VisuMap Microscopy Extension
VisuMap.Microscopy is an extension package for VisuMap
software system, it provides additional services for microscopy related
data analysis. Modern microscopy technology
has enabled people to investigate objects not only in
ever shrinking scales, but also to
explore increasingly larger number
of objects due to the rapid development of
high content scanning (HCS) technologies. As large
amount of data become available, there is a growing
demand on methods and tools to process and analysis
Data collected from microscopy study is often of high
dimensional nature. For instance, in biological and pharmaceutical
research datasets are often biochemical and morphological parameters
about large number of entities, like cells from
cellular system. VisuMap.Microscopy aims to help people to analysis
such high dimensional data by leveraging the visual analytics services
in VisuMap software system.
VisuMap.Microscopy provides the
following services to support microscopy
related data analysis:
- An plugin for VisuMap that exposes
essential services of VisuMap system through the SOAP (simple object
access protocol) protocol, so that third party systems or software applications
can communicated with VisuMap from local or remote
- Implementation of a set of microscopy
specific data analysis services. These services are made accessible to
the end user through VisuMap's scripting interface.
- A collection of plugin modules for
third party software applications to simplify communication with
VisuMap. Currently the following third party applications are supported:
- ImageJ: a
widely used open source software application for image processing and
(Konstanz Data Miner): a popular open source data exploration
platform that especially targets the field of data mining.
a software application derived from KNIME that especially targets the
field of high content screening and high throughput screening.
is implemented as a plugin module for the VisuMap software system, and
it is deployed through a single windows setup program
MicroscopySetup.msi. The installation procedure of the plugin
goes normally as follows:
- Install VisuMap main software on the target machine.
Make sure that the software is running probably with a valid license.
- Install the third-party software (e.g. ImageJ, KNIME
or HCDC) that VisuMap.Microscopy is going to support.
- Obtain VisuMap.Microscopy setup program
( e.g. MicroscopySetup.msi ) and run the setup program. The
setup program will normally install appropriate components depending on
the location of VisuMap installation and of third-party applications.
- Start VisuMap and perform needed post configuration.
After installed the plugin module, the main window of VisuMap
will get a new menu with the label "Microscopy". The new menu
enables users to configure the plugin and access other services.
This software package is released under
open source license. Please notice that associated third
softwares, like ImageJ and KNIME, are released under different license