3D/4D reconstruction software

Software for 3D and 4D rendering, object and spot quantification and tracking and other capabilities.

• Imaris – also has Filament Tracer for neurons and blood vessels. Support for Matlab and Fiji plugins.
• Volocity – also has a deconvolution module (see below)
• Amira – See Electron Microscopy staff members for more information

Deconvolution software

Deconvolution improves resolution and signal to noise ratio by computationally reassigning out-of-focus light to its correct focus plane.

• Huygens – deconvolution modules available for confocal, STED, widefield, spinning disc and multiphoton microscope images
• Volocity – deconvolution module works best for high signal to noise ratio confocal data

Free and open source software

Software you can download and use on your own computer.

• Fiji – popular scientific image analysis software based on Supports proprietary file formats, has a range of built-in plugins and an updater
• Cell Profiler – analysis pipeline software written for high-throughput screening data, but can be used with smaller datasets

Offline analysis versions of microscope software

Can be used for analysis or to browse and export files. Often required for specialised analysis (e.g. super-resolution reconstruction)

• Zen (Carl Zeiss) – specialised modules for PALM and SIM reconstruction and Airyscan
• LASX/LASAF (Leica Microsystems)
• NIS-Elements (Nikon) – specialised modules for N-SORM analysis and iSIM deconvolution
• SlideBook (3i)
• SID4Bio (Phasics) – specialised offline analysis software for interferometry
• FV10-ASW viewer (Olympus)