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