Denoising and deconvolution
- Patch based denoising nd-safir
- Huygens (SVI) http://www.svi.nl/HuygensDeconvolution
Segmentation
- iLastik (by interactive learning) http://www.ilastik.org/
Tracking and cell lineage reconstruction
- Keler lab software https://www.janelia.org/lab/keller-lab/software/fast-accurate-reconstruction-cell-lineages-large-scale-fluorescence
Annotation and visualisation
- Vano http://vano.cellexplorer.org/ (free)
- Vaa3d http://www.vaa3d.org/ (free)
General
- ImageJ http://rsbweb.nih.gov/ij/ (free)
- Fiji http://fiji.sc/ (free)
- Icy http://icy.bioimageanalysis.org/ (free)
- Amira http://www.vsg3d.com/amira/overview
- Imaris http://www.bitplane.com/
- Volocity