Difference between revisions of "VolViewerOMERO"

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It is possible to build VolViewer with support for reading images directly from an OMERO server.  
 
It is possible to build VolViewer with support for reading images directly from an OMERO server.  
  
The viewer can read/write XYZC image stacks with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.
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The viewer can read/write XYZC image stacks from OMERO with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.
  
 
For the C++ implementation details of the OMERO loader please refer to the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.h h] / [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.cpp cpp] files from the SVN.
 
For the C++ implementation details of the OMERO loader please refer to the [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.h h] / [https://cmpdartsvr1.cmp.uea.ac.uk/banghamlabSVN/VolViewer/VolViewer/VolViewer/src/OMEROLoader.cpp cpp] files from the SVN.

Revision as of 16:41, 2 April 2012

Overview

It is possible to build VolViewer with support for reading images directly from an OMERO server.

The viewer can read/write XYZC image stacks from OMERO with up to 3 channels (C). Minimal metadata such as the image dimensions, physical voxel size and channel min/max threshold values are also supported. Currently the viewer supports the following OMERO data types: uint8, uint16, int8, int16.

For the C++ implementation details of the OMERO loader please refer to the h / cpp files from the SVN.

Requirements

To build VolViewer with OMERO support you will require the following:

How To

  • Start by checking out the latest VolViewer source code from the SVN: VolViewer SVN
  • Next build the OMERO cpp libraries following this guide: OMERO cpp libraries
    • To build the OMERO cpp you will require the ICE libraries. Note that these exist in binary form for certain platforms. NB You should only use version 3.3.1 of ICE with OMERO.
  • Now that you have the OMERO cpp library built you are ready to build VolViewer with OMERO support. VolViewer is built using qmake so it is relatively straight forward.
  • Start by enabling the OMERO support in the source code by editing the MyDefines.h file and un-commenting the line:
//#define OMERO_SUPPORT => #define OMERO_SUPPORT
  • Next we turn on OMERO support in the scr.pro project file by adding omero in the CONFIG variable:
CONFIG += qt thread x86_64 => CONFIG += qt thread x86_64 omero
  • Lastly we are now ready to run the qmake command. You will need to set your own paths for the environment variables ICE_HOME and OMERO_HOME.
    • Example build scripts can be found for:

Example Server side scripts

Screenshot

OMERO / VolViewer integration.