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Computers & Software

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 of computers below provides further information about the specifications of the computers and the software installed. Computers must be booked using the Faces Scheduling System and training can be provided for anyone unfamiliar with the software.

Training

Please reserve a training session for the following software packages through the light microscopy facility:

  • Bitplane Imaris - 3D reconstruction and quantification
  • PerkinElmer Volocity - 3D reconstruction and quantification
  • SVI Huygens - Deconvolution
  • Media Cybernetics AutoQuant - Deconvolution
  • Fiji - Basic to advanced image processing

Please reserve a training session for Amira through the electron microscopy facility

Computers

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 login 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 Burrden or Ian White for training on Amira and Andrew Vaughan for training on Volocity. This machine is administered by the Electron Microscopy Facility and login 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

Huygens Essential on WOPR

Huygens Essential uses SVI's Maximum Likelihood Estimation (MLE) deconvolution algorithm in combination with a calculated or measured Point Spread Function (PSF) to model the way blur degrades the microscope image and then re-assigns light back to its correct focal plane. It can be used for both widefield and confocal data sets. The software has a wizard interface where the user checks or adjusts microscope parameters, measures or estimates background and signal-to-noise ratio and can apply a measured or calculated PSF before carrying out the deconvolution operation. The following options are installed in this copy:

  • Widefield Deconvolution
  • Confocal Deconvolution
  • Spinning Disc Deconvolution
  • PSF Distiller - To generate measured PSFs
  • Time Series support - to automatically deconvolve time series
  • Chromatic Shift Correction - To automatically correct for shifts between channels caused by aberrations and misalignments
  • Various Viewers - Slicer, Twin-slicer, Ortho-slicer, Volume-renderer

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

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

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)

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