To everyone interested in software control of microscopes

Cross posting from (

Creative new microscopes most often need dedicated software for operation. Creating these software solutions is laborious, and many of us recognize that we can all help each other, facilitate re-use and avoid duplication. Raghav Chhetri, Stephan Preibisch and I organized a workshop about this topic that took place in February 2020 at the HHMI Janelia Research Campus. Workshop participants showed a great desire to build a community (much larger and more inclusive than the Workshop participants) to work together towards modular tool-sets for microscope control that can be used from multiple computer programming languages and platforms.

We summarized some of the ideas that arose during the workshop in a white paper available on arXiv ( ), and started a temporary github repository ( ) to provide some means for communication and collaboration. We are partnering with Kevin Eliceiri (LOCI, Univ. Wisconsin, Madison) towards creating a website that can act as an umbrella hub for all open source projects concerned with software control of microscopes, including the Micro-Manager project.

Looking forward to seeing your input/suggestions/encouragement/criticism here or on Using a github account, you can also respond to to make it easier to update you of future developments.


Great to see there is so much interest in bringing data acquisition to the next level! I really hope someone manages to rally the people behind common projects and the efforts get synchronized.

Can I ask you about the history behind Micro Manager? How did it start, how was it funded, how many people involved, etc? I think there is a lot to learn from that experience, not only from the software point of view.

1 Like

Great question, and maybe one day I’ll write down the full story. Big lessons learned:

  • Initial development needed to be fast in order to have something useful so that we could apply for real funding
  • Development always took place close to actual users of the software, and feedback from the lab to the developers was always critical.
  • MM had 7 years of NIH funding, however, it became quite clear that it is untenable to fund a project like this solely using government grants (at least in the US). Big problem is retention of good developers if the threat of not being funded is always there.
  • We tried a couple of times to operate MM from a company, and this never worked well. It may be possible to do so, but that is not an easy route either.

Great summary! Thanks!

Indeed, moving an open-source program to a company is tough. You rely, normally, on services paid by a community used not to pay.

Another route would be if a company picks up the development. I mean, a hardware company which currently uses Micro Manager (I’m thinking someone like But, convincing a CEO of doing open-source is tough, very tough.

It also has the danger that competitors of said company will be less interested in supporting their hardware in Micro-Manager. Uniting microscope hardware vendors while competing with them is pretty difficult!