][ImageJ Macro]: How to save plot profile data in a text file?

plot,macros,imagej
I want to make a simple ImageJ macro that draws a profile plot along a given linescan and saves the results in a .txt file. So far, I have: run("Plot Profile"); saveAs("Text", "/path/to/file/Values.txt"); This creates the plot in a new window, but then returns an error, stating that a TextWindow...

getResult() returns NaN for everything but “Area”

imagej,imagej-macro
I'm trying to get the centroid's X and Y values from the Results table, but I can't use getResult() with anything but "Area". All other columns (which are regularly displayed on the table) return NaN. I'm not using any special plugin, the table is created using "Analyze Particles..." Any idea...

Selection problems after Bio Format Importer, czi and zvi Files, ImageJ

plugins,selection,imagej
Hello I'm using ImageJ to analyse -czi and -zvi files. I'm using an automatic selection with "create selection" or "analyze particle"s. It's working well when openening/importing the files with ImageJ. But when I try to use the Bio-Format importer Plugin with the same pictures, it's not working. Not my intended...

Image processing approach

python,image-processing,image-segmentation,imagej
In the following greyscale image,I am trying to identify the objects that I have manually labelled in red. Does anyone have suggestions of how to do this? I have attempted to use a gaussian blur and thresholding but cannot exclusively identify these particles. Would edge detection be a good approach?...

Running fiji/imagej macro from terminal

imagej
I have made a macro in fiji/imagej that i would like to activate via the terminal in a shell script. As it now stands, the macro does not need any inputs, I just want to make fiji run the macro when activated from the terminal, and save its output in...

Image registration b-spline opencv

python,opencv,image-processing,imagej
Here is my question: My optical system is made of a camera plus a circular plexiglass "lens" that changes its curvature depending on pressure (radial bending). This curvature induces a deformation of the image captured by the camera. To correct this deformation, images need to be calibrated. Calibration can be...

Imagej filter larger than the default 3x3

java,imagej
Is there a way using the Imagej api to apply a smooth filter using a larger area than the default 3x3. When you run Imagej and select filters you can specify a size, but I can't find that functionality in the api. Thanks in advance for any help....

Use Weka from ImageJ macro: 'path' is required but unset

macros,weka,imagej
I have tried Calling Weka from an ImageJ(Fiji) macro: run("Trainable Weka Segmentation", "open=C:\\input\\test.tif inputfile=C:\input\test.tif path=[Ljava.lang.String;@77e655d8"); But when I run that I get an error message: 'path' is required but unset This line is exactly the line I get when recording a macro and opening test.tif when the Trainable Weka Segmentation...

ImageJ, adding a scale bar to ImagePlus

java,plugins,imagej
I am trying to add a scale bar to ImagePlus but I can not. When I was using windows I used the following commands: IJ.selectWindow("window_name"); IJ.run("Set Scale...", "distance=1 known="+pixelSize+" pixel=1 unit=um"); IJ.run("Scale Bar...", "width="+barSize+" height=3 font=12 color=Black location=[Upper Right]"); I hope someone can help me, I let the code to...