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 runs in Windows, Mac and Linux operating systems. Basic image processing steps such as merging colour channels, editing stacks and making movies are simple and you have a lot of control over the output. The file formats of the major microscope manufacturers are well supported using the Bioformats Importer plugin. ImageJ is the basis of the Fiji analysis suite, μmanager device control software and OpenSPIM light sheet software, so the ImageJ software architecture is the de facto standard in biological imaging. | 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/ |
| Fiji | Yes | N/A | Fiji is an extended version of ImageJ with two major advantages. Firstly, it has an updater that allows you to keep versions constant, making troubleshooting at lot easier. Secondly, it comes bundled with pre-installed plugins so many analysis features are already in there and you don't need to install them yourself. If you do need to install plugins this is just as easy as it is for ImageJ. I currently recommend Fiji as the software that all staff members should use for basic image processing procedures. | Fiji comes bundled with plugins but these seem to be heavily weighted towards certain applications that aren't necessarily cell biological. This probably simply reflects who is writing software for it. It is therefore likely that from time to time you will need to instal a plugin. This may be fine but some plugins may have dependencies (e.g. Java 3D) that aren't necessarily installed with Fiji. | http://fiji.sc/Fiji |
| Volocity | No | Network | The principal advantage of Volocity is that it natively analyses data sets in 3D rather than as stacks of 2D slices. There are 500 free core licences on the LMCB network licence server as well as a handful of licences available for the analysis modules Restoration, Visualization and Quantitation. Restoration is a deconvolution package, but I find that Huygens or Autoquant perform better on most data sets. Visualization is a 3D reconstruction and rendering package with volume and surface rendering and a ray tracer. Quantitation is a measurement package that can be used to apply a 'pipeline' of analysis steps to process data and extract measurements. Basically this means thresholding and segmentation, binary style procedures like erosion and dilation, object identification, filtering by object features, measurement and colocalisation, etc. | I find that the Restoration module is not great at deconvolving data with lower signal to noise ratios, so I tend to use Huygens and AutoQuant for deconvolution. The Quantitation module is difficult to use, but all pipeline analysis tools are difficult and require a lot of trial and error. The analysis and charts tools in the Quantitation module are not intuitive at all so most of the time I export data as a spreadsheet for analysis in other packages (e.g. Excel). The Tracking tools for measuring objects moving over time seem to be a lot more flexible and user friendly in Imaris. | http://www.perkinelmer.com/pages/020/cellularimaging/products/volocity.xhtml |
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.