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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.

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How to work around ImageJ run("HSB stack") error/ bug?

I am working on a macro for ImageJ. The goal is to take colour scans with several seeds on them and crop around the seeds to get several equally sized images with one seed on each. This is the basic idea for the macro: prompt to select folder with…
Josephine R
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SimpleITK.Show() generates error in ImageJ on Macbook

I'm struggling with imagej on Jupyter. This is part of the code that i'm running: def ImageGen(a,b,x_0,y_0, sigma_x, sigma_y, theta ): g=GaussianFunc(x_0,y_0,sigma_x,sigma_y,theta) g2=sitk.GetImageFromArray(g) res=a*g2+b if…
zahra ameli
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Loading a large tif file but only first slice is loaded in openCV

I'm in a process to write a code in order to process my tiff files . I manage to load tif files with 20 to 30 slices but when I proceed to work on my original files with 4000 slices only first slice is loaded . I don't get any type of error. I even…
Jerika
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Is there a built in function to find the operating system?

So I want to navigate the file system from within a Fiji script, and create files. macOS uses / as a separator while windows uses \ as a file separator. I can't for the life of me find an easy way to do this given the poor search ability of the…
Omar Alamoudi
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Why when running Fiji/Imagej in headless mode, the parameters get cached from the previous time?

So if I run the the following example (keeping the #@String param1 line at script.groovy): ImageJ-win64.exe --headless --ij2 --console --run script.groovy "param1='value1'" the param1 is available through the script.groovy code (as expected..) But…
tanovsky
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Adjust Threshold Within Macro ImageJ

I'm looking to write a macro which requires user input to segment kidneys through thresholding. I'm currently running this: selectWindow("Cortex"); //run("Threshold..."); title = "WaitForUserDemo"; msg = "If necessary, use the \"Threshold\" tool…
George Bruce
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Run BackgroundSubtracter in jython script for Fiji

I am trying to create an Imagej/Fiji script to analyze microscopy images. As part of the pipeline, I want to use the rolling ball BackgroundSubtracter supplied in Fiji. According to the Imagej API, that should look something like…
Jorik van Rijn
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How to batch process ImageJ macro within a specific folder within multiple directories

I have a nested file structure where a parent folder contains multiple folders of different types of data. I am using an ImageJ macro script to batch process all of the image files within one of those folders. I currently need to process each folder…
ashcrashbegash
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Import of 3D affine transformation build in Java to R

I have a question related to affine transformations (between the tags). I am extracting the following two affine transformations from an xml file (full xml file here) created with the BigDataViewer Fiji plugin created with Java, using the…
Marion
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Interfacing with ImageJ/Fiji

What options are there for interfacing with / controlling ImageJ/Fiji from another program? I need to use some image filters that are available in Fiji. However, I cannot have Fiji be the centre of my workflow. I am using another system (scripting…
Szabolcs
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Viewer for very large image sets

I'm looking for a viewer that can view thousands of images selectively. For example, I have a set of photos from 1-1000. Due to the magnitude of the photos (8MB per image), I only wish to view photos 20-40. This is to be done with selecting specific…
cheesyang
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Printing Array Items by Index Number in ImageJ (Fiji)

I'm trying to figure out how I can access an item in an array by it's index number. I've written a script which will generate an array, with some number of variables. There's an old script on the imageJ mailing list archive (shown below) which is…
J. Kovacs
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How can I execute an R script from imageJ/Fiji?

I have written an R script (that perfectly works on R) that I would like to run in Fiji. I see that Fiji can understand the R language, but mine doesn't seem to do anything when I hit "run". Is there a line code to specify at the beginning of the…
Sounette
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Can not "link"SimpleITK::Show() with FIJI

I am running on Ubuntu. When calling the Show method of SimpleITK I am not being able to view such image in my FIJI ( ImageJ2) window. Given that FIJI is a portable application, is it necessary to perform some more process in order to properly link…
Francisco Cunha
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How can I specify a specific channel to set B&C for in FIJI?

I've written a primative FIJI script which opens up my 16-bit 3 channel images and allows me to crop regions of interest. However, I can't figure out how to set the brightness and contrast automatically. At the moment I have to do this manually by…
Yasmeen Al-Mufti
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