Images produced by the light microscopy team at The Crick.

Introduction

Fundamental to the success of any image analysis workflow is the provision of appropriate image data as input. In other words, the more time invested in optimising sample preparation and image acquisition, the more fruitful the analysis of the resultant images is likely to be.

We therefore strongly encourage researchers to discuss their projects with us, prior to acquiring any image data, to ensure the necessary criteria for a successful imaging experiment are met. We have two members of staff dedicated solely to image analysis, who in addition to providing software training, can furnish researchers with custom pipelines and algorithms to address specific biological questions, potentially fostering long-term partnerships between researchers and the CALM STP.

Our preferred analysis platforms tend to be those of the open-source variety, such as FIJI, CellProfiler and Ilastik, but we also support a number of commercial packages.

To find out more, why not come along to one of our Imaging Help Desk sessions, which we run twice per month. This provides researchers with the opportunity to informally discuss and sketch out their projects with experienced members of the CALM team, who can provide advice on experimental design and the various challenges associated with quantitative imaging.

Workstations

IM 1 ( SW303)

Windows 10 workstation

Software Installed:

FIJI,  Imaris (Node-Locked License), Prism, MATLAB, Micro-Manager, Zen Black, Zen Blue

Book IM1

Cost: £ 10.09/h

IM 2 (SW311)

Windows 10 workstation

Software Installed:

FIJI,  Imaris (Node-Locked License), Prism, MATLAB, LAS X FLIM, SimFCS4

Note: Neurolucida moved to CAMP computer

Book IM 2

Cost: £ 10.09/h

IM 3 (SE402)

Windows 10 workstation

Software Installed:

FIJI,  Imaris (Node-Locked License), Nikon Elements

Book IM 3

Cost: £ 10.09/h

ZN1 (SW311)

Windows 10 workstation

Software Installed:

Zen Black, Zen Blue, Vutara (Offline), FIJI, QuPath, Prism, MATLAB

Book ZN1

Cost: £ 10.09/h

CAMP PC (Remote)

 

Windows 10 remote workstation for fast access to CAMP.

Software Installed: Huygens, Imaris (Floating License), Neurolucida

Book CAMP PC

Cost: £ 10.09/h

Livecyte Analysis (Remote)

 

Windows 10 remote workstation for analysis of Phasefocus Livecyte data.

Book  LiveCyte Analysis pc

Cost: £ 10.09/h

CP 1 (SE402)

Windows 10 workstation

Software Installed:

CellProfiler, Ilastik, FIJI, QuPath, Imaris (Floating License), Prism, MATLAB

Book CP 1

Cost: £ 10.09/h

CP 2 (SE402)

Windows 10 workstation

Software Installed:

CellProfiler, Ilastik, FIJI, QuPath, Imaris (Floating License), Prism, MATLAB, PhaseFocus Cell Analysis Toolbox (Remote Connection)

Book CP 2

Cost: £ 10.09/h