Acquisition Computer

Modern scientific cameras are capable of capturing images at very high frame rates. For example, the Orca-Lightning from Hamamatsu, when imaging a region of interest of 4608x128, can image at 2203 frames per second, totalling 1.3 terapixel per second. It is important to have a computer that can handle this data rate. For many applications, we recommend Colfax International’s SXP9000 workstation, which includes several convenient features, including:

  • A large number of high-speed peripheral slots. While originally designed to host GPU cards, these slots can be used for other high-speed peripherals, such as frame grabbers.

  • A high-speed NVMe SSD, which can achieve upwards of 20 GB/s under ideal conditions.

  • 10GbE LAN - 10G Ethernet or faster, if supported by your institution, is highly recommended for transferring data to and from the computer. This computer provides this high-speed connection without necessitating an additional network card, freeing up precious space in the computer.

  • USB-C ports that can be used for image display, keyboard, and mouse. Again, by eliminating the need for a graphics card, available space is available to other peripheral devices.

  • Redundant power supplies - in the event of a power supply failure, the computer will continue to operate. Moreover, they will be able to drive some of the more power-hungry components, such as frame grabbers.

  • Aggressive cooling - the computer is designed to handle the heat generated by the high-speed components.

Standard Specifications

A general build for a imaging computer is as follows:

  • Windows 10 Pro. This is the most common operating system for scientific imaging applications.

  • 2x Intel Xeon Silver CPUs Total of 16 Cores/32 Threads @ 3.2GHz. Higher speeds, and a greater number of cores is advantageous but expensive.

  • 128 GB of 3200 MHz DDR4 RAM. This is more than sufficient for most applications.

  • 800 GB M.2 NVMe SSD. Used to host and run the operating system.

  • 20 TB 7200 RPM SATA HDD. Used as a ‘cold storage’ for long-term data storage.

  • NVIDIA T1000 Video Card. This is a low-end video card that can be used to drive displays and perform some basic image processing. The priority for this computer is driving the microscope and acquiring data, so a high-end video card is not necessary.

  • Intel X710-T2L 10GbE Card. If the motherboard does not provide 10GbE, this card can be used to provide high-speed network connectivity.

  • 7.68 TB NVMe SSD. Used as the primary data drive.

Note

Recently, Hamamatsu released a Linux driver for their cameras. Linux provides several advantages to Windows-based operating systems, including read and write operations with lower overhead. This is especially important for next-generation file formats, such as N5, OME-Zarr, and Zarr, all of which break large images up into smaller ‘chunks’ that can be read and written independently. To learn more, we recommend reading Moore et al. 2021, and Moore et al. 2023.

Configuring Power Management Settings

On modern platforms, the computer’s power management configuration (Windows power plan, chipset/firmware drivers, and BIOS/UEFI power features) can materially affect throughput, latency, and run-to-run stability. By properly configuring the computer, navigate will operate more deterministically and at higher performance. Below is a step-by-step guide to optimize these settings.

Protocol: Windows configuration

1. Update baseline software and firmware

  1. Ensure the system is on a supported Windows release (Windows 10/11 or Windows Server).

  2. Apply your vendor’s recommended BIOS/BMC/firmware updates (Supermicro/HPE/Dell/etc.).

  3. Reboot after firmware updates.

2. Set Windows to a performance-focused power mode

General Power Settings - We recommend setting Windows to a performance-oriented power plan to minimize power-saving features that can impact performance. This includes the high performance plan or, where available, the ultimate performance plan. To change these settings via the GUI, navigate to: Control Panel → Power Options → select High performance (or Ultimate Performance).

Minimum Processor Settings - Additionally, adjust the processor power management settings to ensure the CPU operates at full performance when plugged in. Set both the minimum and maximum processor states to 100% and disable PCI Express Link State Power Management. This can be done via: Control Panel → Power Options → Change plan settings → Advanced power settings:

3. Install chipset platform drivers (including Intel Management Engine)

The Intel Management Engine (ME) provides platform management capabilities independent of the OS. Install the latest ME drivers, which can be found https://www.intel.com/content/www/us/en/download/682431/intel-management-engine-drivers-for-windows-10-and-windows-11.html

  1. Install your vendor chipset driver bundle (preferred for servers/workstations).

  2. Install the Intel Management Engine Interface (MEI) driver package (vendor-supplied).

  3. Reboot.

Confirm MEI is installed: Device Manager → System devices → look for Intel(R) Management Engine Interface.

Protocol: BIOS/UEFI configuration

The exact BIOS menu paths vary by vendor and CPU generation, but the concepts are consistent.

1. NUMA and Node Interleaving

  • Disable Node Interleaving (recommended for modern NUMA-aware OSes). When enabled, firmware interleaves memory across sockets and presents a UMA-like view, which typically reduces NUMA locality benefits.

Important

Some platforms do not expose an explicit Node Interleaving toggle (or it is hidden when the platform defaults to NUMA mode). In that case, verify NUMA is active in the OS (multiple NUMA nodes visible) and proceed with the remaining power settings.

2. Power and idle-state controls (C-states, P-states)

These settings are commonly found under:

Advanced → Advanced CPU Configuration → Advanced Power Management Configuration

The intent is:

  • Keep Turbo + P-states enabled (fast frequency scaling).

  • Disable deep core/package C-states (avoid wake-up latency and jitter).

  • Disable autonomous hardware power management (keep behavior deterministic).

References