[Q&A] for master thesis

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I'll list the questions and answers that the audience might ask here

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IPython Kernel, Python Kernel, and pyimagej environment:

Q1: You are saying, now we can run ImageJ with Python kernel, why there's pyimagej beside it?

• To avoid confusion, I've removed all IPython Kernel and used Python Kernel instead.

• First let's see what's a jupyter kernel, a kernel is a programming language-specific engine that drives code execution in Jupyter notebooks.

• IPython is the project name for the default Python kernel they created intending to provide Interactive Python computing

• The pyimagej beside this Python kernel, indicates I am using the IPython kernel in a Python environment that I named as pyimagej. This environment contains the specific version of Python and other packages (like PyImageJ) that I installed when I created the environment.

• Thus, we are still using the default python kernel, just in a python environment where I installed pyimagej and its dependency

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How many ImageJ plugins do you support in Chaldene, all of them?

• headless mode limitation
• https://github.com/imagej/pyimagej/blob/main/doc/Troubleshooting.md#known-limitations

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• ImageJ2 https://imagej.net/software/imagej2/#imagej2-is-more-than-just-an-application

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How do you deal with the different Image Datatype in Java and in Python?

https://github.com/imagej/pyimagej/blob/main/doc/04-Retrieving-Data-from-Java.ipynb

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what's the relationship among PyimageJ, imglyb, scyjava, Jpype?

The relationship among PyImageJ, imglyb, scyjava, and JPype is that they work together to provide interoperability between Python and Java, particularly for image processing tasks. Here’s a brief overview of each and how they interact:

• PyImageJ: This is a Python library that provides a bridge between Python and ImageJ, which is a Java-based software package widely used for scientific image analysis. PyImageJ enables two-way communication between ImageJ and Python by initializing Java as a subprocess of Python.
• imglyb: This is a Python module that interfaces with the Java-side ImgLib2, a powerful n-dimensional data processing library in Java. It uses JPype to access NumPy arrays and expose them to ImgLib2.
• scyjava: This is a Python library that provides the foundational components such as JVM configuration and type conversions. It uses JPype to create the Python-integrated JVM that will run the ImageJ2 software stack.

• -JPype: This is a Python module that allows Python programs to fully access Java class libraries. It’s used by scyjava to initialize the Java Virtual Machine (JVM), and by imglyb to interface between Python’s NumPy and Java’s ImgLib2.

In summary, these libraries work together to allow Python code to interact with Java libraries, particularly for image processing tasks. This allows developers to leverage the powerful image processing capabilities of ImageJ and ImgLib2 directly from Python scripts.