Kelly Rogers - Image processing and analysis

Kelly Rogers - Image processing and analysis

Researcher: 

Software packages available

Imaris x64 v7.4.2:

Visualisation and analysis software ideal for 3D and 4D datasets. Only available on “Jupiter” workstation in Image Analysis room (C4.18).

Metamorph v7.7.7.0:

Analysis software for 2D microscopy data. Including options for advanced cell scoring and filtering, Integrated Morphometry Analysis and Nuclei Counting modules. Available on “Neptune” workstation.

Volocity

3D/4D data visualisation and analysis package. Full version available on all Image Analysis workstations, and 6 seat site licence (see “software for your computer” section below. Demo version freely available.)

Matlab R2012

Mathematical programming suite available for specific numerical analysis of image data. Speak with Image Laboratory staff for advice or access.

Living Image 3.

For analysis of IVIS Spectrum (whole animal imaging) data.

Attovision

Capture and analysis of data from BD Pathway.

Zen 201

Acquisition software for Zeiss confocals.

Axiovision 64bit

Deconvolution of widefield data.

Analysis hardware

“Jupiter”

“Imaris” Machine.

HPZ800 workstation. 64bit Windows OS. 24GB RAM.

Intel(R) Xeon(R) X5675 Processors.

Asus EAH6970 Graphics Card. 

“Neptune”

Also known as the “Metamorph” machine.

HPZ800 workstation. 64bit Windows OS. 24GB RAM.

Intel(R) Xeon(R) X5570 processors.

NVIDIA Quadro FX 4800 Graphics Card.

“Triton”

Laboratory laptop and “Matlab” machine.

(Not generally available to users, see staff for access).

Dell Precision M4600. 64bit Windows OS. 16GB RAM.

Intel(R) Core(TM) iz-2860QM processors.

NVIDIA Quadro 1000M Graphics Card.

Microscopy server

Network storage available for storing and moving large microscopy data sets.                        

Current capacity 10TB. For access see laboratory staff.

Software for your computer

ImageJ / Fiji

Open-source image editing and analysis software. Many plugins and options available. We suggest downloading Fiji preferentially (Fiji IJust ImageJ) as it has useful prepackaged plugins and a few other minor advantages. Can open almost any image file format, including raw formats direct from microscope capture software.  

Photoshop / Gim

Image manipulation software (Gimp is free and open-source equivalent of photoshop). Beware – image manipulation can make your images look nicer, but it may destroy any scientific merit they have. Speak with laboratory staff if you’re unsure what you may, and may not, do to your data.

Volocity

Demo is fully featured and freely available, but will have watermarks across all images and will not allow printing. Network licence is available to allow you to use full version from your desktop, speak with staff for access instructions.