Choosing an OpenSPIM Computer

Greetings all,

To preface, I am pretty new to microscopy and optics. I am currently working on an OpenSPIM setup and am curious what the key considerations are for selecting a computer to run this kind of setup (minimum processor specs, storage recommendations, cable connections, operating system, etc.).

I would greatly appreciate any guidance and wisdom you can share in this area.

Thank you in advance for your help.

Best,
Joseph

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Hi Joseph

I am not knowledgeable enough about acquisition to make any recommendations. Though I assume transfer and storage speed will be important. Also some acquisition software only works on specific operating systems. Hopefully someone knowledgeable about acquisition will respond.

If you are running post processing software you will want to understand if the software runs mostly on the GPU or CPU or both. Personally I’ve found a fairly new i7 based processor and a new NVIDIA (RTX) card are impressive and “somewhat” cost efficient (you can probably get a good gaming machine with both for apr. $2000 USD). Of course “cost efficient” is relative.

If I need more firepower than a gaming machine can provide I use AWS virtual machines. Though there is a cost to this, and it takes time to transfer the data.

I concede my answer is a bit vague and fuzzy… Hopefully others respond. I’m interested myself in hearing people’s strategies for putting together a good Microscopy setup.

Brian

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Hi there!

Minimum requirements is an entry level desktop. Acquisition is fast and saved for each plane, last I remember, so the acquisition machine needs very little processing power as long as it has a good usb3 for the camera(s).
But it will really all depend on processing if you want to work on SPIM data on that machine, and also storage if you’re planning many many experiments.

I’d suggest you answer some of the questions below so that me and others can help guide you better.

How large are the samples you want to acquire? How often will you be imaging? Where do you wish to store the acquired data?

Depending on the answers, it could be that a good high end desktop PC with some extra storage is enough, or perhaps you need a beast of a machine linked to a NAS via 10Gb ethernet.

Looking forward to hearing from you!

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