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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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How to achieve the Fiji "HiLo" colormap in matplotlib image plots, to mark under and overexposed pixels

Matplotlib's colormaps do not provide the HiLo colormap for images, which is often used in microscopy. HiLo shows a gray-level gradient from low to high values, but values at the low-end are shown in blue and ones at the upper end in red. How can…
stevosn
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Resize and crop an image using ImageJ

I'm trying to resize and crop an image using ImageJ. Here's the code: ImagePlus ip1 = IJ.openImage("_Pic.jpg"); ImagePlus ip2 = IJ.openImage("_Pic.jpg"); ImageProcessor imgP1 = ip1.getProcessor(); ImageProcessor imgP2 =…
vtomic85
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How to use ImageJ in Android?

I am developing an android application in which I am trying to replicate the mapir plugin of fiji. I have searched on internet and I came to know that ImageJ2 can be useful for this. How to use it in my android project? And is ImageJ2 and ImageLib2…
Jay
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ImageJ Macro: saving csv file

I'm trying write a macro to save the profiles from a sequence of images. Sadly, it's not working: the images open and close correctly (and the correct profile is drawn) but the .csv is nowhere to be found. This is the code: function action(input,…
odo22
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How does rawPy reads DNG frames

This question is the follow up of my previous one dng-raw-pictures-imported-as-16-bit-deep-but-unexpected-plt-show-result after which I continued my search. Due to the replies obtained the visualization in 16 bit but channel per channel works well.…
noste99
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Running Jython script from terminal with parameter

I want to invoke Jython scripts from command line, p.e. $ /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless little_jython_script.py I know about Python's (and therefore Jython's) capability to take parameters by import sys params =…
Karl der Kaefer
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Find pixel coordinates of grid intersection points

I am trying to find a repeatable process to find the coordinates of grid intersection points from an image. The image is a montage of many smaller images. Each 'tile' of the montage has inconsistent contrast, so my naive methods are failing (the…
Shaun_M
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Error in running a plugin in imageJ

I am using imageJ (Fiji) version: 2.0.0-rc-43/1.50e I installed a IHC_Profiler (https://sourceforge.net/projects/ihcprofiler/) And when I run it, it shows a console with this: Compiling 1 file in …
pill45
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How do I save the XY coordinates of a Binary Image in R?

I am trying to save the XY coordinates of a binary image in R similarly to the save "Save XY Coordinates" function in ImageJ. I've looked through several image analysis packages available for R, but haven't yet figured out how to accomplish this.
Tim Lehmberg
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Matching Colour/Lighting between Images using a Colour Standard in GIMP

I am working on a project where colour is an important component. I need to compare the colours of subjects between photos, however the lighting between photos is not absolutely consistent and so the colours are inconsistent and skewed. I have a…
Andrew Grass
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Incompatible types in DELPHI and Opencv

I am trying to find contour into a picture. I implement as follows but i get Incompatible types: 'ocv.core.types_c.pCvMemStorage' and 'UWaterShedSegment.pCvMemStorage' error. type pCvMemStorage = ^TCvMemStorage; pCvSeq = ^TCvSeq; …
FishCoder
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imagej image type conversion

I am new to java programing. I am trying to write a java application using netbeans that uses imagej jar to open a dicom image & process it. I was able to do that using the following java code: public class user_interface extends java.awt.Frame…
Mat Al-Tamimi
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multiple object detection and tracking

I am new to image processing and I'm working on a project multiple object detection(any object in frame) and tracking. I read few of the detection algorithms and thought of implemnting Gaussian mixture model for detection and tracking using kalman…
Pratul Jn
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MATLAB vs. FIJI statistical region merging algorithm speed: why is FIJI faster?

I have assembled an algorithm in MATLAB and as part of that am using statistical region merging. I have versions of this in MATLAB and Fiji (ImageJ), both included below. Both versions are based on the Nock and Nielson model and seem similar…
user3470496
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R and ImageJ sync issues

I have a script in R (written by someone else) which calls ImageJ for image analysis using shell() with '-batch' switch: shell("C:\\ImageJ\\imagej.exe -batch [args]") The analysis indeed begins, but it seems that R continues to perform the next…
Inbal H
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