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VisuMap Microscopy plugin
VisuMap Microscopy Extension

Overview

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 those data.

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 sites.
  • 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 analysis.
    • KNIME (Konstanz Data Miner): a popular open source data exploration platform that especially targets the field of data mining.
    • HCDC: a software application derived from KNIME that especially targets the field of high content screening and high throughput screening.
Installation

VisuMap.Microscopy 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:

  1. Install VisuMap main software on the target machine. Make sure that the software is running probably with a valid license.
  2. Install the third-party software (e.g. ImageJ, KNIME or HCDC) that VisuMap.Microscopy is going to support.
  3. 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.
  4. 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.
License

This software package is released under the MIT open source license. Please notice that associated third party softwares, like ImageJ and KNIME, are released under different license agreements.

Downloads

VisuMap Microscopy

The installation program for the binary version of the VisuMap.Microscopy extension package.

ImageJ Plugin Source

The source code of the ImageJ plugin.

KNIME Plugin Source
The source code of the KNIME plugin.

      Screenshots

PCA view of particle analysis results of ImageJ:
PCA view of particle analysis results of ImageJ.


Linked data views for data table from KNIME:
Linked data views for data from KNIME




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