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Computers & Software

The LMCB light microscopy facility and electron microscopy facility have a number of computers optimised for image processing applications. These are located in room 2.19A in the Medawar Building. There is also a wide range of free and commercial software packages for image processing operations such as 3D reconstruction and rendering and deconvolution. The machines must be booked using the MRCLMCB_EM Faces Scheduling System group. Please contact Jemima Burden, Ian White or Andrew Vaughan for a login and training session.

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

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

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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