Stack Overflow
Stack Overflow

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).

885 questions
2
votes
2 answers

Image registration b-spline opencv

Here is my question: My optical system is made of a camera plus a circular plexiglass "lens" that changes its curvature depending on pressure (radial bending). This curvature induces a deformation of the image captured by the camera. To correct this…
mugenop
  • 23
  • 6
2
votes
2 answers

ImageJ package for R

I'm looking for an integration of ImageJ and R. There was a package called RImageJ as referenced in [1][2] for previous versions of R (I'm using R 3.1.2 (2014-10-31) -- "Pumpkin Helmet" ) but it isn't available anymore. Basically what I'd like to…
drgalindog
  • 35
  • 1
  • 6
2
votes
1 answer

Auto threshold in ImageJ/FIJI with Python

I'm trying to write python scripts in ImageJ and I'm having problems with autothresholding. It won't let me use the IJ.setAutoThreshold("Default dark"). An example bit of code is below (with a few things left out for clarity): from ij import IJ,…
Dave'o-Telephone
  • 113
  • 1
  • 11
2
votes
1 answer

Bandpass filter of FFT applied image. (Like ImageJ bandpass filter algorithm)

There is a good function that I need, which is implemented in the Java program: ImageJ. I need to understand the algorithm used there. The function has several parameters: link text And before using FFT it converts image to a special one: The…
maximus
  • 4,201
  • 15
  • 64
  • 117
2
votes
2 answers

Java: ImageJ alternative

I'm looking for some kind of alternative to ImageJ (http://imagej.nih.gov/ij/). For those who don't know, ImageJ is great for analyzing and creating these tif files from scripts that the user writes. However I noticed that using it in a java project…
Sam
  • 405
  • 2
  • 5
  • 13
2
votes
1 answer

Match histogram - ImageJ

Given two ImagePlus or BufferedImages (I don't care) how can I match the histogram of the first to the second one? By matching I mean: Matching the cumulative distribution function (CDF) of one image to the CDF of the other.
DeMarco
  • 599
  • 1
  • 8
  • 26
2
votes
2 answers

Create JavaFX Image from PGM or TIFF as fast as possible

I'm capturing images from a scanner device with java. The input format ist PGM or TIFF. I have to show up live results in the user interface. Actually I'm using ImageJ to read the source input stream as tiff, because ImageJ can also handle…
user3529469
2
votes
1 answer

ImageJ round method not working properly?

I've been testing this for about an hour and I don't understand what's going on. In imageJ, if I say: i = 3.5; print(round(i)); I get 4. However, If I say: …
Ogen
  • 6,499
  • 7
  • 58
  • 124
2
votes
2 answers

Difficulty counting cells due to clustering and pixel value cut off

EDIT: I have continued working on my problem among other things and have made significant process. Using one Dr. Ashby's macro provided on ImageJwiki, and using some of my own makeshift code I can now do batch processing of images taken of Hoescht,…
user3707646
  • 21
  • 3
2
votes
1 answer

Image J 16 bit Signed Buffered Image

So my question is how to get 16 bit bufferedImage from ij.ImagePlus...? If am trying to get using ShortProcessor it change my signed image to unsigned so i am not getting original image...Thanks in advance can any one provide solution. How ImageJ…
Kamlesh
  • 517
  • 3
  • 10
  • 28
2
votes
1 answer

Java for ImageJ. How to convert an image from RGB to 8 bit using code?

I am currently working on Connected Component Labelling. This is a process which takes an image and tells you how many separate objects are in the Image. My problem is that at the very start I need to be able to take any image (specifically RGB…
Liam Barrett
  • 45
  • 1
  • 7
2
votes
1 answer

Trouble integrating ImageJ into Android App

I am creating an Android app that can filter photos. To perform the image processing necessary for these filters, I use ImageJ's API. The user selects the filters to apply to a photo collection in a dialog box. Upon pressing "OK," however, the app…
user3507655
  • 23
  • 3
2
votes
1 answer

Renaming ROIs in ImageJ based on their x coordinate value in order to create a sequence

After I few hours of intensive search, I need to ask you. So, I few days ago I was provided with macro that effectively creates ROIs based on radius and function (Maximum). Link My starting point is the following image:…
JerryTheForester
  • 456
  • 1
  • 9
  • 26
2
votes
1 answer

ImageJ library is failing to open tiff images

I have written below code to open one tiff image. Actually I am trying to use imageJ (ImagePlus) library in one of out java application. But it is giving error message. "ImageJ cannot open TIFF files compressed in this fashion (4)" Any help would be…
user3409976
  • 31
  • 1
  • 4
2
votes
2 answers

running fiji jython script from command line

I am using Fiji for medical imaging purpose.I had written a jython script and would like to run the same from command prompt in windows 7.I tried out different ways for running the script but could not do so.Somebody please help in achieving the…
user3277971
  • 21
  • 3
1 2 3
…
58 59