Biomedical Engineering Reference
In-Depth Information
Open microscopy environment (OME)
http://www.openmicroscopy.org
The main drawback of ImageJ or FIJI plugins are that the meta-data for each
microscope are differently formatted and all the information cannot be made
available in one universal format. The OME aims to bridge this gap and strives
for a universal imaging format.
XCOSM
http://www.essrl.wustl.edu/
∼
preza/xcosm/
http://www.ucalgary.ca/styslab/imagetrak
Technically speaking, the XCOSM was the earliest known deconvolution software
available freely on the public domain. Although this software is not updated
anymore and the source is unavailable in the public domain, it served as the
predecessor for some of the other commercial and open-source softwares (like the
ImageTrak) that were developed later.
MATLAB
R
codes
http://bioimageanlysis.org/
∼
praveen/rltv/
There are other stand-alone open-source packages that are command-line based.
One of it is the RL-TV algorithm implemented in this chapter. Although this is
implemented in the commercial software MATLAB
R
, the codes are available as
open-source.
DECONV
https://www.lsdcas.engineering.uiowa.edu/
http://code.google.com/p/iocbio/wiki/IOCBioMicroscope
Other examples of deconvolution algorithms run on command line are the DECONV
[
76
] written in C++ accessible from the LSDCAS website, and the IOCBioMicro-
scope written in Python.
BioImage XD
http://www.bioimagexd.net/
BioImage XD is a collaborative open-source free software project, designed and
developed by microscopists, cell biologists and programmers. It can be used for
analysis and visualization. While writing this chapter, a deconvolution algorithm
was unavailable but it is a feature that might be included in the next release.
Code acceleration by using GPUs
http://gp-you.org/
As mentioned earlier, some of these codes could be accelerated on some graphics
cards. A starting place to look for them are the free GPU toolbox for the NVIDIA
graphics card.
4.4.3.2 Commercial Packages
While the above packages are open-source, commercial microscope manufacturing
companies have their own versions of visualization softwares that are free to
download and use. Here are a few of them:
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