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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).

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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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How to find number of images in a DICOM study?

Is it possible to find number of images in a DICOM study by reading a DICOM header of a file in that study? I am developing a Java application that receives DICOM studies from different sources. I just want to check if a study has been received…
Arash
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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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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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Synchronize Windows feature in ImageJ

I'm using the Synchronize Windows feature in ImageJ 1.47. To support some debugging, I want to be able to see the pixel values at the cursor location in all my windows simultaneously. By default the "master" ImageJ window displays the RGB values…
LWixson
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Fiji/ImagJ command line argument input and return?

I am wondering if I am running Fiji under --headless mode, what is the best way to pass the parameters to some macros? And what is the best way to return some message (ex. macro execute is done, or some error message) For example, I have a macro…
Nick X Tsui
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Is there a way to call imagej macro (.ijm) from java (i.e. have macro stored as string and execute it using a java control of imagej)?

It is reversed problem to: How can I call/execute a java program from an ImageJ macro? Whenever I write imagej I refer to fiji. Of course a trivial solution is to create a .ijm from java string and call imagej using a system call with .ijm as an…
stymek
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