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hardware:computer [2015/07/27 23:27]
Jon Daniels created
hardware:computer [2021/02/13 21:28] (current)
Jon Daniels [Acquisition]
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 ====== Computer  Requirements ====== ====== Computer  Requirements ======
-==== Acquisition ====+===== Acquisition =====
-The main constraints is sufficiently fast disk write speed to handle the camera data.  Worst-case is 100 fps with full frame, or 800 MB/s (only one camera is used at a time).  Usually this is solved by using SSDs in RAID0 configuration (e.g. 4 SSDs in RAID0 can achieve <1 GB/s).  If you aren't using full frame or fastest imaging speed this requirement is relaxed.+Make sure to get a computer with sufficient PCI/PCIe slots for the camera framegrabber cards (usually 2 cameras/cards for dual-viewplus whatever other peripherals you need.
-==== Data Analysis ====+Otherwise the main requirement having sufficiently fast disk write speed to handle the camera data.  Depending on the use case, solid state drives (SSDs) and/or RAID0 with SSDs may or may not be required.  Individual users should consider their requirements.
-Ideally get a computer with GPU/graphics card because some of the data analysis software can take advantage of it to speed the computation Howeverthis is a nascent area and depends on software supportmany developments in data analysis are forthcoming so it'hard to say exactly what will be the best in the long run.  Having lots of RAM also helps the analysis so that the entire dataset can be held in active memory.+The sCMOS cameras used with diSPIM can generate 800 MB/sec (100 fps at 4 MP, 16 bits per pixel).  However the maximum possible frame rate of the camera is not achieved for diSPIM.((Light sheet illumination only occurs during global exposure, and camera-limited frame rates occur without any global exposure time.))  Typical maximum acquisition speeds are 1024x1024 at 50fps or 512x512 at 200 fpsboth these situations both generate 100MB/sec.  The average data rate, and hence hard drive speed requirement, is usually even less because most commonly acquisition occurs in bursts (i.e. there is time between successive time points) and a RAM buffer initially holds images so the hard drive needs to keep up with the average data rate.  Usually only one camera works at a time, though there are schemes where both cameras could be used simultaneously and thus double the data rate or else multiple cameras could be used for simultaneous multi-channel recording.
-==== Specific suggestions ====+100 MB/sec is typical for a magnetic hard drive.  300 MB/sec is typical for a single SSD.  If the data rate is too high for a single SSD, use SSDs in RAID0 configuration (e.g. 4 SSDs in RAID0 can achieve >1 GB/s).  Lately M.2 drives with PCIe interface with comparable speeds to a RAID0 with SSDs have become available and might be a good option.  To benchmark your PC's hard drive write speed you can use [[http://crystalmark.info/?lang=en | Crystal Disk Mark]].  I'm pretty sure the relevant score to diSPIM acquisition is the "Seq" "Write" score (Sequential (Block Size=1MiB) Read/Write with single Thread), at least for Micro-manager software with typical acquisition settings.
-ASI has successfully used Dell Precision T3600 with 8-core Xeon CPU, 4x SSDs in RAID0, 64 GB RAM, Nvidia Quadro K4200, and enough PCIe slots (2 camera framegrabber cards, graphics card, and RAID controller).+ 
 +===== Data Analysis ===== 
 +Having lots of RAM speeds the analysis; ideally the entire dataset can be held in active memory.  Ideally get a computer with CUDA-capable graphics card because some of the data analysis software can take advantage of it to speed the computation (OpenCL is a competing framework for GPU computation).  This is a nascent area and depends on software support; many software developments data analysis are forthcoming so it's hard to say exactly what will be the best hardware in the long run. 
 +===== Specific suggestions ===== 
 +In 2018 ASI has successfully used use a Dell Precision 7920 tower with 6-core Xeon CPU, one SSD for the OS/applications and a RAID0 drive with 4 SSDs for data, 64 GB RAM, and Nvidia P2000.  This has spare PCIe slots even with 2 camera framegrabber cards, the graphics card, and RAID controller. 
 +Previously (~2016?ASI has successfully used Dell Precision T3600 with 8-core Xeon CPU, 4x SSDs in RAID0, 64 GB RAM, Nvidia Quadro K4200, and enough PCIe slots (2 camera framegrabber cards, graphics card, and RAID controller).