Image Analysis
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
Workstations for image analysis:
The image analysis workstation is located at the Centre for Computational Biology (seat 40) at the read 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 (microscopy@imm.ox.ac.uk) 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 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].
References
[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