Biomedical Engineering Reference
In-Depth Information
Zeiss LSM Browser and ZEN
http://www.zeiss.de/ZEN
The Zeiss LSM image browser as the name implies is the Zeiss' older version of
the image browser for it's proprietary 'LSM' file format. The old version has been
around for quite some time and was recently replaced by a new version, called ZEN.
Both these versions can be downloaded from the Zeiss web site. However, we found
the older version more intuitive to use than the newer version!
Leica LAS AF Lite
ftp://ftp.llt.de/softlib/LCSLite
Leica LAS AF Lite is the equivalent software for browsing the Leica SP2 and SP5
confocal images. The software can be downloaded from the FTP site of Leica.
Scientific volume imaging (SVI)
http://www.svi.nl/Download
http://www.svi.nl/FrontPage
http://www.svi.nl/BackprojectedPinholeCalculator
http://www.svi.nl/NyquistCalculator
Scientific volume imaging (SVI) are the foremost leaders in high-quality restoration
and analysis programs for microscopy. Huygens software refers to the different
image processing packages that are intended for restoration, interactive analysis
and volume visualization of 2-D, 3-D, multi-channel and time series images
from fluorescence microscopes. The deconvolution software is based on either
the classical ML or the Tikhonov-Miller algorithm, and they need a commercial
licence. However, they also have the freeware versions-the HuygensEssential and
FreeSFP, which can be used for image reading/writing in many file formats, volume
visualization, and a few basic image processing operations. This light version can
be downloaded from their site. Apart from their softwares, they also have a public
wiki site that provides a detailed explanation to the most frequently asked questions
along with support tools such as Backprojected pinhole radius and Nyquist rate/PSF
calculator.
MediaCybernetics AutoQuant
http://www.mediacy.com/index.aspx?page=AutoQuant
Other than SVI, the other commercial and popular vendor is MediaCybernetics
that markets the AutoQuant deconvolution software. One of the essential features
in this package, which Huygens does not have is AutoDeblur-the adaptive blind
deconvolution routine for restoration. AutoQuant also added many other extensions
for acceleration, constraining the estimation, and noise reduction.
Amira for scientific visualization and processing
http://www.amira.com/
Another commercial software for scientific visualization and processing is the
Amira software. This boasts of a list of features such as slice alignment, image
registration, Z-drop correction, etc that are not present in the above softwares.
However, we found the 3-D deconvolution in Amira to be not very user friendly.
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