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hardware:computer [2015/08/06 20:02] Jon Daniels [Data Analysis] |
hardware:computer [2016/05/21 17:39] Jon Daniels [Acquisition] |
===== Acquisition ===== | ===== Acquisition ===== |
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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-view) plus whatever other peripherals you need. |
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| 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. |
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| 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 fps; both 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. At present only one camera works at a time, though in the future there are schemes where both cameras could be used simultaneously and thus double the data rate. |
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| 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). 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. |
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===== Data Analysis ===== | ===== Data Analysis ===== |
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Having lots of RAM also helps the analysis so that 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 developments in computation/data analysis are forthcoming so it's hard to say exactly what will be the best hardware in the long run. | 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. |
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===== Specific suggestions ===== | ===== Specific suggestions ===== |