Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 13 Next »

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

Son of Beast

WOPR

Dell Precision T5400 running Windows 7 64-bit with Intel Xeon X5460 3.16 GHz quad core processor, 28 GB RAM and a 1 TB hard drive.

Software installed:

  • SVI Huygens Essential 4.5
  • PerkinElmer Volocity 6.3
  • Leica Microsystems LAS AF 2.6
  • Fiji 64-bit

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

Volocity on WOPR

Volocity

Deep Thought

Zen

Orac

  • No labels