To everyone interested in software control of microscopes

Cross posting from Image.sc (https://forum.image.sc/t/to-everyone-interested-in-software-control-of-microscopes/37280)

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 (https://arxiv.org/abs/2005.00082 ), and started a temporary github repository (https://github.com/nicost/uScopeControl ) 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 Image.sc. Using a github account, you can also respond to https://github.com/nicost/uScopeControl/issues/1 to make it easier to update you of future developments.

7 Likes

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.
2 Likes

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 http://www.confocal.nl/). 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!