T-SPIM (dual axis illumination) acquisition options

Hi all,

We have build a T-SPIM but not sure if there is any way to operate with the FIJI plugin other than to have illumination from both directions simultaneously. Even if i could run a device that could shutter the laser to each side consecutively I don’t know how i could configure an acquisition in the SPIM plugin to image the channels on each side interleaved i.e. Z plane 1, left axis, channel 1, channel 2, Z plane 1, right axis, channel 1, channel 2, Z plane 2, left axis, channel 1, channel 2 etc etc or indeed how to do the z stack of one axis first then the second but this would not be the preferred approach. Is anyone doing this in Micro-Manager?

Thanks for any advice,


Hi Matt,

I think it’s possible in Micromanager. I would do it by adding two optical chopper wheels to your OpenSPIM and controlling them with a microcontroller such as Arduino but I never tested this. You could configure it by creating many channels in the multidimensional acquisition tool. Thereby you could image any z-step twice (channel1: 488 left-illumination; channel2: 488 right-illumination) or four times in case of two laser lines (channel1: 488 left-illumination; channel2: 488 right-illumination; channel3: 561 left-illumination; channel4: 561 right-illumination). How do you image right now with two laser lines?




Hi Johannes,

In our case both axes illuminate simultaneously and we just have one channel per wavelength. Now that you put it like that it does seem quite straightforward to create channels to switch illumination on each side. I was considering using some epi shutters we have spare to block the light alternately but I can’t yet control them in Micro-Manager as they’re made by Nikon and there is no device adapter. Investigating if an Arduino could be used in combination with TTL to signal open or closed. Whether a shutter is a good way to do it I’m not sure. I’ve seen flip mirrors can be used but thought they would be slower than shutters.



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