Introduction

Version 6 of Plaque Simulator (PS6) is designed for relatively recent (2013 models or later) Apple Macintosh computers with Apple silicon M-series and/or Intel Xeon, Core i5, i7 or i9 multicore x86 processors that can install OSX version 10.12 or greater.

As of March 2022, Eye Physics recommends running PS6 on the fastest M series processor Apple desktop computer that you can afford with at least 8 processor cores, >= 16 GB of RAM and MacOSX 11 (Big Sur) or 12 (Monterey). Support for MacOS 10.13 (High Sierra) requires PS6 version 6.6.1 or later and MacOS 10.14 (Mojave) requires PS6 version 6.6.7 or later. Support for MacOS 11 (Big Sur) on Intel cpus requires PS6 version 6.7.7.

Apple silicon M series system on chip (SoC) models are faster and far more energy efficient than models that use Intel processors and M series models are very highly recommended. However, because SoC copmuters are not upgradeable, be sure to order as powerful a version as you can possibly afford with an absolute minimum of 16 GB RAM.

In 2022, Intel Xeon and Core i series processors should be considered as obsolete. They consume far more energy than Apple silicon processors, run very hot resulting in thermal throttling and deliver poor battery life in laptops. Some Intel CPUs are hyper-threaded which means that for each processor core that is physically present, the operating system addresses two virtual or logical cores, and shares the workload between them when possible. The Intel Core i5 and later generation i7 processors found in many older iMacs and Mac laptops have less cache and are not hyper-threaded. PS6 will run on the Core i5 processor but dosimetry performance will be slower than on an i7 or i9. Find a computer with as many cores (>= 6) and threads as you can afford.

Plaque Simulator version 6.2 and later leverages multicore processors when performing all 2D, 3D and histogram dosimetry calculations. For instance, when running on a hyper-threaded 4 core Xeon processor, PS6 distributed its dosimetry calculations uniformly and concurrently amongst 8 logical cores, resulting in a 5X acceleration compared to running on a single logical core. The acceleration factor is about 7X on a 6 core processor and at ≥12X on a 12 core processor. Performance per core is much better on Apple silicon SoCs.

Eye Physics recommends running PS6 on the fastest multicore processor that your institution can afford in order to achieve the best overall user experience possible. For any given processor speed, increasing the number of cores will proportionally increase the speed of multidimensional dosimetry calculations, resulting in more rapid image reconstruction, isodose line, isodose surface and dose histogram comparisons of alternative plan options. OSX leverages the GPUs on the video card to accelerate some graphics and many features of the operating system, so choosing the most powerful video capability offered at the time of purchase is also desireable.

The software development systems as of March 2022 include a 2021 M1 Mac Mini with 16GB RAM and 1 TB SSD running Mac OS12 (Monterey) and a 2019 Mac Pro desktop tower running MacOS 11.6.3 (Big Sur). The Mac Pro is configured with a 4 GHz, 16 core Xeon W processor, AMD Radeon Pro Vega II 32 GB graphics card, 96 GB RAM, 4TB secure boot SSD, a pair of secure 2TB WD Black SN750 MVNe M2 SSDs on a dual PCIe adapter for fast image and patient file storage, 4 TB of SSDs configured in RAID0 on a PCIe adapter for fast scratch storage, a pair of internally mounted 14TB Seagate Barracuda Pro spinning hard drives for archival storage, 25 TB of external Thunderbolt3 connected RAID5 DAS storage, and 32 TB of privately managed Synology and WD MyCloud NAS servers. Peripherals include a USB3 connected optical DVD/CD drive for loading CT images from disc, a trio of Dell 30" ultrasharp UP3017 display monitors, an Epson 4870 Photo flatbed scanner with VueScan software, an HP Color LaserJet Pro M254dw printer, a Logitech 4K Pro Webcam for online teaching and meetings, a Yeti Nano USB3 microphone and various USB and analog connected speaker systems. The Eye Physics office has a 1 Gbps symmetric (upload and download) fiber-optic internet connection.

For training, video production, 3D printing and as backup treatment planning systems, Eye Physics uses several 2009 and 2010 Mac Pros desktop computers which have been upgraded from their stock configuration to firmware MacPro5,1 and a pair of 3.46 GHz 6-Core Intel Xeon processors (total 12 physical cores, 24 logical cores), an 802.11ac+Bluetooth_4 mini PCIe card, a Sapphire Radeon Nitro+ RX 580 8GB GDDR5 Dual HDMI / DVI-D / Dual DP w/ Backplate Special Edition (UEFI) PCI-E Graphic Card 11265-21-20G. This card works fine for dual 30 inch monitors and MacOS 10.14 or greater, and can be flashed for MacOS booting. An inexpensive dual 6-pin to single 8-pin power adapter is required. These older Mac Pro systems also incorporate 4 port USB3 PCI cards, Samsung 970 EVO plus NVMe M2 SSDs on PCIe adapter cards as fast boot drives, Samsung 860 SSD drives mounted on a PCI SATA3 adapter cards for intermediate speed storage, 4 WD Black series 6TB spinning hard disks for archival storage, a DVD-RW optical drive, and 96 GB RAM running under MacOS 10.15.5 (Catalina). All of the Mac Pro 5,1 upgrade components are available on ebay and/or from various other internet vendors.


Hardware recommendations, in order of preference:
  • Computer:
    • Desktop:
      • Best: The 2022 Mac Studio with M1Max or M1Ultra cpu, >= 32GB RAM and >= 1TB SSD.
      • Good: A 16-core 2019 Mac Pro tower is what Eye Physics uses for software development and treatment planning. It is absolutely ideal for these purposes because it has loads of PCIe and memory expansion capability, but it is also very expensive.
      • Good: The 2021 M1 Mac Mini with 16GB RAM and >= 1 TB SSD.
      • Okay: The 24" iMac with M1 cpu with 16 RG RAM and >= 1 TB SSD.
      • Okay: Recent generation 27 inch iMacs or iMac Pros with 6, 8, 10 or more core i7, i9 or Xeon W processors running at least 3 GHz feature reasonable computing power, large screens and cost effectiveness.
      • Laptop: 16" MacBook Pros with M1Pro or M1Max cpu, >= 32 GB RAM and >= 1 TB SSD.
      • Other models: Avoid models with processors slower than 2 GHz and dual-core processors such as older Mac minis, MacBooks, MacBook Air and any others that are only available with dual-core processors and of course avoid all older models that can't run OSX 10.12 or later.
    • Models with Apple silicon CPUs: these are VERY powerful and efficient system on chip (SoC) computers and hence can not be upgraded so order as fully configured as you can afford
      • M1: with >= 16 GB RAM.
      • M1-Pro: with >= 32 GB RAM.
      • M1-Max: with >= 32 GB RAM.
      • M1-Ultra: with >= 32 GB RAM.
    • Models with Intel CPUs: Intel CPUs are obsolete in 2022 because they are energy inefficient and thermally throttle but some are still useful. In 2022, Eye Physics still uses a couple of 2018-2019 era Macs that run on Intel CPUs.
      • Xeon: Configurations such as the Mac Pro 2019 with >= 16 cores are very good.
      • Core i9: >= 6 core versions of the i9 cpu are okay.
      • Core i7: >= 4 core versions of the i7 cpu are okay.
      • Core i5: The i5 processor has less on-board cache than the i7 or i9 and its 4-core version is not hyper-threaded, but it is adequate.
      • Other models: Dual-core processor variants work but are not recommended.
    • Speed: Fastest affordable (e.g. ≥3.46 GHz), 2.6 GHz minimum.
    • Cores: Six or more processor cores are recommended, 4 cores minimum.
    • RAM: ≥32 GB is recommended, 16 GB minimum.
    • OS: As of early 2022, Eye Physics uses MacOSX 11.6.3 (Big Sur) for routine treatment planning and we test with MacOS 12.x (Monterey). MacOS 10.14 is supported by PS6 versions >= 6.6.7. MacOSX 10.12 is the minimum supported OS version.
    • Graphics: Any Apple supplied standard or upgraded graphics configuration that is compatible with your computer and OSX version is fine. The 2019 Mac Pro tower comes with several graphics card options. Eye Physics uses the AMD Radeon Pro Vega II 32 GB graphics card in our 2019 Mac Pro tower.
    • Displays: Apple computers work best with Apple provided "Retina" screens and/or 3rd party screens that have pixel densities of about 110 ppi. We do NOT recommend using 3rd party 4K (or greater) screens for treatment planning. Screens in the 24" and larger class greatly enhance the user experience when working with text and CT reconstructions using PS and/or OsiriX, fundus photo collages and fusions using Photoshop, and for treatment planning in general. iMacs and laptops with 27 inch Retina displays are fine. Eye Physics uses a trio of Dell UP3017 30 inch displays with our Mac Pro 2019 tower. The UP3017 screens feature 2560x1600 pixels, 0.251 mm pixel pitch and 101 pixels per inch (ppi). For our Apple silicon M1 Mac Mini and M1-max Mac Studio desktops we use Dell 34" curved displays. These are wide quad high definition (WQHD) models with 3440x1440 pixels, 0.2325 mm pixel pitch and 109 ppi.
      • Mac Pro: One or more "2K" class 24" to 34" monitors are recommended.
      • Mac Studio: One or more "2K" class 24" to 34" monitors are recommended.
      • Mac Mini: One 32" QHD or 34" WQHD monitor is recommended.
      • iMac: Models with 27" screens with 5K Retina display panels are recommended, smaller screen versions are okay.
      • MacBook Pro: 14" or larger retina screen recommended, 13" screen is okay but really cramped.
      • Retina display: PS works best when the display resolution preference is set to "default". Image quality and performance degrade slightly if any of the other scaled resolutions are selected in order to display more (or fewer) logical pixels. Retina display iMacs and laptops are highly recommended.
      • Apple desktop displays: The 27" 5K Studio Display and 32" 6K Pro Display XDR are both Retina displays and are recommended but are expensive.
    • Flatbed Digitizer: A "high-quality" flatbed scanner with 8x10 inch transparency option and USB or firewire connection (e.g. Epson Perfection V700 Photo). Only the most recent Apple hardware supports USB3, and recent models no longer include firewire ports, so verify in advance that your computer is compatible with whichever scanner you select. These scanners usually cost less than $700.
    • Input devices: PS6 is designed to work best with a wired USB multi-button mouse with a scroll-wheel or scroll-ball such as Apple's "mighty" mouse. Eye Physics uses a 3rd party SteelSeries Rival 710 mouse with its desktop systems. Apple's wireless bluetooth "magic" mice and/or trackpads (version 2) with forceTouch are also higly recommended add-ons. These "magic" devices enable PS6 to respond to modern finger gestures such as pinches, swipes, and rotation gestures when running OSX 10.11 (El Capitan) or later. Current Apple laptops come equipped with forceTouch trackpads and touch bars. Eye Physics uses a Magic Mouse 2 with its 2018 MacBook Pro laptop.
    • Keyboards: Eye Physics recommends wired USB keyboards. We prefer mechanical Cherry MX switch keyboards from Das Keyboard such as the Model 4 Professional for Mac. Eye Physics also uses various USB wired and Bluetooth wireless keyboards manufactured by Apple.
    • Printer: Eye Physics uses an HP Color LaserJet Pro M254dw printer, but any MacOSX compatible printer, either networked or directly connected, will work. MacOS 10.13 and 10.14 compatible drivers for the HP M254dw are available online from HP.
    • Example: As of June 2022, the Mac Studio desktop illustrated below is an example of an entry level hardware configuration, similar in computing power to the systems Eye Physics uses for development, planning, testing and training. More powerful versions of the Mac Studio are recommended if you can afford them. All Eye Physics owned Mac Studio desktops are configured with M1-Max 10-core cpus, 32-core GPU, 64GB RAM and 2 TB SSDs. Eye Physics recommends the largest screen you can afford. Eye Physics uses multiple Dell 30", 32" and 34" 2K-class screens.

      Example of 2022 entry level Mac Studio computer and the optional 27" Studio Display

      MacStudio2022

      Example of a 2022 Dell 34" WQHD display to use with Mac Studio or Mini desktop or as additional screen to use with a laptop.

      Dell34screen


Additional software recommendations

To get the most from Plaque Simulator you will want to do image based planning. Eye Physics uses the following well known 3rd party software solutions to prepare CT, MR, ultrasound and fundus images for export to Plaque Simulator.

  • DCMTK: The DICOM toolkit DCMTK is a collection of cross platform libraries and applications implementing large parts the DICOM standard for Unix operating systems including MacOS. To install DCMTK you must first install a package manager for MacOS such as Homebrew. Follow the instructions on the Homebrew web site. Once you have installed Homebrew, you can then install DCMTK from a MacOS terminal window using the command brew install dcmtk. Be sure to make note of the Unix file path at which DCMTK was installed, it may differ slightly depending upon your version of MacOS. The file path is typically something like usr/local/bin.
  • OsiriX: The multiplanar reconstruction functionality of OsiriX is now available in PS version 6.8.6 and later once you have installed DCMTK. For versions of PS prior to 6.8.6 please download the latest version of OsiriX that is compatible with your OSX version. OsiriX, a well established open source DICOM viwer and listener, is used by Eye Physics to create anonymized image series for teaching purposes and to export multiplanar reconstructions (MPR) of the eye from 3D CT and MR sources to Plaque Simulator versions that do not support DCMTK. There are a couple of "free" alternatives to OsirX which are based on code forks from older OsiriX distributions; HOROS and Miele-LXIV.
  • Photoshop: Adobe Photoshop for Mac, a component of Adobe Creative Suite for Mac is used by Eye Physics when creating fundus collages and fusions, editing CT, MR and ultrasound images, and cropping and otherwise preparing pictures of plaques and seed carriers for inclusion in plaque model files.
  • Vuescan: from Hamrick Software is a superior application for Windows, Mac OS X, and Linux that replaces the software that came with your flatbed scanner.
  • BBEdit: from Bare Bones Software is a great text file editor that can be used to view and edit the .xml files created by PS6 and DCMTK.
  • Excel: Microsoft Excel:Mac, the spreadsheet component of Microsoft Office for Mac was used by Eye Physics to create and edit the tab delimited text physics files used by Plaque Simulator version 5 (PS5). PS6 can open and save PS5 (.iphys) physics files, but prefers the newer xml versions (.iphys6) of these files.