Blog from September, 2021

This is not a strictly a microscopy technic. It is more a method for sample preparation in which the sample is embedded in a Gel matrix which is digested and physically expended. Conventional microscopy acquisition is then applied to the expanded sample.

See

https://pubmed.ncbi.nlm.nih.gov/25592419/

https://en.wikipedia.org/wiki/Expansion_microscopy

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

Proprietary

• Zeiss
• manufactured by for  . It comes in 2 flavours: Basic Research, Advanced Research plus some options Confocal, High-Content and Artificial intelligence (Ai) add-ons.
• Leica
• Evident / Olympus
• PicoQuant
• MBF BioScience
• Visitron
• Inscoper

Acquisition software

Free and Open-source

• by Nico Stuurman and Mark Tsuchida

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