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Image analysis has become an integral part of planning and running microscopy experiments.

Currently we have no image analysist who can support users, but we are in the processs of recruiting a new team member.




Commercial software:

Imaris — 3D volumetric reconstruction and analysis software, located on the Image Analysis computer in the Image Analysis office of the MRC WIMM.

Huygens — Deconvolution for wide-field, confocal and STED images, based on the Osprey server (managed by Dominic). For access to the imaging server resources please create an Imaging Account.


Servers for image analysis:

Osprey server: Dell PowerEdge C6220 II Server: 2x Intel Xeon E5-2697v2, 128 RDIMM RAM

Harrier server: Dell PowerEdge R730 Server: 2x Intel Xeon E5-2650, 256 RDIMM RAM, NVIDIA Tesla K80 GPU.


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