Exsiting PyImageJ only Support ImageJ2

[xp1632]

https://nbviewer.org/github/guiwitz/neubias_academy_biapy/blob/master/14-PyImageJ.ipynb

[xp1632]

ImageJ based on python interpreter as a base line for evaluation

https://imagej.net/scripting/pyimagej https://www.nature.com/articles/s41592-022-01655-4

[xp1632]

PyImageJ enables two-way communication between ImageJ and Python by initializing Java as a subprocess of Python, such that any Java-based functionality can be used from Python programs, and new Python-based routines can be written to augment Java programs.

[xp1632]

PyImageJ paper (https://www.nature.com/articles/s41592-022-01655-4.pdf):

- Why?

- Accessibility of Python libraries for researchers at various programming proficientcy level
- ImageJ : a Java-based open-source software package and platform widely used for scientific image analysis.
    - allow researchers to perform image-processing and analysis tasks
    - operations can be combined to construct complex workflows in the form of macros and scripts
- Communities across both languages require a bridge enabling seamless feature integration without
    duplicated effort

----

- To address this need:
- PyImageJ: Python-based package built on ImageJ2 that provides fundamental interoperability between Python and ImageJ

---

- Features:

- Enables two way communication between ImageJ and Python by initializing Java as a sub-process of Python.
- ImageJ2 consists of two key layer 
- SciJava(infrastructure https://scijava.org/, https://github.com/scijava/scyjava ), 
- ImgLib2(image data model)
    - Accordingingly, PyImageJ is built on two fundamentalPython packages
    - scyjava( https://github.com/scijava/scyjava) 
    - imglyb ((https://github.com/imglib/imglyb))
    - as Python-based intergration layer for Java-based SciJava and ImageLib2 respectively

- PyImageJ offers access to **ImageJ2 API**
- PyImageJ supports **headless mode** with GUI that enables workflows on systems without monitor(such as a remote server)
---

- Technical details:

**For scyjave Layer**:
- It utilizes two parts:
    1. To retrieve ImageJ2 java libraries:
        - **jgo**: Launch Java code from the CLI, installation-free (https://github.com/scijava/jgo)
    2. To create a special Python-intergrated Java environment to include the libraries:
        - **jPype**: a Python module that let python call JAVA via jar within Python by intergrating JVM into pythonruntime         
        - (https://blog.csdn.net/u013250861/article/details/120383456)
        - (https://jpype.readthedocs.io/en/latest/)
- Functionalities:
    - download and cacheJAVA libraries from remote online repositories
    - start java environment as a sub process in python
    - warp java classes as dynamically generated Python classes with same functions
    - convert common data structures between Java and python
--- 
**For imglyb Layer**:

- Using shared memory to store image data and exchange image between Python and ImageJ
- ImageJ images can be converted into Python type that is NumPy or xarray

[xp1632]

Example notebook of using PyImageJ:

https://nbviewer.org/github/guiwitz/neubias_academy_biapy/blob/master/14-PyImageJ.ipynb

[xp1632]

https://py.imagej.net/en/latest/Initialization.html#how-to-initialize-pyimagej https://github.com/imagej/pyimagej