Microscope for automated acquisition (software and hardware), some advice?

Hello everybody, and thank you all for creating such useful communities on image analysis world.
I am a cell biologist and I’m approaching to image acquisition and analysis automation on fixed and living samples.

In my former lab, to automate the selection and the acquisition of specific field or phenotype, I used successfully the Nikon NIS software with JOBS module with a Nikon Ti eclipse microscope.
Now, I have to put on a brand new system in a new lab and I’m wondering if there are other comparable and maybe freeware options.
What I’m interesting in is a microscope with a software able to create acquisition pipelines (preferably with user friendly interface).
To better explain what I’m looking for, with Nikon JOBS I could create a pipeline like this:

Selection of 20x objective
Selection of acquisition area size
Autofocus on dapi
Acquisition and analysis to look for mitotic cells (based on dapi signal)
If mitotic cells are in the field:
- selection of 63x objective
- acquisition with z-step on multiple lambda channels
If mitotic cells are not in the field:
- move to next field

Do you have experience and/or advice on alternative Microscope/Software combination?
I think that uManager could be a good freeware option but I’m concerned about compatibility with the microscope and on the time I will consume learning code for pipelines creation.

Sorry for the probably naive issue!
Thanks a lot!

A powerful/flexible freeware solution that doesn’t take time to learn is definitely a tall order! :sweat_smile:

Curious to hear if anyone else has anything in mind, but I’m not aware of anything else out there (in the free software world) that is as user friendly (with as broad device and multi-language support) as micromanager. Provided you’ve already got the mitotic cell detection code already written, it would be relatively straightforward to set up such a pipeline (once you get the hang of micromanager). If you’re currently using prebuilt JOBS routines for analysis, and need help actually recreating some of those algorithms in python or java, etc… I’d recommend going to forum.image.sc for help on that bit.

Thank you talley,
I’m not afraid of learning new software or coding (but definitely it’d be a problem for other member of the lab :D).
btw, besides freeware solutions, what about company platforms (alternative to Nikon NIS) that could be a good compromise?
I have tried Zeiss Zen and Leica LASX but, at least the version I’ve tried, they provide only a tilescan function. Before asking to the various company specialist I would like to know your experience.

Yeah, if you’re comfortable with the code, i think you should be able to make something usable by non-coding members of your lab with a little work. Probably nothing with the polish that the mega-companies can pull off with their R&D, but something that will get you the data you need :slight_smile: . It really all depends on the environment you like to code in. If you like python, I’ll mention that both pycro-manager and pymmcore would let you take advantage of all of the device support offered by micromanager, while being able to code the core pipeline sequences in python.

pinging @nico.stuurman here, he may have specific thoughts on JOBS-style pipeline-building GUIs or other approaches using micromanager.

As for commercial solutions, I have no experience to comment on Zen or LASX, but I would have naively assumed that you’d need to be on that specific company’s hardware to take advantage of their software packages… maybe I’m wrong? There is metamorph, which supports a broad range of devices, and offers some degree of customizability with their “journals”, but that’s far from freeware.

Anyway, personally, I’d go to micromanager… but maybe others can chime in here with additional ideas.

Very biased opinion here (as a co-creator of Micro-Manager): this is very doable with Micro-Manager. In fact, I wrote a plugin (called “Intelligent Acquisition” for more or less this scenario many years ago. Regretfully, it has not been exercised very much, so I have no idea if, and how well it will work for you. The plugin has acquisition settings (MDA settings) for both the “exploration” and “imaging” phase, which you could use to define the objective and channels. The user can define an ImageJ macro for analysis (i.e. locate the mitotic cells). I forgot what it should return, but happy to investigate if you are interested.

More generally, you have the following options with Micro-Manager:

  • write a Beanshell script
  • write a Micro-Manager plugin in Java with full blown UI (for instance based on the “Intelligent Acquisition plugin”
  • Write Python code only using the MM device abstraction layer through pymmcore
  • Interact with a running MM GUI using pycro-manager, and your own Python code.

The nice thing is that your code will work with more or less any hardware that works with MM (and the Nikon TI happens to work very well, not the least since our lab has a couple), so that you can share your code with others (and move it to other hardware). Users I talk to seem to like the UI (with the exception of the multi-window concept inherited from ImageJ), there are various ways of executing scripts from buttons, plugins have their own UI, and it should surely be possible to build simple and nice UIs when using something like the pycro-manager bridge.

Hope this helps!

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