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Expansion Microscopy
List of Software for Microscopy
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Blog
2021
September
12
Jira links
List of Software for Microscopy
Created by
Nicolas Stifani
, last updated on
Feb 09, 2024
2 minute read
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
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
Bulk Rename Utility - Free File Renaming Software
VLC
Official download of VLC media player, the best Open Source player - VideoLAN
FFMPEG
FFmpeg
R
The Comprehensive R Archive Network (r-project.org)
R Studio
RStudio - RStudio
Atom
Atom
GitHub
GitHub: Where the world builds software · GitHub
Teams
Download Microsoft Teams Desktop and Mobile Apps | Microsoft Teams
Zoom
https://zoom.us/support/download
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