Hello from Wei and some questions about ImageJ


#1

Dear Curtis,

This is Wei from the ImJoy team, I am currently working in Emma Lundberg’s group, SciLifeLab | KTH Stockholm, as a postdoc. As you know that we recently announced the beta release of ImJoy and also joined the image.sc forum as a community partner. Thanks a lot for offering such a great platform for the community. And what you did for LOCI, FIJI, ImageJ2 and the forum is just amazing, I also read your recent effort to bring ImageJ to python and allow it to run in Jupyter notebook, that would be greatly accelerate the development.

I think the motivation behind making ImJoy is somewhat close to your work with pyimagej, we would like to bring the recent advancements of the web (rich industrial level UI, mobile support, data visualization, browser based computing with WebAssembly and WebGPU etc.) to the bioimaging, we natively support python and use conda to manage plugin dependencies and virtual environments.

Different from jupyter notebook which provide an interactive coding interface with docs for programmers/beginners to learn and experiment idea, ImJoy focus more on the deployment and distribution part. We try to help develpers to transform their code/jupyter notebooks into ImJoy plugin with interactive UI and push to github, and get a plugin url, then the user can access the plugin immediately. Thus, I think ImJoy and yours are complementary work towards the same goal.

You may already see this post ( Need help to bring web interface to Fiji/ImageJ with ImJoy ), where I think it would be meaningful and feasible to make ImJoy and fiji work together, especially for running imagej on different host, or a imagej server, but still keep the real-time interactivity with a web GUI in ImJoy.

I would like very much to hear what do you think about these.

One thing I would like to ask in particular is about Fiji update. As mentioned in my post, ImJoy uses conda to manage virtual env and solve dependency automatically, this essentially get rid of the command line interface which is a big barrier for a regular user to use. Ideally we would like to have the same system as pip/conda for imagej plugins. I saw you recently added the imagej.init() method which can pull imagej and fiji plugins from http://maven.imagej.net/. And I am wondering will this imagej.init be the pip for imagej? Would it be possible to use conda itself to manage Fiji update? Since it’s a language-agnostic platform?

Looking forward to hear from you.

Best,
Wei


#2

Thanks for reaching out, @oeway!

Would you be willing to have this conversation in public? I think others than only us would be interested in hearing about it, and maybe adding thoughts and ideas to the discussion. If you are OK with it, we can mark this thread as public. What do you think?


#3

Hi @ctrueden, Thanks for your response.
That would be fine with me, it would be even better to hear more thoughts and ideas.


made this topic public #4