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Questions tagged [fiji]

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

Fiji is just ImageJ. It 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 Fiji usage as well as Fiji-specific questions, the ImageJ forum is the best place to ask.

111 questions
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System.getProperty("plugins.dir") return null

I am trying to run imageJ project in eclipse but while running the project i am getting "null" value while printing this "System.getProperty("plugins.dir")" in my console, i already included imageJ jar(ij.jar) but still getting this error.
Mukesh Gupta
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How to standardize conversion to binary of images with differing brightness and contrast

I'm working with microscopy samples that feature a 'web' of dark lines. I want convert the images to binary so only the dark portions show up, but I'm uncertain of how to standardize this process. The images have varying brightness and contrast so…
R. H.
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Error in ImageJ macro to lay outlines of particle analysis over original image

I am trying to write an imageJ macro that will 1) Open and split an image into two channels 2) Perform particle analysis on each image and save measurements 3) Save the original image with the particle outlines overlayed So far I have realised I…
Eloise Lockyer
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ImageJ / Fiji shows wrong number of frames in video (FFMPEG import)

I am counting the number of animals in a an area using Fiji. I import the video through the FFMPEG plug-in (videos are mp4 with mpeg-4 codec). However, I noticed that when I import the videos Fiji uploads the wrong number of frames, and I cannot…
locoric_polska
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Trying to create a Mosaic in ImageJ and I get this Java error

I am trying to stitch images using the MosaicJ plugin in Fiji (ImageJ), however, I get the error in the code below. Does anyone know what it means and how I can fix this please? I have no experience using Java at all. I am using a MacBook by the way…
Tobi Lawal
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remove or minimize the overlapping in image

I am working on a project where there is a high chance of overlapping particles in the images as partciles are coming down from the conveyor belt in the mining industry. I am also working on the hardware system to minimize the overlapping but none…
Salman
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