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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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convert tiff video into set of images in FIJI / IMAGEJ

How can I convert tiff video into set of images, should I use plugin？ and export images types should be tif as well, please give me any guide!
Marktwinkle
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How do I pass an argument to an ImageJ macro from within an ImageJ Java plugin?

I am trying to pass an argument from an ImageJ plugin to an imageJ macro. Basically, I call the macro from within my ImageJ Java plugin to open a stack of images and would like to be able to pass an integer value to the plugin to be able to append…
user3716193
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how to display a list of images on one side of the split pane

I want to make a split pane where on the left hand side it displays a list of images, and once you click on those images it should then display the image in a bigger size on the right hand side. I was wondering if anyone knows how to do this because…
selena
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ImageJ2 customized GUI

I am trying to put the imageJ window inside a desktop pane that I have created but I am having trouble doing this. How do you use imageJ2 source code in order to make a customized GUI where the imageJ window is inside the desktop pane? This is for…
user3605351
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Running commands from fiij menu in java code

I need to run a command from fiji menu in java code developed using netbeans IDE. The command is Image--Color--RGB to CIELAB. I used "IJ.run" to run commands from ImageJ menu like Fill Holes(i.e. IJ.run(imp,"Fill Holes","")). But I don't know how…
Safaa Al-Haj Saleh
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ImageJ: Listener on point selection tool

I want to set up an own programm using ImageJ as a library. So this will not going to be a plugin. The user can open an image and then mark a spot with the point selection tool provided by ImageJ. When the user does this I want my measurements to…
user2599141
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Gradle Could not find method compile

I am trying to use gradle for the first time. What I want to do is to use ImageJ with gradle. I took the example file from imageJ website and a java code from the examples on the imageJ github. Gradle says it can't find the method compile for…
Bubble
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Register two .tif images in Imagej, align z-axis and rotation

I am working with Fiji on my image analysis. I have two *.tif stacks from a microscopic sample, one of them is slightly rotated and has a z-axis offset. It's like a screw being screwed in to a different amount than the first one. How can I align…
Idontcare
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Denoising an Image using ImageJ Macros

I would like to ask how to denoise this image using ImageJ macros. I know it's like coding in C but i want to know what is the algorithm that i can use to denoise this picture.
user3388464
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Java with ImageJ

I am using ImageJ in java code for doing segmentation of objects in images using LevelSet. I imported the jar file called "levelsets.ij.LevelSet". But I get an error as 'unidentified command' in the string field 'Level Sets' in the run command.…
Feminna Sheeba
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Counting Regions of Interest in a Picture

I need to count the number of strips (as labeled) in the following photo: I have hundreds of photos that I need to analyze and I am curious if there is a way to automatically isolate the regions of interest and perform a simple count for each…
BillyBoy
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Imagemagick: How to increase the number of colors in binary image?

It is a black-and-white image. Its palette consist from only two colors. When I try to threshold this image in ImageJ (Fiji), it cann't do this because of the image has only two colors. (I don't know why it cann't do this.) So, the questions is:…
Ivan Z
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How to select the bubbles inside the droplet correctly

This is Wendy.Image processing related question. I have to select the bubbles properly to analyze its size and calculate the velocity among image sequences. original image enter image description here image sequences enter image description…
Wendy
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C Programming turning array into an image

I am using C to run a phase retrieval algorithm on images. I am using ImageJ to convert the .png into a text image that I then read into my code and run the code. At the end I have printed the output to a text array, and then have to read it from…
Chris U
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How to use ImageJ with NetBeans

I have ij jar file. How can I adopt the help of this jar file in my code. I want to create an image auto selection tool. Is ij or javacv better?
Don Chakkappan
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