Substage for 2-photon microscopes

Hi there OFM folk!

Hope everyone is doing well these days.

I am not sure if this would be better suited for any other topic section in the forum so please feel free to move it or to point me in the right direction…

As the thread title says, we (currently Filip Janiak and me, at the University of Sussex) are re-visiting the substage part of 2 photon microscopes, in hopes to make them more efficient, customisable, affordable and of course, Open Source.

In our current design, we are using a delta stage to hold and position our sample. The stage will be connected to the substage part of the collection path and we would like to hook up the control part of the stage to software used by a lot of users in our field. Namely, ScanImage (this is not completely open, nor it would be my first choice, but we are trying to make the integration as seamless as possible for users).

We tested some things already using a motorised version of the stage connected to the “standard” drivers of the recommended motors connected to an Arduino Nano, and issuing commands over the serial port using the Arduino IDE.

Now, we would like to move on to integrating things, which leads me to the following questions:

  • What is the current stable/mature version of the Sangaboard? v0.3 or v0.4?
  • Assuming control of the board works by sending serial commands to it, what would you recommend for integration with 3rd party software? Should we get a RPi, connect it to the Sangaboard and then use ScanImage to interact with the Pi? or a simple connection between the Sangaboard to ScanImage would be the most straightforward way to do things?

Thanks! and sorry for the long post!

Welcome to the Forum. I don’t know about the needs of 2-photon microscopy in particular. The Sangaboard versions are still v0.X so not stable or mature. However they are really just a different form-factor for an Atmega microcontroller running the Arduino bootloader - so the ‘nano + motor controllers’ version is no different in function. Sangaboard v0.4 contains useful power supply elements to tidy up overall supply to the microscope and the Pi.
Connecting directly would seem to make most sense - the connection from the Pi to the Arduino will be serial anyway. If you want to use a different interface, the Pi can do a conversion - for example the Openflexure Server gives you access to move commands using web requests.

Thanks for the fast reply!

ok, sounds pretty much like what I had in mind.

The reason I asked about the Sangaboard version is that I read on a couple of other threads that v0.4 still had some bugs that had to be ironed out? Is that now resolved? (granted the messages reporting the bugs are from ~1year ago, but I did not see other messages stating that v0.4 was the preferred version nowdays)…

v0.4 did have some bugs that ended up taking a long time to find. I believe the latest iteration now works, but I don’t know whether any changes are reflected in the Kitspace listing.

None of the Sangaboards have been widely available, but all being well that will change. v0.4 being in Pi HAT form factor is particularly useful for keeping things tidy, and tidy helps reliability. Unfortunately having a custom board is likely to be more costly than using a generic Arduino because of smaller volumes.

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