Plugins to support

[ctrueden]

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]

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.