Software

 

Below a list of software available to all users of the Advanced Imaging Facility.

List of free software available to the microscopist


Guidelines for Best Practices for image processing.
Digital Imaging: Ethics.
Designing a rigorous microscopy experiment: Validating methods and avoiding bias (2019) Jost and Waters, J Cell Biol. DOI: 10.1083/jcb.201812109.

Free viewers to view and extract your images:

Leica TCS SP5 confocal laser scanning microscope (PC): A free viewer can be downloaded from here.

Olympus FV1000 confocal laser scanning microscope (PC): Select 'Laser Scanning Microscopes' from this page. Please contact me (krs5) for a serial number if you cannot find it on the microscope.

Nikon NIS-Elements (PC/Mac): A free viewer can be downloaded from here.

Volocity (PC/Mac): to access data files from the Nikon microscopes 1 and 2 and Olympus cyto system a free viewer can be downloaded from the here.


Software available in AIF

The microscope suite in the Henry Wellcome Building (room 3/51) has 3 PCs for data analysis. You can book a PCs via the calendar system.

Leica LAS AF software Extra copy of LAS AF software to analyze data from the Leica SP5 confocal laser scanning microscope

ImageJ

Fiji

Free image processing and analysis software (Fiji = Fiji Is Just ImageJ).
MS Office
Adobe Photoshop
Volocity
High Performance 3D-4D image analysis and reconstruction software 
NIS-Elements
Analysis software for Nikon microscope 4


The microscope suite in the Adrian Building (room G1A) has three PCs for data analysis. The following software is available:

Imaris Software Suite modules: Imaris, Imaris MeasurementPro, ImarisTrack, ImarisColoc and ImarisVantage.
Imaris Basic Extra license for Imaris (basic) on the deconvolution PC
Huygens Essential deconvolution Deconvolution package
Scan^R analysis software
Cell^R analysis software
Adobe Photoshop CS3

ImageJ 

 Fiji

Free image processing and analysis software. (Fiji = Fiji Is Just ImageJ).

In the RKCSB is an analysis computer with an extra copy of NIS-Elements.

Software available via the University network (UOL computers) via Program Installer:

ImageJ Explanation how to install on UOL computers
Fiji Explanation how to install on UOL computers
Gimp (free software) Image editing software
Graphpad Prism Scientific graphing, curve fitting and statistics
Irfanview Image viewer
Mathematica Data analysis
MatLab Data analysis
Photoshop Image editing software

List of free software available to the microscopist

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