Computers & Software
There is a wide variety of software packages available to LMCB staff for image processing and analysis. Some software is free and can be installed on any computer including personal laptops but other software must be paid for and is either only installed on certain computers or is available under a network licence scheme where any computer able to connect to the licence server can run the software. The information below deals only with software used for scientific image processing and analysis. I have not included photo-editing software such as Adobe Photoshop and Gimp, or vector graphics software such as Adobe Illustrator and Inkscape, although there is a certain amount of overlap between the functions - especially when it comes to preparing images for publications and posters.
The LMCB light microscopy and electron microscopy facilities have an image processing suite currently consisting of 6 computers located in room 2.19A in the Medawar Building. There are a number of different image analysis software packages installed on the machines. The list below provides further information about the specifications of the computers and the software installed. Computers must be booked using the and training can be provided for anyone unfamiliar with the software. I have only included commercially available software in the list but the computers will also have Fiji or ImageJ installed.
Image Processing Software
| Software | Free | Licence | Key Features | Minus Points | Website |
|---|---|---|---|---|---|
| ImageJ | Yes | N/A | It's free. It is written in Java and so runs in Windows, Mac and Linux operating systems. | Most of ImageJ's functionality comes from plugins, which means you must install extra plugins whenever you need to do anything advanced. This can lead to one person's installation of ImageJ being different to another's, making any problems hard to troubleshoot. If a feature is not available in ImageJ you may need to write a macro or plugin yourself. ImageJ can and does handle 3D and 4D stacks very well but the available tools for 3D rendering and visualisation have not been as easy to use as those in other software when I have tried them. I don't think there are any tools for making measurements on a 3D volume. | http://imagej.nih.gov/ij/ |
Beast
Processor: 2x Intel XEON CPU X5650 2.67 GHz, 6 cores, 12 logical processors
RAM: 96 GB
Software: Imaris 7.6.5, Volocity 6.3, Amira 5.4.1, LAS AF Lite 2.4.1
Contact Jemima Burden or Ian White for training on Amira and Andrew Vaughan for Imaris, LAS AF and Volocity. This machine is administered by the Electron Microscopy Facility and booking is through the MRCLMCB_EM Faces Scheduling System group.
Son of Beast
Processor: 2x Intel XEON CPU X5650 2.67 GHz, 6 cores, 12 logical processors
RAM: 96 GB
Software: Volocity 6.3, Amira 5.4.2
Contact Jemima Burden or Ian White for training on Amira and Andrew Vaughan for training on Volocity. This machine is administered by the Electron Microscopy Facility and booking is through the MRCLMCB_EM Faces Scheduling System group.
WOPR
Processor: Intel Xeon X5460 3.16 GHz, 4 cores, 4 logical processors
RAM: 28 GB
Software: Huygens Essential 14.06.1p5, Volocity 6.3, LAS AF 2.6.0
Contact Andrew Vaughan for training. This machine is administered by the Light Microscopy Facility and booking is through the MRCLMCB_LSM Faces Scheduling System group.
Deep Thought
Processor: 2x Intel XEON CPU E5-2620, 2 GHz, 6 cores 12 logical partitions
RAM: 32 GB
Software: Autoquant X3 3.0.2, Metamorph 7.7.6, Volocity 6.3, LAS AF Lite 3.1.0
Contact Andrew Vaughan for training. This machine is administered by the Light Microscopy Facility and booking is through the MRCLMCB_LSM Faces Scheduling System group.
Zen (UCL Super-Resolution Facility)
Processor: 2x Intel XEON CPU E5-2643, 3.3 GHz, 4 cores 8 logical processors
RAM: 64 GB
Software: Zen 2012 SP1 (Black Edition) release version 8.1
Contact Andrew Vaughan for training. This machine is administered by the Super-Resolution Facility (SuRF) and booking is through the MRCLMCB_LSM Faces Scheduling System group.
Orac (UCL Super-Resolution Facility)
Processor: Intel Core i7-4770K CPU, 3.5 GHz, 4 cores 8 logical processors
RAM: 16 GB
Software: LAS AF 3.3.0, Huygens Professional 14.06.1p5 (confocal and STED licence)
Contact Andrew Vaughan for training. This machine is administered by the Super-Resolution Facility (SuRF) and booking is through the MRCLMCB_LSM Faces Scheduling System group.