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hardware:computer [2018/10/16 23:32] Jon Daniels [Specific suggestions] |
hardware:computer [2021/09/10 21:21] Jon Daniels [Acquisition] added link to Arxiv paper |
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. | 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. | 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. 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. |
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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. | 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. |
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| Light sheet can generate lots of data very quickly, and it is important to have a plan to deal with the deluge. This often involves support from the institution's IT department. A helpful discussion of the challenges and options is the article [[https://arxiv.org/abs/2108.07631v1|Biologists need modern data infrastructure on campus]]. |
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