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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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FIJI: How do I impose a Directory from inside a Macro? Automatic, not "choose directory"

I have a long code with various outputs. I am saving the customized results table in the directory where the image I am working on is: dir = getDirectory("image"); but I would like to save that .txt file also in a new directory, newdir, which is…
LJR
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.nd2 to .tif using fiji bio-formats windowless

thanks for stopping by. I am trying to process ~50 images from .nd2 to .TIF, but the exported images are not what I expect and I'm not sure what is wrong. My .nd2's have two channels and I would like the final .TIF to be an image of both channels.…
SJK
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How to equalize intensities in different images with OpenCV (Python)

I googled for this about a day. I have 50 images, all showing the same background. Unfortunately, they are all slightly differing in brightness / intensity due to slight changes in lightning during the picture aquisition. Now I want to equalize the…
Bendaua
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How can Use IADF-IAVFF 1.0 Fiji-Plugins Java/python

A new Fiji-plugin for visualizing intra-annual density fluctuations and analyzing intra-annual theoretical volumetric flow rate fluctuations along wood cross-sections hello to you all, I try to use this new fiji-plugin to perform the analysis of my…
Eric Brazeau
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How can we compute log values of numbers less than 1...? using java

I am in a situation that I need to calculate something like log(1/1400). I have tried Math.log method in java but no luck. actually how can we calculate something like this in java? Math.log1p also I have tried since it give the log value of 1+x…
user9644596
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GenericDialogPlus - saving FileField as a new variable?

Newbie to scripting here. I’d like to create a dialog window that prompts user to choose 2 files (“pos”, and “neg”). I’d also like to store these file paths as a variable to use later on. I’m having trouble storing the file paths. Instead of…
moxed
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How to create a convex hull of all binary spots in ImageJ

I have a binary image of separated spots. Is there any ImageJ plugin that could construct convex hull of all spots? Or could you recommend another program, not ImageJ, that can do this?
Ivan Z
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ImageJ Script: How to add one image to an existing image

In Fiji (ImageJ) I have two images open (Img1 and Img2). I want run a script that adds both images and stores the result in Img1. I'm boing to do this in a sequence of images so I would like to try to avoid creating and closing many images. Would…
Miguel
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Multiplying two images together in ImageJ

I'd like to do some image processing in FIJI / ImageJ but not sure how to go about it. I have a first image, call it "imageA" and would like to perform several operations on it. I know you can go to Process->Math and have some options for operations…
Harry B
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How to do a line selection in fiji (imagej) using specified coords

How to select a line in an image using ImageJ/Fiji by setting its start and end points? As in not drawing it over the image, but inputting the coordinates directly somewhere.
Mali Remorker
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imageJ/FIJI: can i add a new ROI in the middle of a ROI manager list of ROIs

I have some code that processes saved lists of ROIs in a specific order. I am trying to go back through and add ROIs where they are missing but can only seem to add them to the end of the list of ROIs in ROI manager. Is there a way to add them into…
user3470496
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weka.classifiers.neural.lvq Not found

Where can i found lvq in weka dev 3.7.11 jar? As while importing this weka.classifiers.neural.lvq, it shows me an error of not found.
Mukesh Gupta
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java.lang.NoSuchMethodError: putMemberOffset

I am working on windows 10 with jdk1.8 I am getting following error. I tried a lot but unable to find the reason why getting this error, error snap is as follows. java.lang.NoSuchMethodError: putMemberOffset at…
rtisne
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fiji imagej crashes on Ubuntu 16.04

I installed fiji (a distribution of imagej) on my Ubuntu 16.04 machine, and double-clicking the desktop icon opened the app for a second, or rather it tried to open, and then died. I looked for an answer online, and found on this page…
excyberlabber
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imageJ macro export results to csv

I am trying to run the Thunderstorm plugin in ImageJ on all files in a folder. Once I perform the localizations and get results, I want to export the results in a csv file such that the first part of the csv file contains the image name. Here is the…
saurCMat
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