Plugin in µManager

Hi everybody!

At the moment I’m trying to realize a plugin for µManager which shows an overview grid of all xy positions (including images) for a multi-dimensional acquisition. Before doing an actual time lapse measurement I’d like to have a quick overview scan of the sample divided in all my pre-selected xy positions. By clicking on a specific position, the stage should automatically move towards there and display a live image.

As there’s still a lot of development potential regarding my programming skills, my question now is where do I have to write such an application. I already tried to get familiar with the different µManager features (script panel, pycro-manager, …) but I’m not sure which feature is suitable to which issue. Do you have any tips to begin with?

My plan so far is to implement my application in the script panel and then insert it as a java plugin (*.jar file) into µManager. Are there any similar examples working with the script panel?

I’d be very pleased to receive suggestions from you :smiley:

Thank you!

You might want to take a look at explore acquisitions in Micro-Magellan (a µManager plugin), as it sounds like it might be usable for your purpose

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Thank you very much, @henrypinkard :grinning:
Micro-Magellan is indeed compatible to my problem, but it might be a little bit too advanced for it. My application is intended to enable uncomplicated timelapse measurements rather than high-resolution microscopy. Mostly it’s just some cells on a slide which I’d like to observe (e.g. for gene expression).
Btw I’m starting to think that pycro-manager provides the functions I need.

It can definitely do that (I have used it a lot for that myself). The documentation is a bit out of date, but let me know if you any questions about how to use.

Pycro-manager and µMagellan are built on top of many of the same components (File format, acquisition engine, image viewer), so it is also definitely possible to use Magellan as a GUI to set things up and Pycro-manager for anything fancier.

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Thanks for your help! Then I’ll definitely give it another shot and keep you tuned if any problems should occur :stuck_out_tongue_winking_eye:

Hi apoptosis,

I’ve written something like this as part of a wider plugin that we’re hoping to put out there at some point when it’s fully functional! I’ve gone down the road of making a plugin UI in NetBeans. Let me know if you’d like to talk about any of the issues we’ve had


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Hi Sunil,

I’m sorry for answering so late. Thank you very much for your response!
Currently I’m getting along quite well with Micro-Magellan as a a stand-alone. So actually there are no issues yet. However, maybe I’m going to have to implement some optimizations at some point later.
Btw I would be really interested in trying out your plugin when it is put out :smiley: