Adding interactive ROIs in lyse

[Shawn Storm]

Hi all,

I am working with single atoms with optical tweezers and I would like to incorporate a feature that would save time. Namely, to position the ROIs over the fluorescence of every atom, I typically have to manually put the coordinates and the box size in python, rerun and see if the position matches where the atoms are. This takes a few iterations and with many atoms and due to daily drifts this accrues a lot of time. I am wondering if it is possible to, in lyse, have interactive ROIs that I can change on the fly so I can just run the experiment, see the fluorescence and change ROIs in lyse. I got this idea from a group that is not using labscript and has their own data analysis program. Attached you can see a video that of what I would like to do in their program. I was thinking of pyqt to do this so I would really appreciate any guidance on this!

[Ian B. Spielman]

Dear Shawn,

This is possible, but not easy, to directly implement in the current Lyse schema. If I were to do this right now, I would use Lyse to communicate with an external helper process (see this https://github.com/rpanderson/analysislib-mloop for an example of how this might be done). The reason for this is that the helper GUI really does not want to use the automatic figure-window managing that Lyse currently implements for figures.

I would say that many of the recent changes to Lyse were implemented with the motivation to increase the flexibility going forward. For example, in-house I wrote a class-based revision of Lyse workers in which each worker process can (if it wants to) create and control its own PyQt window. This process still receives messages like Lyse workers currently do, but they are instead dispatched to class methods, and the state of the class persists between shots.

It would take a bit of time to get this going again with the recently lyse update, but it could be done.

— Ian

NIST Fellow
Group Leader, NIST laser cooling and trapping group
Fellow, Joint Quantum Institute

National Institute of Standards and Technology and the University of Maryland

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> On Dec 17, 2025, at 04:39, Shawn Storm <shawn...@unifi.it> wrote:
>
> Hi all,
>
> I am working with single atoms with optical tweezers and I would like to incorporate a feature that would save time. Namely, to position the ROIs over the fluorescence of every atom, I typically have to manually put the coordinates and the box size in python, rerun and see if the position matches where the atoms are. This takes a few iterations and with many atoms and due to daily drifts this accrues a lot of time. I am wondering if it is possible to, in lyse, have interactive ROIs that I can change on the fly so I can just run the experiment, see the fluorescence and change ROIs in lyse. I got this idea from a group that is not using labscript and has their own data analysis program. Attached you can see a video that of what I would like to do in their program. I was thinking of pyqt to do this so I would really appreciate any guidance on this!
>

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