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Questions tagged [imagej-macro]

89 questions
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ImageJ macro make new folder and save output in new folder

I modified the following macro I found on an ImageJ message board to batch split channels, create a new folder called "OneChannel" and save the output in the new folder. The code works as expected: it creates the new folder, it splits the channels,…
Nick
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how can I modify the brightness&contrast automatically on my images with fiji macro?

I try to write a very simple macro with Fiji in order to merge channels and enhance contrast automatically. dir = getDirectory("Select input directory"); out = getDirectory("Select destination directory"); files = getFileList(dir); //foreach…
EaudeRoche
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ImageJ stack to images & rename images

I have a small problem with imagej: I have .tif files in a folder, which consist of three different files (blue channel, green channel, red channel). I would like to convert them to separate pictures, then to only keep the green one I want to do…
DCZ
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Setting different thresholds dependent on what filename ends with in ImageJ macro

I have a folder containing many images. These are grouped into sets of three images where one filename ends in dsRed).tif, another filename ends in FITC).tif and the other filename ends in DAPI).tif. How can I tell ImageJ to do different stuff to…
Simon C
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File open dialog in ImageJ Javascript Script

I want to write a macro/script to open a file open dialog, and then import the selected image using BF with various options. I found this JS script for doing the latter part here:…
abalter
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ImageJ Macro for converting multichannel Tiffs to Tiffs with only specified channels

I have a quite simple programming question I was hoping somebody could help me with. I'm working with Tiff files with several channels (all contained in a .lif file, which is Leica format). I want a way to easily convert all my Tiffs to Tiffs…
Johannes Holm
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How do I batch process Z-stacks or all open images on ImageJ/Fiji?

I've really only needed the basics of ImageJ so far, but now I have Z-stacks with 400-500 raw images in each stack. They're already separated by colour, but I can't seem to get a macro to recognize the Z-stack file, convert stack to images, and then…
Tsum
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ImageJ getHistogram function output

I'm trying to understand why the output of the getHistogram function is different from what is displayed when I click on the List button at the bottom of the histogram window. For testing, I created a simple jpeg image in paint - it has a white…
David Newman
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SelectWindow in ImageJ

All, I am new to scripting with imageJ and have run into a problem I cannot get past. I have multiple files open at once and would like the code to cycle though them, do an analysis, create a new filtered image, save that image and close it along…
Rich Hamm
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Subtraction of fluorescence from two images representing the same sample

I am an oceanographer and I have a problem in my research. I am working on the FIJI software (Image J) and I have to process many images to do some quantification. I have images of samples taken with different Fluorescence : CY3 ; TxET , and DAPI I…
ArthurCo
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FIJI/ImageJ Macro not saving every analyze particles results and summary table

I have a folder of multiple Tif images, that I wish to analyze the particles, using analyze particles function. I need one channel, with all of its z-stack slices to be analysed and saved into a folder. My problem is that only every second summary…
MM1
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Can't run function in ImageJ

I am a beginner with imageJ. I wanted to start using scripting tools, I started with writing a simple function as shown below, to mark a single pixel as white on the image already loaded into imageJ function MarkPixel(x,y) { setColor("white"); …
fahd
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ImageJ Macro script to batch process with color thresholding fails to save output tif files

I've written a script in ImageJ Macro in order to batch process a large number of images with color thresholding and particle analysis, modified from this tutorial. Most of the time the thresholding works automatically, but sometimes has to be done…
mws
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Add LUT table into the plugin jar package for ImageJ

I am developing JAR package with a plugin for ImageJ. I tend to use one LUT (lookup table for coloring grayscale images) file, which is not default part of ImageJ/FIJI instalation. I would like to include the lut file into the jar package so that I…
VojtaK
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ImageJ macro has loop error during ROI analysis

I am trying to analyze confocal microscopy image for cFos analysis. From maxstacked image, I took ROI of DAPI and enlarged the ROI to detect the degree of expression of transgene marker. So I can find whether expression of transgene Piezo1 is…
Chypark
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