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Questions tagged [imagej]

ImageJ is a Java-based open-source image processing program that is used extensively in scientific image analysis, particularly life sciences. Please consider asking ImageJ-specific questions on the Image.sc forum: https://forum.image.sc/tags/imagej. This tag should be used for questions about programming in/for ImageJ.

ImageJ is a Java-based open-source image processing program that is used extensively in scientific multidimensional image analysis, particularly life sciences. This tag should be used for questions about ImageJ-related programming.

For questions regarding general ImageJ usage as well as ImageJ-specific questions, the Image.sc forum is the best place to ask.

ImageJ supports plugins written in Java and scripts in several languages (i.e., JavaScript, Python, BeanShell, Groovy, Clojure, Ruby, and the ImageJ1 macro language).

885 questions
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Detecting hexagonal shapes in greyscale or binary image

For my bachelor thesis I need to analyse images taken in the ocean to count and measure the size of water particles. my problem: besides the wanted water particles, the images show hexagonal patches all over the image in: - different sizes - not…
homework
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How can I call/execute an imageJ macro with R?

I've written a macro in imageJ that spits out a data frame which I then analyze in R. I'd love to be able to have the whole procedure work in R without having to first run the macro manually in imageJ. Currently the macro prompts the user for the…
ACG
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ImageJ - ScaleBar in Java

I have opened an image with this code: this.imp = IJ.openImage(imageFilePath); imp.show(); And now, I need to set the scaleBar. I need to set it after imp.show() because the user has to draw a line before (and later set the scale). But it only…
David
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ImageJ - Convert image format without saving file

I'm using ImageJ API to convert some 24-bit TIFF images to 8-bit JPG. After the conversion I need to do other processing on these images. I made this: ImagePlus img = IJ.openImage(f.getAbsolutePath()); // Open image new…
kennyFF92
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Importing classes from the root of external jars (.jar) in Intellij (Maven Project)

I'm using IntelliJ 2016 and I have some Maven dependencies (for ImageJ plugin development) that I added successfully, the two external libraries show up in the form of jar files . I've added them in project structure -> module -> dependencies and…
Youcefhd
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imageJ plugin argument

Hello I am trying to pass arguments to my ImageJ PlugIn. However it seems no matter what I pass, argument string will be considered as empty by the program. I couldn't find any documentation on the internet about THAT issue. My Java plugIn looks…
kaligne
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Are ImageJ Maven dependencies in maven central?

I am planning to use ImageJ for a webapp but it seems ImageJ maven dependencies are not in the central maven repository. Am I right? Is this going to change when ImageJ 2.x is released?
balteo
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How to change white background for black

In a recent project I have to manipulate images, but since this is new to me I am kind of lost. I need to scan the hand using a regular scan device. I could acomplish this but the background is white and I need it to be black. After several days of…
Ivan Perales M.
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ImageJ macro code to change directory

I am learning how to write macros in ImageJ. I have the user select a folder where data is stored, e.g., path=getDirectory("Choose a data folder"); Once the user has selected the folder, e.g., path = D:\data_superfolder\data_folder I then need to…
Alna
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Overlay of multiple colors in ImageJ

I'm writing a little plugin for imageJ and I am drawing several regions as an overlay on the image. I'm using this code: ImagePlus imp = getImage(); Overlay ov = new Overlay(); for (int r=0; r
nico
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Running fiji/imagej macro from terminal

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…
MatsZissou
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How can I do batch image processing with ImageJ in Java or clojure?

I want to use ImageJ to do some processing of several thousand images. Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically? For example, say I want to take my thousand images and apply a polar…
Robert McIntyre
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Image Analysis: Finding proteins in an image

I am attempting to write a program that will automatically locate a protein in an image, this will ultimately be used to differentiate between two proteins of different heights that are present. The white area on top of the background is a membrane…
Samuel Barnett
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Dicom: Matlab versus ImageJ grey level

I am processing a group of DICOM images using both ImageJ and Matlab. In order to do the processing, I need to find spots that have grey levels between 110 and 120 in an 8 bit-depth version of the image. The thing is: The image that Matlab and…
Prometheus
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Automatically release unused memory in ImageJ / Fiji

I use Fiji/ImageJ on Windows and encountered the following problem: when I close a file, the memory allocated for that file is not released. ImageJ keeps that memory allocated, and reuses it when other files are opened. So this is not strictly a…
hthms
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