Software

Image Analysis Software and Computers

General Information

• Tutorial: guidance for quantitative confocal microscopy by James Jonkman, Claire M. Brown, Graham D. Wright, Kurt I. Anderson and Alison J. North. Nature Protocols 2020
• A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments by Jen-Yi Leea, and Maiko Kitaokab. Mol Biol Cell.  Jul 1;29(13):1519-1525 2018
• Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images by Douglas W Cromey. Sci Eng Ethics  2010

Analysis PC's

• Analysis Computers - There are two analysis workstations availible to book, one for each campus, for demanding image processing and analysis (free to use for registered FILM users).

Open Source Software

• Software - FIJI (FIJI is just ImageJ)  - general image handling - a maintained version of ImageJ (Windows , Linux  and , MacOS). 
• Software - ICY for general image handling,  good for cell segmentation and tracking (Windows, Linux, MacOS) - Pasteur Institute.
• FLIMfit  - Fluorescent lifetime analysis software (Windows and MacOS) - developed at Imperial College London.
• ImageJ  - general image handling and analysis  - (Windows, Linux and MacOS) - NIH -  see FIJI 
• CellProfiler and CellProfiler Analyst - software for quantitative analysis of biological images (Windows and MacOS) - Broad Institute Inc.
• Ilastik - the interactive learning and segmentation toolkit (Windows , Linux  and , MacOS). 
• QuPath is a powerful, flexible, extensible software platform for whole slide image analysis.

Commercial Software

• Software - Huygens  - Deconvolution software, 3D rendering and analysis  (Licenced Server).
• Software - Imaris  - 3D visualisation/rendering and analysis (Windows - Licenced Server).
• Software - Volocity  - Good for 3D visualisation/rendering and movie contruction (Windows - Licenced Server).
• Software - Definiens - Object-based image analysis package (Windows - Licenced Server).
• Omero - Image database - view, organise, analyse and share your data - (Research computing service - enquiries to rcs-support"at"ic.ac.uk) (Web Based).