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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).

794 questions
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Matlab only opens first frame of multi-page tiff stack

I've created multi-page tiff files with a macro in ImageJ, and I'm now trying to open it using matlab, but I can only access the first frame. Here is the result of imfinfo(filename). Accordingly, I get length(imfinfo(filename)) = 1 Filename:…
user3049481
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How to merge different stacks together in ImageJ?

I'm trying to find out a way to merge two stacks together. For example I'm taking some 60X images about the soma of a neuron and then I'll take another stack at 60X for the basal dendrite. Then how can I combine them together?
Daniele Piccolo
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ImageJ Overlay Stacks

Basically what I am trying to achieve is overlay one stack with another, in a layer that maybe displayed or not. I know it is possible to overlay 2D images but is there a function to overlay stacks. I have a stack in .raw format containing a 3D uCT…
William Grimes
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imageJ how to get pixel rgb value?

i have a simple plugin which saves the polygon coordinates: Roi roi = imp.getRoi(); Polygon p = roi.getPolygon(); for (int i = 1; i <= p.npoints; i++) { // létrehozzuk az onvif féle vector-t org.onvif.ver10.schema.Vector myVector = new…
David
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ImageJ compatibility with BufferedImage

Can I use BufferedImage objects from java.awt.image.BufferedImage with ImageJ class instances? For example can I use BufferedImage object instead of an ImagePlus object?
buwaneka
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OpenCV vs ImageJ which one to chose if you want to develop in Java?

I would like to use a library to detect objects in an image such as a chair, a bed... Which library would you recommend OpenCV or ImageJ?
Adel Boutros
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Display non-ASCII character in ImageJ

Simple question but I can't find the answer anywhere. No search strategy so far has worked for me. I have an ImageJ macro that opens a dialog for users to set the size of an image overlay. The dialog prompts users to provide the size of the overlay…
dr.nixon
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Exception `java.lang.IllegalStateException: zip file closed`, when running code from Fat-JAR/Uber-JAR

I have an issue with my software, when building and running it as an FatJAR/UberJar built with Maven. In this case I get this error: Uncaught error fetching image: java.lang.IllegalStateException: zip file closed at…
packoman
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how do I perform image stitching with a reference image as a guide?

image stitching with a reference image. I have multiple images of subject(bone), the images are of different sections of the subject as on a 3x3 matrix. I would like to stitch them together but the problem is they don't have any common feature, as…
Palash
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Exception during Fiji/ImageJ launching from Python

I want to write some code in Python that will be used for manipulating data in Fiji. I followed the instructions to install the library "imagej" so that I can access Fiji via Anaconda-Python. This is how the two lines look like: import imagej ij =…
pedro_galher
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How to obtain the scale of an image automatically in imageJ

I need to measure leaf area in a large set of leaves. The problem is that each image has a different scale since they were made with a camera at different heights. Next to each sheet I put a graph paper as a scale. Is there any method / macro of…
David Alonso
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scikit-image read 8-bit image as 16-bit

I am using both ImageJ and scikit-image to analyze 3D images. My original image is 16-bit and it is very big. I converted 16-bit image to 8-bit image in imageJ so that I can work easily. Now when I am reading the image with scikit-image module both…
ankit agrawal
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Error with an import module jnius while using imagej in python

I am trying to connect a headless imageJ library to my python application. Unfortunately, the dependency error list goes on endless and I am now stuck at an import error involving the import of a java wrapper called jnius. So far I have installed:…
abk
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How to modify the code of the dependencies of a maven Project

I just started to do some work on the ImageJ project. This software is developped in Java using Maven as a build system and is split intp numerous sub-projects/modules. I would like to work and modify some of these sub/projects and have them compile…
M. Desharnais
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Calculate binary optimal threshold ImageJ based on foreground/background mean

I was researching on how to calculate an Optimal Threshold for ImageJ and found this explanation of the Otsu Thresholding, which I thought made perfect sense for me to use. I've struggled with implementing it though, and after some thought I found a…
gizmo
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