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All-in-one software (acquisition, processing, analysis)

Proprietary

• Zeiss

  Link in New Window
  linkText Zen software href https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html

• Link in New Window
  linkText NIS-Elements software href https://www.microscope.healthcare.nikon.com/products/software/nis-elements

  manufactured by

  Link in New Window
  linkText Laboratory Imaging href https://www.laboratory-imaging.com/en

  for 

  Link in New Window
  linkText Nikon Microscope href https://www.microscope.healthcare.nikon.com/

  . It comes in 2 flavours: Basic Research, Advanced Research plus some options Confocal, High-Content and Artificial intelligence (Ai) add-ons.

  Link in New Window
  linkText NIS Element package comparison href https://www.microscope.healthcare.nikon.com/products/software/nis-elements/package-comparison

• Leica

  Link in New Window
  linkText LAS-X Software href https://www.leica-microsystems.com/products/microscope-software/p/leica-las-x-ls/

• Evident / Olympus

  Link in New Window
  linkText CellSens software href https://www.olympus-lifescience.com/en/software/cellsens/

• PicoQuant

  Link in New Window
  linkText SymPhoTime 64 software href https://www.picoquant.com/products/category/software/symphotime-64-fluorescence-lifetime-imaging-and-correlation-software

• MBF BioScience

  Link in New Window
  linkText Stereo Investigator href https://www.mbfbioscience.com/products/stereo-investigator

• Visitron

  Link in New Window
  linkText VisiviewR Software href https://www.visitron.de/products/visiviewr-software.html

• Inscoper

Acquisition software

Free and Open-source

• Link in New Window
  linkText Micro-Manager software href https://micro-manager.org/

  by Nico Stuurman and Mark Tsuchida

  Link in New Window
  linkText credits href https://micro-manager.org/Credits

Visualization, Processing and Analysis software

Free and Open-source

• ImageJ (NIH)
• FIJI (Fiji Is Just ImageJ)
• MorphoGraphX https://morphographx.org/
  Dedicated to 4D analysis
• ICY Home - Icy – Open Source Image Processing Software (bioimageanalysis.org)
• Ilastik https://www.ilastik.org/ Pixel Classification
• Cell Profiler https://cellprofiler.org/ Image Analysis and Quantification
• Qupath QuPath on Github
• Napari Napari

Proprietary

• Spot Imaging
  Used to control Spot cameras with some analysis capabilities. Software ranges from 500$ to 1000$
• Imaris Oxford Instruments
  Dedicated to multidimensional visualisation and analysis. Requires a License.
• Image-Pro (MediaCybernetics)
  To be tested.
  Seems to be also sold by Asia Imaging
• AutoQuant (MediaCybernetics)
  Used for deconvolution. Fast, Simple and Accurate. Requires a license.
  Seems to be also sold by Asia Imaging
• Amira (Thermo Fisher Scientific)
  To be tested
• Metamorph MetaMorph® Software Suite Knowledge Base (moleculardevices.com)
  Soon to be retired
• Volocity Volocity Software (volocity4d.com)
• Huygens HomePage | Scientific Volume Imaging (svi.nl)
• VisioPharm VisioPharm
• MicroVolution: Very fast deconvolution

Utilities

• Bulk Rename Utility

• Free

• renaming utility
• VLC media player

• Free open-source cross-platform media player
• FFmpeg Free open-source cross-platform video transcoder command line
• Handbrake Free open-source cross-platform video transcoder with user interface

• R The Comprehensive R Archive Network (r-project.org) Free open-source and cross-platform coding language and environment for statistics and much more

• RStudio Free user interface for R programming language

• Atom

• GitHub Repository for programming scripts