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Ticket #163 (closed enhancement: moved)

Opened 2007-08-01T16:51:27-05:00

Last modified 2014-01-09T13:13:14-06:00

Expand VisBio as a toolkit with scriptable components

Reported by: curtis Owned by: curtis
Priority: critical Milestone: visbio5.0
Component: visbio Severity: serious
Keywords: Cc:
Blocked By: Blocking:

Description (last modified by curtis)

VisBio already has some connectivity with ImageJ, and with MATLAB, but this functionality is far from complete. As VisBio is modularized (delegating much of the import, export, caching and thumbnailing logic to Bio-Formats; relying on OME Notes for metadata editing; etc.), it should be fairly straightforward to create hooks to access this modular functionality from a variety of infrastructures:

  • ImageJ, as a series of plugins, and macro function wrappers for those plugins
  • MATLAB, from within the environment
  • Jython (Python in Java)
  • Jacl (TCL in Java)

For each infrastructure, it should be possible to construct a script that imports microscopy data, does some computation, and exports and/or visualizes the result, using the VisBio infrastructure as appropriate.

As a proof of concept, one or more "VisBio lite" scripts will be created for each supported infrastructure that build and display a stripped down VisBio GUI demonstrating some of the functionality possible within that infrastructure.

Change History

comment:1 Changed 2014-01-09T13:13:14-06:00 by curtis

  • Status changed from new to closed
  • Resolution set to moved
  • Description modified
  • Severity set to serious