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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.

111 questions
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How to specify colormap when saving tiff stack

I'm using tifffile in python to save out 3-channel tiff stacks, which I then want to read into ImageJ or FIJI. These tiff stacks open as composites in ImageJ with each channel assigned a (presumably default) colormap/LUT. However, the colors that…
holastello
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Detected JDK Version: 11.0.8 is not in the allowed range [1.8.0-101,1.8.9999]

I'm trying to build fiji software from it's source code.here's the github page:fiji source code I started with building project using maven from ubuntu's terminal and I faced with this error: ali@ali-All-Series:~/Downloads/fiji-master$ mvn WARNING:…
Ali Rayat
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1 answer

How to save ImageJ tiff metadata using Python

I'm trying to save a tiff stack using tifffile and using this solution to add ImageJ tiff metadata tags and values. The code runs with no errors, but when I open "image info" in ImageJ, I don't see the new tag I created. I don't really know how Tiff…
bobby_dandan
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How to subtract one stack from another in FIJI (ImageJ)?

Is there a way of how to subtract one stack of images from another stack using FIJI (ImageJ)? To be more specific, I would like to find a quick way for such a subtraction, where first image of the first stack is subtracted from the first image of…
Capo Pavel Mestre
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2
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1 answer

String format in imageJ macro

I would like to convert an integer into a string with leading zeros in ImageJ / Fiji macro editor using String.format() function. With this code: s = String.format("%04d", 13); print(s); I get the following error: Unrecognized String function in…
NicoH
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1 answer

Convert image datatype from uint16 to uint8

I have a tiff image stack in uint16 datatype and I’d like to convert this to uint8 datatype. I’m not sure how to do this in Fiji. I have loaded the stack in Fiji and I tried to change the datatype while exporting. But I couldn’t find any tab in Fiji…
Natasha
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Exception during Fiji/ImageJ launching from Python

I want to write some code in Python that will be used for manipulating data in Fiji. I followed the instructions to install the library "imagej" so that I can access Fiji via Anaconda-Python. This is how the two lines look like: import imagej ij =…
pedro_galher
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Extracting data from java class model in MATLAB

I am writing a script that allows me to automatically analyse my image data sets in MATLAB by using MIJI and the TrackMate plugin. I am able to successfully run an analysis but I cannot get the tracking data out from the java class…
Eppicurt
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1 answer

How to run imageJ from terminal at current folder?

I need to run a Fiji(imageJ) script from terminal on a macOS. Using the code below. /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless -macro ~/desktop/testing.ijm.ijm And the Fiji script I need to run is dir = getDirectory("Where I…
Geyao Li
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2 answers

Incorporating a plugin into an ImageJ/FIJI Macro (bUnwarpJ)

I am trying to integrate the plugin, bUnwarpJ into an ImageJ macro I have been writing. The aim is to call this plugin, allow the user to define the parameters and run it. This plugin has an option to save the user defined parameters, i.e.,…
Pradeep R
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1 answer

How to achieve the Fiji "HiLo" colormap in matplotlib image plots, to mark under and overexposed pixels

Matplotlib's colormaps do not provide the HiLo colormap for images, which is often used in microscopy. HiLo shows a gray-level gradient from low to high values, but values at the low-end are shown in blue and ones at the upper end in red. How can…
stevosn
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2
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1 answer

Error in running a plugin in imageJ

I am using imageJ (Fiji) version: 2.0.0-rc-43/1.50e I installed a IHC_Profiler (https://sourceforge.net/projects/ihcprofiler/) And when I run it, it shows a console with this: Compiling 1 file in …
pill45
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How can I save an image, change the contrast/brightness, display the change then restore the original image, displaying those all in the same window?

The idea of my program is similar to the adjust brightness/contrast built-in plugin. I want to have the image in one window where you can see it with varying b/c values. The original image should be saved before I make any changes to it so that I…
MxIhsaan
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1 answer

Combining two .AVI movies with OpenCV unsuccessful

I am trying to use OpenCV to combine two .AVI videos, but having little success. I want a combined final video that plays the two videos sequentially. The two input videos were created with Fiji's TrackMate algorithm. They are 6.6 and 6.2 MB, each…
Steven Basmith
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0 answers

How to remove multiple ROIs in the same general area on Fiji

I am wondering if anyone knows how to delete multiple ROIs in the same general area of an image. I'm using Fiji. I am looking for an easy way to delete all ROIs in a given area. For example, the multi-point selection tool has the ability to delete…
brendav
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