imagej | Open scientific N-dimensional image processing | Machine Learning library

I have a little command line utility rjp2tif that extracts radiometric data from a jpeg file into a tiff file. I was hoping to be able to pipe the filepath to ImageJ on the command line and have ImageJ open the tiff file. To this end, rjp2tif writes the filepath of the tiff file to standard output. I tried the following in bash:

$ rjp2tif /path/to/rjpeg | open -a imagej

and

$ rjp2tif /path/to/rjpeg | open -a imagej -f

The first opens ImageJ but doesn't open the file. The second opens ImageJ with a text window with the filepath in it.

This is on macOS Monterey, but I don't think that matters. Anyone tried to do this and been successful? TIA.

I have an array with dimension (5000, 5000, 12) representing X, Y and color. It is already dtype=uint16.

I would like to create a tiff stack from this array so I can load it in ImageJ. My approach so far:

I have below code. print(image.GetDimension()) works and prints the output (512, 512, 17). But sitk.Show(image) doesn't work.

My Code

this is really easy question for someone to answer, but I can't seem to resolve it. I downloaded the source code (.java) for the Microscope_Scale plugin (https://imagej.nih.gov/ij/plugins/microscope-scale.html). I edited the file by adding the calibrations for several microscope objectives. I can't seem to figure out how to compile (?) the .txt file into a plugin that ImageJ (also tried FIJI) can run. This is such a fundamental concept, I really can't understand why it doesn't work.

Question is how to convert a previously edited .java file (that is now a .txt file) into a plugin?

The unedited .class file works perfectly well.

Thanks very much, I really appreciate your help!

-jh

Below is the code for the edited plugin:

I have a microscopy image and need to calculate the area shown in red. The idea is to build a function that returns the area inside the red line on the right photo (float value, X mm²).

Since I have almost no experience in image processing, I don't know how to approach this (maybe silly) problem and so I'm looking for help. Other image examples are pretty similar with just 1 aglomerated "interest area" close to the center.

I'm comfortable coding in python and have used the software ImageJ for some time.

Any python package, software, bibliography, etc. should help.

Thanks!

EDIT: The example in red I made manually just to make people understand what I want. Detecting the "interest area" must be done inside the code.

I am new to ImageJ macros and I want to use a macro in Fiji. The code for the macro is from this source.

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 the second stack. Then second image of the first stack is subtracted from the second image of the second stack and so on.

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:

I'm using OpenCV version 4.1.1 in Python and cannot get a legitimate reading for a 32-bit image, even when I use cv.IMREAD_ANYDEPTH. Without cv.IMREAD_ANYDEPTH, it returns as None type; with it, I get a matrix of zeros. The issue persists after reinstalling OpenCV. os.path.isfile returns True. The error was replicated on another computer. The images open in ImageJ, so I wouldn't think they're corrupted. I would rather use Skimage since it reads the images just fine, but I have to use OpenCV for what I'm working on. Any advice is appreciated.