Microsocpe automation/adaptive microscopy using Nikon microscopes

Dear community,

I would like perform adaptive feedback microscopy experiments using a Nikon wide-field system (Ti2) (@VolkerH, @aquilesC, @nico.stuurman, @Nicholas_Sofroniew). For instance change the acquisition settings or talk to another hardware (e.g. using a NI-card and TTL-signals) in response to image processing.

Our first start was using NIS-elements and JOBS. The reason is that the interface is quite user-friendly and we managed to do quite a lot of things. For very simple image processing using the GA-module we were successful. Unfortunately, we have not gone far using GA3 or external analysis software. Currently we we do not manage to import XYZ coordinates from GA3 or ImageJ into JOBS in order to move the stage and launch a different experiment. Do you have any experience for I/O using JOBS?

We are also looking into open source solutions such as micromanager/pycro-manager https://pycro-manager.readthedocs.io/en/latest/. Do you have any experience on how to perform decisions upon image processing using opensource software?

Thanks for your help


Hi Antonio,

I do have experience with computation feedback in Java (for instance: https://www.biorxiv.org/content/10.1101/2020.06.30.179648v1), but I think that you are looking for more Python-based solutions. Henry Pinkard designed Pycro-Manager for that exact purpose. I do not think he is on this forum or image.sc (edit: he is @henrypinkard on image.sc), but he will certainly respond to issues on https://github.com/micro-manager/pycro-manager

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