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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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Find number of spots in a noisy image

I want to automatically count the number of spots in this type of image where spots are very close to each other such that many are considered as a single spot: I thought of using MATLAB's local maxima function/algorithm such as imregionalmaxima…
tselios
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display a dicom image in a java application using ImageJ

I am experimenting with ImageJ Library and I found that ImageJ could be used in a java application as well. Is there a specific tutorial to display a dicom image using imageJ? Also, does ImageJ support dicom RT structures?
chrisrhyno2003
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ImageJ API: how to display an image with zoom and drag to scroll features active in the image window?

If I use Fiji application to open an image, then the image is displayed in a window where I can use + and - keys to zoom in and out, also I can hold down the space bar and drag the zoomed image with mouse to scroll through it. I want to implement…
croset3
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how to control ImageJ from Python 3.4.2

I am trying to use Python 3.4.2 to control ImageJ what I want to do is from python code , I want to sent orders to imageJ to analayse some images, detecting edges, contrast, noise etc there is a similar question here How to connect ImageJ to…
Jose Fernando Gomez Davila
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SaveAs in a loop with ImageJ

I'm brand new to imageJ and its macros, I can't save a Results file from Particle Analyze in a loop. Here is my code, made of what I just learned on internet and I just can't include [i] in the saveAs function and there is a mismatch with the saving…
Sarahdata
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Opening raw images on Python resulting in a different image compared to ImageJ

I wrote this script to open a raw image and do some processing. import numpy as np import matplotlib.pyplot as plt PATH = "C:\Users\Documents\script_testing_folder\\" IMAGE_PATH = PATH…
WingZ_of_Silence
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ImageJ (plugin Java): auto threshold method doesn't work

I try to write Java Plugin to ImageJ, which should: Load image (24-bit). Do some preprocessing operations. Threshold the image in numerous of methods. Do some other operations. I have problem with threshold operation. Part of my code looks like…
trojek
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Error loading OpenCV in Java for Image Processing

I am facing a problem in loading OpenCV in Java(Eclipse, Mac OSX). I am new to Java and my main target is Image Processing.I have checked several examples online but....I have few queries actually: 0) Can you actually instruct me how to use OpenCV…
Psi Lambda Delta
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Image processing approach

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…
William Grimes
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Estimation of line length using Skeleton

I'm using ImageJ and Skeleton to estimate line length and density, but the problem is that I have an agglomerate of lines that I need that to be considered as different lines, before I can use the Skeleton plug in. Has anyone have any idea of how to…
Marina Rocha
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Case sensitive string comparison Image J Macro

String comparisons are case insensitive using Image J Macro. For example, the following will print "True": if ("c" == "C") { print("True"); } Does anyone know of a workaround to make case-sensitive comparisons in image J macro?
RainbowMonkey
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ImageJ - how to ensure two images are directly comparable (what scripting command?)

I need to present some microscopy images side by side and ensure they are directly comparable by eye in a presentation. The pictures were all taken with the same exposures, gain et cetera so the underlying pixel values should be comparable.…
IJQ
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Get the pixels in an ROI only, how?

Trying my hand at scripting and so far I have a function that returns an ROI derived through thresholding. PA.setRoiManager(roim) paOpt = PA.CLEAR_WORKSHEET +PA.SHOW_NONE +PA.INCLUDE_HOLES +PA.EXCLUDE_EDGE_PARTICLES + PA.ADD_TO_MANAGER #…
Liam_Stubbington
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Image Segmentation, watershed, waterfall, p algorithm

I was wondering if anyone is aware of any currently available packages for segmentation using the waterfall method or p algorithm. I've looked in github, CRAN, and Fiji and haven't found anything despite published literature discussing the benefits…
Harry B
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Crop Custom Shape in ImageJ or equivalent (TIFF video file)

I have a .tiff video file with growing fibers that look like the image below Now imagine that this fiber will constantly grow and shrink in a straight line. Now I'd like to somehow crop out the region of the video that contains just the fiber…
Amateur Math Guy
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