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Plugins to support #48

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ctrueden opened this Issue Aug 18, 2014 · 1 comment

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ctrueden commented Aug 18, 2014

Some OME users have requested that we endeavor to make ImageJ2 compatible with certain plugins. If possible we should preferentially support them. This ticket is a placeholder feature ticket. More specific blocking tickets should be hatched as plans for the support of these plugins is planned.

The list of mentioned plugins include:

  • Image/stacks/Z project
  • Image/stacks/orthogonal views
  • stacks/tools/combine
  • stack/tools/slice remover
  • image/transform/ "all the different options"
  • image/adjust/threshold
  • process/binary/make binary
  • process/math/ "all the different options"
  • process/image calculator
  • analyse/tools/ROI manager
  • analyse/set measurements
  • analyse/measure
  • process/macros/run "used with custom macros"
  • denoising (bilateral filter)
  • deconvolution (deconvolution lab and/or Bob Dougherty's iterative 3D)
  • normalization (normalize local contrast, quantile-based?)
  • enhance local contrast (CLAHE in 3D)
  • 3D spatial filters (mean, median, gaussian, convolve)
  • 3D FFT and bandpass
  • registration (stackreg, turboreg)
  • SPIM registration & multi-view fusion
  • FeatureJ (Laplacian, Hessian) and/or surfaceness, tubeness, vesselness
  • Weka machine learning / segmentation
  • Tracking (TrackMate)
  • colocalization: coloc_2, JACoP
  • batch macro runner

For more context regarding the specific plugin list and the history of these ideas see http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2013-March/002375.html.

Migrated-From: http://trac.imagej.net/ticket/1878

@ctrueden ctrueden added this to the 1.1.0 milestone Aug 18, 2014

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ctrueden May 31, 2018

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Many of these will now work from ImageJ scripts on the server side. Users need to do a little bit of legwork to create such scripts. Any commands above that do not work headless will not work (and will never work as such), though similar headless-friendly commands could be created. That would be outside the scope of ImageJ-OMERO, though.

I'm going to close this general issue, but please open issues for specific non-working commands that you would like to help getting supported by ImageJ-OMERO.

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ctrueden commented May 31, 2018

Many of these will now work from ImageJ scripts on the server side. Users need to do a little bit of legwork to create such scripts. Any commands above that do not work headless will not work (and will never work as such), though similar headless-friendly commands could be created. That would be outside the scope of ImageJ-OMERO, though.

I'm going to close this general issue, but please open issues for specific non-working commands that you would like to help getting supported by ImageJ-OMERO.

@ctrueden ctrueden closed this May 31, 2018

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