Biomedical Engineering Reference
In-Depth Information
Image Database from La Jolia, California
http://ccdb.ucsd.edu/data/index.shtm
The Cell centered database (CCDB): The CCDB (La Jolla, California, USA) is a
web accessible database for high resolution 2-D, 3-D and 4-D data from light and
electron microscopy, including correlated imaging. Techniques range from wide
field mosaics taken with multi-photon microscopy to 3-D reconstructions of cellular
ultrastructure using electron tomography. While many of the data sets are derived
from the nervous system, the CCDB contains data from many systems. For each
dataset, the CCDB makes available the raw data, reconstructions derived from the
raw data and any segmentations and analysis performed on the data. They also
accept contributions of data from the scientific community.
4.4.3 Software
A large variety of software packages are available for deconvolution and visualiza-
tion. The softwares can be either commercial or open-source packages, and each
have their pros and cons. Roughly, deconvolution algorithms currently available in
the market can be classified into two types. The first category increases the net
contrast but might not remove the out-of-focus light. These are fast, involve
moderate number of calculations, but the obtained images are non-quantitative.
The second category represents more advanced image restoration algorithms that
removes the out-of-focus light and conserve the quantitative fluorescence intensities.
4.4.3.1 Open-Source Packages
ImageJ developed at National institutes of health (NIH)
http://rsb.info.nih.gov/ij/
The single most widely used open-source package for microscopy is the Java-based
engine ImageJ developed at the NIH. The ImageJ, when introduced, was truly
revolutionary because it is light, easily portable and works on multi-OS without
installation. The only requirement is that Java needs to be pre-installed. The software
that is available online is the basic version and does not support all the microscope
image formats. However, any additional feature can be easily added with the help of
some 'plugins' and individuals can write their own 'macros' to automate the tasks.
McMaster Biophotonics plugin database
http://www.macbiophotonics.ca/downloads.htm
The ImageJ users community contributed a lot to the development of many plugins.
A compiled list of some of the essential ones can be found at the McMaster
Biophotonics facility site along with the instructions for the installation.
FIJI
http://fiji.sc/
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