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Questions tagged [imagej]

ImageJ is a Java-based open-source image processing program that is used extensively in scientific image analysis, particularly life sciences. Please consider asking ImageJ-specific questions on the Image.sc forum: https://forum.image.sc/tags/imagej. This tag should be used for questions about programming in/for ImageJ.

ImageJ 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 ImageJ usage as well as ImageJ-specific questions, the Image.sc forum is the best place to ask.

ImageJ supports plugins written in Java and scripts in several languages (i.e., JavaScript, Python, BeanShell, Groovy, Clojure, Ruby, and the ImageJ1 macro language).

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How to count the number of spots in this image?

I am trying to count the number of hairs transplanted in the following image. So practically, I have to count the number of spots I can find in the center of image. (I've uploaded the inverted image of a bald scalp on which new hairs have been…
B Faley
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Twain device (scanner) control in Java

I want to scan a number of papers through Java. I found the mm's computing twain library. When I run the example TwainExample.java at the site, I receive this error. uk.co.mmscomputing.device.twain.TwainIOException: Cannot load Twain Source…
Any Thing
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How can I use ImageJ as a library for a separate Java application?

In a regular Java application, I have a BufferedImage that I would like to manipulate with ImageJ. I have a macro that is exactly what I need to execute. I suspect that the first step is to make an ImagePlus object, but I am not sure how to then run…
eiowmqui
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Calling ImageJ from Mathematica

From Mathematica, I wish to pass an image to an ImageJ plugin and get the result sent from ImageJ to Mathematica. JLink is the tool that will help, but I am familiar neither with it nor with ImageJ (making it hard to leverage existing related…
Matthias Odisio
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color match in images

I have two images (slices) which were taken by two camera sensors to complete one image. However, due to some differences in sensors' performance, the colour/tones of them are different and I need to match them to make one unified image. I used the…
gin
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Java - How to write a very large (20,000x20,000 px or larger) tif image

I am working with extremely large tif images that I am composing into a large single image. I have a library that was created by a colleague of mine that generates the image pyramid and provides a very handy tool for visualizing the image pyramid. …
Jameshobbs
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Image processing: Rotational alignment of an object

I have a stack of images with a bar close to the center. As the stack progresses the bar pivots around one end and the entire stack contains images with the bar rotated at many different angles up to 45 degrees above or below horizontal. As shown…
user1863037
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ImageJ Brightness & Contrast over a stack of images

I'm looking through a dataset set of images in ImageJ (a stack of .tif images, about 130 frames), and I have a problem with the dataset. It's a series of microscope images, with each frame being a plane about 3-4 micrometers above/below the previous…
Magsol
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How to connect ImageJ to python?

I am using Python to design a software, and the image processing is one of the steps. I am using ImageJ to realize this. Since there is a Jython interpreter within ImageJ, which can be opened within ImageJ software, there must be a way to connect…
Jarvis Du
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Run Fiji from command line?

Here is what I want to do: I want to run Fiji from command-line, to do something like batch image processing. I imagine by typing some command at some console, some batch file can be launched to execute some macro. In this case, the Fiji GUI will…
Nick X Tsui
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How to find number of images in a DICOM study?

Is it possible to find number of images in a DICOM study by reading a DICOM header of a file in that study? I am developing a Java application that receives DICOM studies from different sources. I just want to check if a study has been received…
Arash
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R/ImageJ: Measuring shortest distance between points and curves

I have some experience with R as a statistics platform, but am inexperienced in image based maths. I have a series of photographs (tiff format, px/µm is known) with holes and irregular curves. I'd like to measure the shortest distance between a hole…
Mikko
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Converting 32-bit TIFF to 8-bit TIFF while retaining metadata and tags in python?

I would like to convert several TIFF files with 32-bit pixel depth into 8-bit pixel depth TIFFs while retaining metadata and TIFF tags. The 32-bit TIFFs are four-dimensional ImageJ-hyperstacks with TZYX axes (i.e. time, z-depth, y-coordinate,…
Otri
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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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SimpleITK.Show() generates error in ImageJ on Linux

EDIT NOTE: This question was originally phrased as How to link SimpleITK.Show() to imageJ in linux? By upgrading SimpleITK 1.0.0 to 1.0.1, I was able to launch ImageJ from SimpleITK.Show(). However, ImageJ is unable to open "sample_mri.hdr". ImageJ…
DottedGlass
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