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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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java.net.URLConnection fails to connect via http or https

I am debugging an issue with my local Fiji/ImageJ installation failing to update through the Help -> Update UI. The ImageJ code that triggers the issue is this updater code:…
SidSethupathi
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JACoP Colocalization Macro Errors Galore

I've tried countless combinations of paths to try and get my macro working to analyze a very large set of images using JACoP. Any suggestions on what might be the issue? this iteration got me closest (I think) to getting it to work. It even loads…
apowell37
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Association of the file type with the plugin in ImageJ to allow drag and drop or click to view

I have created ImageJ plugin by modifying https://imagej.nih.gov/ij/plugins/raw-file-opener.html I managed to get it associated with the ImageJ menu by providing new item File->Open Format When I want to open this format, I have to click File->Open…
VojtaK
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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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How can I plot large volume in 3D plots?

I tried plotting image data of tiff arrays (150,500,500) and so far none of the plotting techniques worked out. I find it frustrating since Fiji imageJ with bioformats can handle everything very fast and is plotting nice images aswell. Can you help…
Qindral
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ImageJ Batch Mode is still opening images

I'm trying to run through a folder in BatchMode but even when I set it to setBatchMode(true) (or setBatchMode("hide")) it still opens the image before setBatchMode("show") and takes forever to open and process. It runs "faster" when I don't use…
DS14
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Setting up ImageJ Macros to batch process lab images

I'm currently trying to batch process a lot of lab images at once using ImageJ/Fiji but I'm having a hard time making it process the images. Whenever a file is pulled up, there are three images which are split into channels and open in separate…
LoveMyoung
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How to save the makeline information (coordinates) in Fiji (imageJ) which comes from the user

I have a macro in Fiji where I am using the waitForUser("For creating the plot", "Make a line along the diameter of the cell and press OK") code and I want to save the coordinates of the line drawn by user, can someone please help as to how this can…
Dhanlakshmi
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Format not supported or reader plugin not found, Fiji ImageJ

I have just downloaded Fiji on Linux 64 bits for visualizing ome.tif files. I haven't modified any setting but it can't open my files. I am getting the error "Format not supported or reader plugin not found". The console indicates:…
salomepx
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Read/Write BigTIFF using BioFormat

I need to I/O large images in TIFF format, so I need to use the BigTIFF format. I tried to use BioFormats (bioformats_package.jar) last version to read an image, using: ImagePlus[] images = images = BF.openImagePlus(io) ; Then, I wanted to access…
FiReTiTi
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ImageJ/Fiji - Save CSV using macro

I am not a coder but trying to turn ThunderSTORM's batch process into an automated one where I have a single input folder and a single output folder. input_directory = newArray("C:\\Users\\me\\Desktop\\Images"); output_directory =…
user18715468
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Write ImageJ ROI file from R

In R, I have a matrix that equals an image, where each cell is 0 if it is background and >0 if it is a ROI. Each ROI has its distinct number, so if it spans several matrix cells all these cells will have the same number. I want to generate ROI files…
NicolasH2
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I am trying to select the last index of a string after splitting an image name from imageJ. I know in python we can do string[-1]

imageName=getTitle(); #This returns a string with the entire path of where the image is. image1 = split(imageName,"/"); #splits the image where "/" is. Based on path, this varies in length image = image1[1]; #I want the last one but it will not…
Karina
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how to open an image in imagej using python?

I want to automatically count cells and I usually do this with ImageJ I can open imagej using subprocess subprocess.Popen(r"path\ImageJ\ImageJ.exe") I want to upload an image into imagej from python Then run an imagej macro (edits image file and…
user17304179
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OrientationJ: Problem saving results from OrientationJ vector field macro

I am trying to write a macro for ImageJ that processes the images in the specified folder through the OrientationJ Vector Field plugin, and then saves the outputted results tables into a separate folder. The issue is that when I run the macro, the…
Charlie M.
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