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- Amira
- Applied Precision
- Arivis
- Autoquant
- Avizo (VSG)
- BioimageXD (free)
- Bioimage Suite (free)
- BioVision
- BioVoxxel (free)
- Bisque (free)
- Bitplane
- Cellprofiler (free)
- Cellenger (Definiens)
- CellCognition Project (free)
- Cell Pie (free)
- CellSeT (free)
- CircuSoft PFRET
- Colocalizer
- Compix (Hamamatsu)
- Endrov (free)
- Farsight (free)
- Fiji (free)
- Gemident (free)
- Iatia (QTm)
- ICluster (free)
- Icy (free)
- Igor Pro (WaveMetrics)
- iLastik (free)
- ImageJ (free)
- Image Processing Toolbox (The MathWorks)
- ImageSurfer (free)
- Imagetool (free)
- ImageTrack (free)
- IMOD (free)
- Improvision (Perkin Elmer)
- Indeed 3D (Amira. Visage Imaging)
- Inovision
- Intelligent Imaging Innovations
- ISee Imaging
- ITG software
- Knime (Free)
- MatLab-Image processing
- Media Cybernetics (Autodeblur, Image Pro, QED Imaging, In vivo live cell imaging …)
- Micropilot (Free)
- Microvolution (Free for Academic license)
- Multi-Image Processing Application (MIPA)
- MIPAV (free)
- MitoBio (free)
- Molecular Devices (Metamorph)
- MosaicSuite (free)
- MVIA
- NeuronStudio and NeuroBioimaging (CNIC) (free)
- ORMFCOSM-XCOSM (free)
- Open Microscopy Environment (OMERO) (free)
- Powermicroscope-Deconvolution
- Scanalytics
- Scientific Volume Imaging
- Scimagix
- Slicer 3D (free)
- Soft Imaging Systems
- Synoptics (Syncroscopy, etc.)
- TGS Visual Concepts
- Virtual Cell-NRCAM (free)
- VisBio: volume rendering (free)
- Visual 3D and Cell counter (free)
- Vaa3D (free)
- Volocity
- Voxx: A Volume Rendering Program for 3D Microscopy (free)
- VTK (free)
- Wimasis
- XuvTools (Stitching) (free)