Stack Overflow
Stack Overflow

Questions tagged [imagej-macro]

89 questions
2
votes
0 answers

How can I feed a string that includes quotes to a system2 call in R?

I have a somewhat niche question that I'm hoping someone can answer for me or help me find a work-around to: I've written a script in R that will run an ImageJ macro for sets of images I produce as a part of my workflow. Because this is work that I…
Kelly N.
  • 51
  • 5
2
votes
0 answers

R and ImageJ sync issues

I have a script in R (written by someone else) which calls ImageJ for image analysis using shell() with '-batch' switch: shell("C:\\ImageJ\\imagej.exe -batch [args]") The analysis indeed begins, but it seems that R continues to perform the next…
Inbal H
  • 33
  • 1
  • 6
2
votes
1 answer

Crop Custom Shape in ImageJ or equivalent (TIFF video file)

I have a .tiff video file with growing fibers that look like the image below Now imagine that this fiber will constantly grow and shrink in a straight line. Now I'd like to somehow crop out the region of the video that contains just the fiber…
Amateur Math Guy
  • 199
  • 2
  • 3
  • 12
1
vote
1 answer

Condition or function to verify if a file is missing when opening files sequentially in ImageJ

I'm using an ImageJ macro that opens and processes a group of images from several samples sequentially named - e.g. sample1_image1.tif, sample1_image2.tif, sample2_image1.tif, (...). I'm using a loop to increment both sequences for the samples and…
Figs
  • 15
  • 3
1
vote
1 answer

How to work around ImageJ run("HSB stack") error/ bug?

I am working on a macro for ImageJ. The goal is to take colour scans with several seeds on them and crop around the seeds to get several equally sized images with one seed on each. This is the basic idea for the macro: prompt to select folder with…
Josephine R
  • 13
  • 3
1
vote
0 answers

Calling an ImageJ/FIJI macro from inside a jupyter notebook

I would like to use ImageJ and some of its macros and call them from inside a jupyter notebook. I am aware of PyimageJ, and I have been able to install it and load an image for display using ImageJ methods. But I am having some difficulties in…
Materia Dura
  • 21
  • 3
1
vote
0 answers

User defined input in a macro

I am trying to create a macro on Fiji (ImageJ). I cannot find how to introduce a user input. I want to sum a stack with z project. Each sum is the result of 10 stacks. But the start is not the same. It varies between 1 and 11. So it would be fine…
Alexander
  • 73
  • 7
1
vote
2 answers

How to batch process ImageJ macro within a specific folder within multiple directories

I have a nested file structure where a parent folder contains multiple folders of different types of data. I am using an ImageJ macro script to batch process all of the image files within one of those folders. I currently need to process each folder…
ashcrashbegash
  • 157
  • 11
1
vote
2 answers

ImageJ macro not waiting for command to finish running

I'm using ImageJ macro to batch process images. Specifically, I'm trying to run a plugin called Log3D on each image. For some reason, ImageJ macro won't wait for the command to finish running before running the next line in the script. Is there a…
Omer Shkedi
  • 41
  • 1
  • 4
1
vote
1 answer

Writing ImageJ Python scripts in PyCharm

I'm able to install Jython (via homebrew), configure PyCharm to use it as my interpreter, but I can't get PyCharm to import ij. /usr/local/bin/jython -Dpython.path=/tmp/python /tmp/python/test.py WARNING: An illegal reflective access operation has…
agf1997
  • 2,668
  • 4
  • 21
  • 36
1
vote
1 answer

Printing Array Items by Index Number in ImageJ (Fiji)

I'm trying to figure out how I can access an item in an array by it's index number. I've written a script which will generate an array, with some number of variables. There's an old script on the imageJ mailing list archive (shown below) which is…
J. Kovacs
  • 157
  • 1
  • 1
  • 10
1
vote
1 answer

Is it possible to set `var` as const in imagej-macro?

Can anyone show me how to secure the value of variable in imagej macro script? In general, there is a key word, such as const, to ensure the variable unchangable in most of programming language, but in imagej macro this optional keyword cannot be…
Yeeson
  • 69
  • 7
1
vote
1 answer

ImageJ Macro and Plugin Paths

I'm using ImageJ on MacOS X. Currently the ImageJ properties utility is reporting the Macros and Utilities directories as "null" IJ.getDir("plugins"): null IJ.getDir("macros"): null I can set the directories using the following command from the…
agf1997
  • 2,668
  • 4
  • 21
  • 36
1
vote
1 answer

ImageJ: NameError when using selectionType() in Python script

I am a newbie to ImageJ and was trying to recreate the following macro using Python (in ImageJ macro editor). s = selectionType(); if( s == -1 ) { exit("There was no selection."); } else if( s != 10 ) { exit("The selection wasn't a point…
alexxei
  • 40
  • 6
1
vote
1 answer

How to crop image for every element in the grid using ImageJ/FIJI

I have 12 images. I am processing with ImageJ/FIJI. Then I made grid (using Analyze -> Tools -> Grid) of size 2923779 ( i.e. Area per point __ pixels ^2) for all images uniformly. It looks like this: What I want to do is to crop the each of the…
neversaint
  • 60,904
  • 137
  • 310
  • 477
1
2 3 4 5 6