http://confocal-microscopy-list.275.s1.nabble.com/Lightsheet-imaging-analysis-Workstation-Specs-tp7590391p7590422.html
works great. Buy a high wattage power supply and 'appropriate' heat sink(s).
p.s two lab users: nice AMD CPU PC desktops for $600 each. Both users
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy> Post images on
http://www.imgur.com and include the link in your posting.
> *****
>
> Hi, quick follow up: Has anyone built a workstation for microscopy analysis
> using AMD hardware? Their price/thread is way better than Intel's (both
> customer- and server-grade CPUs) and the only downside seems to be that
> they run a little hotter. Is there limited support in the various software
> packages? Or is it just a matter of legacy infrastructure? Thanks, Francesco
>
>
> On Thu, Jan 16, 2020 at 9:50 AM Olaf Selchow <
[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>>
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>> Post images on
http://www.imgur.com and include the link in your posting.
>> *****
>>
>> Hello everybody,
>>
>> Happy to share a bit of my experience on this:
>>
>> - Re the multiview deconvolution by Preibisch et al - with GPU
>> enhancement: It works but my experience also is that it could be a bit
>> easier to get the installation done. CUDA support is not depreciated
>> though, to my knowledge.
>>
>> - Typical data set size in what I have done in Light Sheet Microscopy in
>> recent years is 500 GB to 10 TB both, in live imaging (long timer series
>> with multiple views) and imaging of optically cleared specimen.
>>
>> - Re the specs of a suitable machine, the following things I would
>> consider (depends on how many people will use it, how many microscopes
>> connected, installation location of the processing computer)
>>
>> 1. With Imaris and / or arivis vision4D to be run on the same machine as
>> Fiji and maybe the manufacturers software (Zeiss ZEN, Leica LAS X, 3i
>> Slidebook, etc) you want to run Windows, I guess.
>>
>> 2. If you want to be able to use it with multiple users in parallel you
>> want/need Windows Server.
>>
>> 3. I would make sure that the microscopes are connected with direct 10
>> Gbit. Over an institutional network, even if 10 Gbit, you might be limited
>> in bandwidth and so you can migrate the data only after acquisition from
>> the acquisition PC to the Storage. This costs time, blocks the acquisition
>> PC and essentially duplicates the required storage capacity you need. I
>> always try to bring the microscopes with the processing & analysis
>> computers in a 10 Gbit subnet that I can manage with a dedicated
>> router/firewall/switch. That prevents interferences with all the other
>> traffic in your institute.
>>
>> 4. I would not use a NAS. Processing data by loading data into memory /
>> software via network (and saving the results / temp data via the same line)
>> can take ages. 10 Gbit is far too slow in my view. I’d use a prcessing
>> machine with a strong RAID controler and a large RAID array directly
>> attached to the processing unit. And I would save the data from the
>> microscopes directly to this volume.
>>
>> 5. if you need super large RAM depends on how many people are supposed to
>> work in parallel on this machine, if you want to use VMs, and what software
>> you use (arivis needs much less RAM than others. Fiji benefits a lot from
>> super large RAM, etc.). But if you choose the right motherboard and OS, you
>> can always and easily upgrade RAM later.
>>
>> 6. CPU: generally, large multicore CPUs speed up things. But some
>> software, even today, doesn’t make much use of parallelization. If you buy
>> a very expensive dual-44-core CPU for thousands of $/€ you might end up
>> with the software not using it. Actual check out the workflows. Some
>> vendors might say „yes, our software uses all cores available“ , but in the
>> end the processing function you are using most might still be running on a
>> single or only 2 cores.
>>
>> 7. Monitor: I have worked with a number of 32 inch UHD 4K (3840 x
>> 2160, 16:9) and 32 inch WQHD 3.6K (2560 x 1440, 16:9) monitors and never
>> had a real problem. But thi smight depend on the GPU you use.
>>
>> 8. GPUs:
>> - if you want to use 3D renderings over remote access (e.g., RDP)
>> sessions, I strongly recommend professional GPUs. I know, they are
>> expensive. But the drivers on the Geforce or other gaming-grade GPUs can
>> give you a hard time when working remotely. I have good experience with
>> NVIDIA Quadro RTX boards (they are, in some GPU CUDA processing tasks, 2x
>> faster than the previous P-seroes that is otherwise also perfectly fine.)
>> For 3D viewing / rendering / analyzing data, make sure the VRAM on the GPU
>> is 11 GB / 16 GB or larger.
>> - for some software and for VMs, it makes sense to think of the option of
>> multiple GPUs. Maybe you just want to make sure you can fit a 2nd or 3rd
>> later on. In SVI Huygens you can, for example, assign instances of DCV to
>> certain GPUs - so multiple GPUs can speed up your work. You need to buy the
>> respective licenses from SVI though.
>>
>> 9. Storage volume: make sure you have multiple (2 or more) fast volumes
>> (RAIDs of HDD or SSDs) to have space for the software where it can save
>> temp data - on an independent volume. Multiple simultaneous read/write
>> processes can slow down even fast RAID configs. Also keep in mind that SSDs
>> are more convenient and faster, but still more expensive and still have a
>> higher failure rate. Mak sure you consider hard drives 7 ssds as
>> consumables. In a RAID of 15 HDDs, it is perfectly normal that you have 1
>> HDD/year in average that fails and needs replacement. SSDs maybe even more
>> often.
>>
>> The Lenovo Think Station P920 is certainly a great hardware. You’ll still
>> have to invest a bit of time and money to get it ready to work for your
>> applications. Networking i, etc.
>>
>> I would also point out that there is commercial options that provide you a
>> turnkey solution with support that can scale / grow with your needs.
>> I have worked with ACQUIFER HIVEs a lot. Check with them or a similar
>> provider if your budget allows a high end solution for 60k (+) $/€ and if
>> you are looking for a solution provider that saves you from configuring
>> network adapters yourself …
>> Note: I used to have consultancy projects with ACQUIFER and might have
>> more in the future. So I am a bit biased, but mostly because I think they
>> have great hardware and services and I worked wit them to position their
>> products and improve them. I do not (!) have a direct financial interest in
>> them selling a platform unit to you!
>>
>> I hope this helps.
>> best regards,
>> Olaf
>>
>> ———
>> Dr. Olaf Selchow
>> --
>> Microscopy & BioImaging Consulting
>> Image Processing & Large Data Handling
>> --
>>
[hidden email]
>>
>