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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).

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Synchronize Windows feature in ImageJ

I'm using the Synchronize Windows feature in ImageJ 1.47. To support some debugging, I want to be able to see the pixel values at the cursor location in all my windows simultaneously. By default the "master" ImageJ window displays the RGB values…
LWixson
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Fiji/ImagJ command line argument input and return?

I am wondering if I am running Fiji under --headless mode, what is the best way to pass the parameters to some macros? And what is the best way to return some message (ex. macro execute is done, or some error message) For example, I have a macro…
Nick X Tsui
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Is there a way to call imagej macro (.ijm) from java (i.e. have macro stored as string and execute it using a java control of imagej)?

It is reversed problem to: How can I call/execute a java program from an ImageJ macro? Whenever I write imagej I refer to fiji. Of course a trivial solution is to create a .ijm from java string and call imagej using a system call with .ijm as an…
stymek
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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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opening a raw with imagej in command prompt

I'm trying to create a .bat file to read .bsv files and turn them into color pngs. The first part of that is using imagej to open the .bsv, and then using a "save all" plugin I added. I tried making a macro but it just gives me errors. How would…
singmotor
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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 silent mode - process without opening images

I need to run Macro, but I don't want to show the image. If I don't call the imp.show(), ImageJ will print to the console There are no images open. So how can I run Macro without showing the image? Thanks in advance. public class MyPlugin…
cernover
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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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Writing Macro in ImageJ to open all files from folder, change B/C, subtract background, assign a threshold

I'm trying to write a macro that: Opens up all .tif images from a folder Converts them all to 32-bit images Adjusts the brightness and contrast to a certain min/max (130/160) Subtracts the background with a rolling ball radius of 15 and light…
noexperiencewithcoding
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How can I feed a string that includes quotes to a system2 call in R?

I have a somewhat niche question that I'm hoping someone can answer for me or help me find a work-around to: I've written a script in R that will run an ImageJ macro for sets of images I produce as a part of my workflow. Because this is work that I…
Kelly N.
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How to subtract one stack from another in FIJI (ImageJ)?

Is there a way of how to subtract one stack of images from another stack using FIJI (ImageJ)? To be more specific, I would like to find a quick way for such a subtraction, where first image of the first stack is subtracted from the first image of…
Capo Pavel Mestre
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