Multi Channel with openspim plugin

Hi everyone,

I am fairly new to the OpenSPIM world. I am working on diabetic nephropathy and a part of my project is to measure the damage done to the kidneys in zebrafish.

I have managed to use the OpenSPIM plugin for Micromanager to take some z-stacks over time. At the time, I was only interested in seeing GFP but now I also want to measure mCherry at the same time.

Is there any way to have a multi-channel acquisition. We want to use the plugin due to its anti-drift function.

Thank you very much in advance.

Kind regards,
Gideon

Hi Gideon,

If you have an additional laser then yes that should be possible and assuming the lasers you have can be controlled by Micro-Manager. When you say image at the same time, it would be sequential acquisition unless you setup two cameras for simultaneous acquisition. We have a Vortran Versalase with 4 separate laser lines.

Thanks,

Matt

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Hi Matt,

Thank you for such a quick reply. Yes I do mean sequential acquisition. So at each z I want to take two images, one for each channel.

I am able to control the lasers through micromanager, specifically I can turn them both on. However, what happens when I do an acquisition both lasers are shining at the same time and only one image is taken.

Our laser system is made by Cairn Research and the camera is a photometrics iris 9.

When you say you have 4 separate laser lines, are you able to define which ones will be captured/used by the Spim acquisiton plugin?

Thank you very much in advance.

Kind regards,
Gideon

Hi Gideon,

Sorry for the slow reply this time, i don’t get an email when when someone posts on a topic and just happened to be on the forum to ask a question myself.

To do multi-wavelength acquisition have you configured multiple channels in your Channel group in Micro-Manager? And have you added them to the channels section of the Multi-D Acquisition window. Because we have different channels defined and one laser line associated with each channel it should be able to snap two separate images switching between the lasers. I have to admit though i know nothing about the Cairn laser. Sorry if you’ve done all this just not sure how familiar you are with Micro-Manager and how its configured.

Thanks,

Matt

Dear Matt,

Thank you very much for your reply.
I have in fact done all of those things. Also, using the multi-d acquisition tool of micromanager I am able to define multiple channels and I can see the laser switching during acquisition.

The real question is if it is possible to do with the Openspim plugin. There only the current channel will be used for acquisition and I have no way of controlling it. We want to use the plugin as it has the anti-drift function wich is essential to keep our sample in sights.

I hope this makes the question more clear.
We want to to multi-channel using the openspim plugin of micromanager.

Kind Regards,
Gideon

Ah ok, I think what i was doing was multichannel z stacks outside of the SPIM plugin just in Micro-Manager, no multiposition or rotation. I just assume it would do the channels that were setup in the MDA window of Micro-Manager.

Thanks,

Matt

There is a manage devices button in the OpenSPIM plugin which has an illumination/detection section and there is a drop down which says “Laser” and “Laser(2)” this almost looks as if it would allow you to do a two wavelength acquisition but my lasers are not shown in the drop down boxes. It might be that this is just for simultaneous acquisition of two channels with two cameras. Hmm our dreams of multi-colour acquisition might be scuppered… Strange as it seems as if it wouldn’t take much for it to be able to do it if it were combined with the micro-manager MDA channel list.

You should be able to fix that by visiting https://forum.image.sc/u/matt_pearson/preferences/emails and changing the settings to your liking.