Introduction

Version 6 of Plaque Simulator (PS6) is designed for recent (2009 models or later) Apple Macintosh computers with Intel Xeon, Core i7, or Core i5 multicore processors that can install OSX version 10.9 or greater. Eye Physics recommends running PS6 on the fastest computer you can afford with at least 4 processor cores, 8 GB of RAM and OSX 10.11.6 (El Capitan). Support for MacOS 10.12 (Sierra) requires PS6 version 6.4.1 or later.

Intel Xeon and Core i7 processors 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 processor found in many off-the-shelf iMacs and Mac laptops has less cache and the 4 core variant is not hyper-threaded. These computers may, however, be ordered with an upgrade to the Core i7 processor at the time of purchase at a slightly higher price. PS6 will run nicely on the Core i5 processor but dosimetry performance will be a bit slower than on the i7.

Plaque Simulator version 6.2 and later leverages multicore processors when performing all 2D, 3D and histogram dosimetry calculations. For instance, when running on the hyper-threaded 4 core Xeon processor, PS6 distributes 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.

Eye Physics recommends running PS6 on the fastest hyper-threaded multicore processor (e.g. Xeon or Core i7) 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 isodose line, isodose surface and dose histogram comparisons of alternative plan options. OSX leverages the GPUs on the video card to accelerate graphics and many features of the operating system, so choosing the most powerful video capability offered at the time of purchase (or as an after-market upgrade for 2009-2012 Mac Pros) is also desireable.

The software development system as of September 2016 is a 2009 Mac Pro desktop (aluminum tower case) which has been upgraded from its stock configuration with a 3.46 GHz 6-Core Intel Xeon processor (6 physical cores, 12 logical cores), an 802.11ac+Bluetooth_4 mini PCIe card, an AMD Radeon HD 7950 3072 MB graphics card reflashed for OSX, a 4 port USB3 PCI card, a 1TB Samsung 850 Pro SSD boot drive mounted on a PCI SATA3 adapter card and several WD Black series 4TB hard disks, a DVD-RW optical drive, and 32 GB RAM running under MacOSX 10.11.6 (El Capitan). Peripherals include a pair of Dell 24" ultrasharp display monitors, Epson 4870 and 4990 Photo flatbed scanners with VueScan software and a Dell C1760nw LED printer. All of the 2009 Mac Pro upgrade components are available on ebay and from various internet vendors.


Hardware recommendations, in order of preference:
  • Computer:
    • Desktop: All Mac Pros manufactured after 2009, and/or iMacs with 4-core i7 processors are strongly recommended. iMacs with 4-core i5 processors are also acceptable. A 2009-2012 Mac Pro (aluminum tower case) running OSX 10.11.6 (El Capitan) should be ugraded with a Radeon 7950 class (or better) video card to leverage the GPUs and possibly an 802.11ac+Bluetooth 4 mini PCIe card in order to work with the new force-touch magic trackpads. 2013 and later Mac Pros (black cylinder case) do not require any modifications.
    • Laptop: MacBook Pros with 2 or 4-core i7 processors are acceptable. PS6 has been tested on a pair of 15" MacBook Pro laptops. Both are equipped with 500 GB SSD drives. The first was manufactured in 2010 and has a 2.66 GHz dual-core i7 processor, 8 GB RAM and an HD display. The second is a mid 2015 model with a 2.8 GHz quad-core i7 processor (up to 4 GHz turbo boost speed), 16 GB RAM and the Retina display. Performance is adequate on both laptops but is notably slower compared to the 6-core Mac Pro desktop equipped with a 3.46 GHz Xeon processor.
    • Other models: Avoid models with processors slower than 2 GHz and dual-core processors such as the Mac mini, MacBook, 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 10.9 or later.
  • Intel CPU:
    • Xeon: A single processor with 4 or more cores is strongly recommended. Using multiple multicore processors tends to require slower variants of the CPU and is probably not worth the additional expense.
    • Core i7: The 4-core version of the i7 is recommended.
    • Core i5: The i5 processor has less on-board cache than the i7 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 GHz), 2.6 GHz minimum.
  • Cores: 6 processor cores are recommended, 4 cores minimum.
  • RAM: 16 GB is recommended, 8 GB minimum.
  • OS: MacOSX 10.11.6 (El Capitan) is recommended. MacOS 10.12 (Sierra) is supported by PS6 versions >= 6.4.1. MacOSX 10.8 is the absolute minimum.
  • Graphics: Any Apple supplied standard or upgraded graphics configuration that is compatible with your computer and OSX version is fine. Only the pre-2013 Mac Pro desktop computers accept graphics card upgrades. A few 3rd party graphics upgrades are available for the 2009-2012 Mac Pros and may work but they are not recommended.
  • Displays: Display monitors in the 24" and larger class greatly enhance the user experience when preparing CT and MRI multiplanar reconstructions with OsiriX, fundus photo collages and fusions using Photoshop, and for treatment planning in general. iMacs and laptops with Retina displays are fine.
    • Mac Pro: One or more 27" or 24" monitors strongly recommended.
    • iMac: Models with 27" screens, with or without Retina display panels, are highly recommended, smaller screen versions are okay but not recommended.
    • MacBook Pro: 15" or larger screen recommended, 13" screen is okay, an external 24" display monitor is recommended for use with all laptops.
    • Retina display: Plaque Simulator has been tested with the ultra high resolution retina display. It works best when the display resolution preference is set to "default". Image quality and performance degrade ever so 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.
  • 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-ball such as Apple's "mighty" mouse. Apple's wireless bluetooth "magic" mouse and/or trackpad (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). Current Apple laptops come equipped with forceTouch trackpads.
  • Printer: Eye Physics uses color LED printers such as the Dell model C1760nw, but any MacOSX compatible printer, either networked or directly connected, will work. Dell released an updated 1760 series driver for OSX 10.11 (El Capitan) compatability in October 2015.

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.

  • OsiriX: 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 and export to Plaque Simulator several multiplanar reconstructions (MPR) of the eye from 3D CT and MR sources.
  • 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.
  • 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.