Selection of computer Hardware

Cockpit is a portable python application that runs on Windows, Linux and macOS. This allows a very wide range of computers to be used to run the main GUI application. That said there are a few considerations to make before selecting the main computer to run the GUI front end for a microscope.

The strongest determinant of hardware and OS selection is often the availability of interfaces for the required devices to connect to the microscope. Many camera have dedicated data transfer cards that require both a PCIe slot in the computer and a software driver to interface to the host OS. In many cases this forces the selection of windows as this is the most widely support OS.

It should be noted that the main controlling computer does not need to be directly connected to the hardware, devices can easily be on a remote computer communicating over the network. The main computer and remote one do not need to run the same OS, eg the controlling computer can be macOS while the computer hosting the hardware can run windows. However, many people want some, or all of the devices connected to the main computer.

CPU requirements

In general cockpit is not very demanding of CPU, the heavy graphics tasks are performed on the system GPU. Cockpit is multi-threaded but runs in a single Python process so is limited by the Python global interlock, the so called GIL. This means multi-core CPUs are unlikely to be fully utilised. However, if you plan to use the same computer to run devices these will run under a separate python process and so will be able to exploit more of the power of a multi-core CPU.

Memory requirements

Cockpit does not use a huge amount of memory, although additional memory may considerably help performance with image stacks. The system stores mosaic images both directly on the GPU for performance and in memory to allow rescaling so large mosaic considerably add to the memory footprint. I would recommend at least 16GB.

Graphics Cards

The system stores mosaics and live or snapped images on the graphics card to allow rapid navigation. This can require substantial ram on the GPU card, especially for large mosaics with 1000’s of images. Any modern graphics card will be able to provide real time scaling and rendering of these simple images, limited only by the available graphics memory to store the images.

Disk Space

The amount and rate at which image data can be collected in fundamentally limited by the disk storage space. For rapid image collection SSD’s are much faster, and this performance can be further increased by using raid to spread the data across multiple disks. Typically a modern CMOS camera takes images of at least 8MB per image, multiple z-planes, colour channels and time points can make extremely large image stacks so ensure you have enough local storage for fast acquisition and then a network data store, with a data backup solution, for longer term storage.

Multi-computer configuration

In general for high performance systems we run the cockpit GUI from one computer and connect the actual hardware to other computers to maximise performance. We connect the computers together with a dedicated internal network which just contains the computers running the microscope and then the main computer has 2 networks connected one for general usage and the other just connecting to the other microscope computers.

To further improve performance while minimising costs we often drive multiple cameras from one computer but provide separate network paths to the front end computer running Cockpit. Both the camera computer and the cockpit computer require multiple network cards but if each card is given a separate IP address and each camera is exported via that address then the large volume of network traffic from the cameras can easily be separated.