...
I find that the Restoration module is not great at deconvolving data with lower signal to noise ratios, so I tend to use Huygens and AutoQuant for deconvolution. It is difficult to set up an analysis pipeline using the Quantitation but all such tools are difficult and require a lot of trial and error, so this isn't unusual. The analysis and charts tools in the Quantitation module are not intuitive at all so most of the time I export data as a spreadsheet for analysis in other packages (e.g. Excel). The Tracking tools for measuring objects moving over time seem to be a lot more flexible and user friendly in Imaris.
How to get a copy of Volocity to use on your computer (LMCB network only)
Volocity online tutorialsChromatic shift correction in Volocity
Volocity Registration Correction
Volocity Acquisition Quick Start
Imaris
| Anchor | ||||
|---|---|---|---|---|
|
Licence: Single licence installed on Beast analysis computer
...
Bitplane Learning Zone (includes video tutorials)
Huygens
| Anchor | ||||
|---|---|---|---|---|
|
Licence: Huygens Essential wide-field, confocal and spinning disc on WOPR computer. Huygens Professional confocal and STED on STED and Orac computers
...
Scientific Volume Imaging's Huygens is a modular deconvolution software package. It has a core program that can be used to open, visualise and export data but additional modules must be installed to deconvolve wide-field, confocal, spinning disc and STED data. Multi-photon data can also be deconvolved but we don't have this module yet. We have Huygens on three machines but the licences vary, so you may not be able to deconvolve your data on all the machines (e.g. wide-field, multi-photon and spinning disc data can only be deconvolved on WOPR, confocal data can be deconvolved on all three machines). Additional modules for 3D rendering and image analysis are available but are not installed on our systems so Huygens is mostly used for deconvolution. Huygens is my preferred deconvolution package because it handles low signal-to-noise ratio images well, it is easy to edit parameters in the deconvolution routine and SVI provides a lot of information on their website. You have to register with SVI and get a login to access much of the content on the website.
...
SVI's YouTube channel - video tutorials
Nikon NIS-Elements
Full NIS-Elements offline packages are available on Son of Beast and Deep Thought. The software is available for PC only but a free NIS-Elements Viewer for PC or Mac is available for download from Nikon's website
Analysis Computers
Beast
Processor: 2x Intel XEON CPU X5650 2.67 GHz, 6 cores, 12 logical processors
...
Contact Jemima Burden or Ian White for training on Amira and Andrew Vaughan for training on Volocity. This machine is administered by the Electron Microscopy Facility and booking 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
Contact Andrew Vaughan for training. This machine is administered by the Light Microscopy Facility and booking is through the MRCLMCB_LSM Faces Scheduling System group.
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
Contact Andrew Vaughan for training. This machine is administered by the Light Microscopy Facility and booking is through the MRCLMCB_LSM Faces Scheduling System group.
Zen (UCL Super-Resolution Facility)
...
RAM: 16 GB
Software: LAS AF 3.3.0, Huygens Professional 14.06.1p5 10 (confocal and STED licence)
...