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Image analysis is an integral part of planning and running microscopy experiments. Please come and talk to the facility team at an early stage of the project, to ensure that your experimental design and image analysis strategy is the most suitable/efficient for your specific question.

 Available software on our image analysis workstation:

Imaris — 3D volumetric reconstruction and analysis software

Huygens — Deconvolution for wide-field, confocal and STED images

ZEN Image analysis and Airyscan image processing software from Zeiss

QPath — Histology section visualisation and analysis software (freeware)

ImageJ/Fiji —  image analysis (freeware)


External software Tutorials and resources

Huygens Imaging Academy

Huygens Webinars


Imaris Learning path

Imaris Tutorials


 Workstations for image analysis:

The image analysis workstation is located at the Centre for Computational Biology (seat 40) at the rear end of the office. The workstation must be booked via Agendo and you need a WIMM IT account to log in and email the Imaging facility team ( to get booking access and an induction.


Workstation information:

CPU: Intel P XEON E5-2630V4 2,2 GHz LGA2011 L3 25MB Box

Graphics: NVIDIA RTX4000 (PNY), 8 GB, Cuda capable, PCI Express 3.0x16 

Memory: 64 GB (4 x 16 GB) included, max. 256 GB RAM; Memory slots: 16 x DIMM slots 

Hard Drives: 6x HDD 12TB, RAID 5 configured to 55 TB data storage volume 

2x Solid State Drive 240 GB for pagefile and operating system 

10 Gbit Ethernet on the motherboard


Specialist software developed within the facility:

FoCuS-scan — Fluorescence Correlation Spectroscopy (FCS) software for analysis of line scan (xt) data [1]

FoCuS-point — FCS software for analysis of single points and TSCPC filtering [2].

GP-plugin — Fiji/ImageJ plugin for Generalised Polarisation analysis [3].

QuantiFly — Software for counting of cells and structures in 2D images [4].



[1] Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data

Waithe D. et al, (2017), Methods, in press

[2] FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting

Waithe D. et al, (2015), Bioinformatics, btv687

[3] Spectral imaging to measure heterogeneity in membrane lipid packing

Sezgin, E. et al, (2015), ChemPhysChem, 16, 1387-1394

[4] QuantiFly: Robust Trainable Software for Automated Drosophila Egg Counting

Waithe D. et al, (2015), PloS One, e0127659