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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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Point selection in pictures with custom scale

I try to analyze images with Fiji. Therefore I first “calibrate” the scale with set scale run(“Set Scale…”, “distance=52.6 known=30 pixel=1 unit=no global”); and then make a rectangle as seen in the picture: Pic 1. Then I execute a measurement with…
maxgotstuck
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How to loop through each point of a multi point selection to get the pixel value?

I'm new to ImageJ and ImageJ macro. I started to make a macro that apply the "Find Maxima" function on an image. Then I would like to test each pixel spotted as maxima to filter them by value. How can I loop through all the points of the selection…
damien200
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Undefined variable error when running macro in ImageJ

I am new to ImageJ macros and I want to use a macro in Fiji. The code for the macro is from this source. macro "MultiRoiMove Tool - C00cT0f16M" { if (RoiManager.selected<2) exit(); …
ceno980
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How to Install a toolset in Fiji or ImageJ

New to FIJI and ImageJ here, so I apologize if this question sounds idiotic to the veterans. I came across a really cool toolset that can deblur laser scanning microscopy images here: http://image.bio.methods.free.fr/lsmtrans.html but it is missing…
Yuji Itadori
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Make ImageJ/ Fiji Jython script with ij and loci classes work from bash script

So far, I exectuted my jython plugins from the script editor in Fiji. I would like to execute my jython scripts from in the command line. When executing jython myscript.py at the line from ij import IJ I get the error: ImportError: No module named…
Lisa B.
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ImageJ plugins with dependencies or uberjar assembly are not available in FiJi plugins

I am writing an ImageJ/FiJi plugin. when I build my project with the following pom.xml and uberjar.xml, I get the following jar…
m.i.cosacak
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WEKA 3.8 won't run on Win10

I can run WEKA 3.6.9 on my Win10 machine, but WEKA 3.8.4 fails. The error is ' Could not initialize the GenericPropertiesCreater. This exception was produced: java.lang.NumberFurmatException: For input string:" ' This problem also is blocking the…
RonDespain
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Create new image stack from merged stack with ImageJ

I have a merged image stack (from two composite stacks), with a screenshot of a slice shown here. This was done in ImageJ. Essentially, the water (blue) was injected into a gas diffusion layer (i.e., a porous material made primarily of carbon…
Esper
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ImageJ Macro: Undefined Variable when saving an image to a directory

When I am changing open image window it forgets the directory, how can I retrieve it to save again This is how I create a direcotry in Stack image folder dir=getDirectory("image"); print(dir) splitDir= dir +…
Z.Grey
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Trying to loop a macro in FIJI/Image J

So this is the second time I've posted a question like this. Last time I got so much help from a user called @quantixed but I need help again. My code isn't working, but it's something to do with me trying to isolate images from a stack because I…
CluelessBiochemist632
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Export Weka Fiji plugin segmentation as ROI

I am using Imagej/Fiji Weka plugin for classifying different regions of the image and I would like to obtain those regions for further processing… (as Rois? a table with the classes?) So in the end I want to get the area for each of the segmented…
tanovsky
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Computing the thickness of branches in a 2D image

I'd like to get a measure of the thickness of branches in an image. The following is the output obtained from Fiji. I'd like to compute an average measure of the thickness associated with each edge. By edge, I mean the segment present between any…
Natasha
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How to prevent error in compiling jar plugin

I keep getting this error when i try to run a a plugin called MicrobeJ in Fiji (ImageJ) Exception in thread "Thread-8" java.lang.NoSuchMethodError: org.jfree.chart.plot.XYPlot.setAxisOffset(Lorg/jfree/ui/RectangleInsets;)V at…
Aditya Iyer
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ImageJ/Fiji change the default colormap

Is there a way to change the default colormap in ImageJ/Fiji? Maybe it is too obvious but I didnt spot it in the options. Or is there a way to run a script automatically after an image has been opened and the script does for example: run("Fire")…
moc
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ImageJ TIFF import image dimensions?

I have a bunch of auto-scanned slides using a slide scanner (Hamamatsu), which I can export from the NDPview software at different magnifications. So far, I have been zooming in to where I get the best resolution of my region on interest and add a…
DS14
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