Computers & Software
The LMCB light microscopy and electron microscopy facilities have an image processing suite currently housing 6 computers reserved for image processing jobs. These are located in room 2.19A in the Medawar Building. The machines must be booked using the Faces Scheduling System. 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)