Interpolator Plugin Help - TEST FOR MECURIAL....


--------------------------

This plugin allows for rapid segmentation of surfaces by automatically generating "interpolated" contours between the "key" contours which you have manually drawn. Each time you add a new contour, press [Enter] (instead of [n]) and the program will generate interpolated contours between any connected key contours either side of the contour you have just added or modified.
Contours are "connected" if they are within "Z Bridge" slices of each other and the computer believes they are part of the same surface as according to the selected "surface method". The shape of interpolated contours depends on which "interpolation type" you have selected.


Click here to see a video tutorial


List of Interpolation Types
--------------------------

  1. None - lets you use normal contour drawing behavior.
  2. Linear - generates interpolated contours with straight lines between key contours.
  3. Spherical - generates interpolated contours in the profile of sphere, and does not deal with branching.
  4. Smooth - generates interpolated contours such they form a smooth, curved surfaces.
  5. Smooth Pts - as previous, but more sensitive to changes on different sides of the contour.


Hot Key Summary
---------------------
[Enter] Interpolate selected contour and start new contour
[n] Start new contour (without interpolating current contour)
[u] Toggle current contour between key/interpolated
   
[g] Find next gap or isolated contour (NOTE: to enable ghosting, try pressing [ctrl+g])
[h] Find next large hole between key contours (ie. a large region of consecutive interpolated contours)




Tips
---------------------

If you are not happy with the shape of interpolated contours you can either undo [apple+u], add/modify more contours, or change the interpolation options and type. Select 'Clear all Interp' to delete all interpolated contours and 'Regenerate Interp' to regenerate all key contours.

All of these interpolation types are intended for use with closed contours and so may give undesirable results for open or scattered point objects which span multiple slices.

Interpolation can become sluggish for objects with numerous contours. To improve performance you should consider adding an extra object and then use 'edit > object > move' to merge the contours into the desired object periodically.

To segment compartments even faster, try using this "Interpolator" plugin in unison with the "Drawing Tools" plugin.

The best settings to use depend on the size, shape and complexity of the surfaces you are segmenting. For relatively round/simple medium-to-large surfaces I suggest 'Spherical' interpolation with a Z Bridge of maybe 40. If your surfaces are highly branched you may want to change the surface method to 'touching', branching to 'merge conts', reduce Z Bridge and use either 'Linear' or 'Smooth' interpolation. In the end, trial and error is the only way to find the best settings - don't forget you can fine-tune some of these settings by clicking the 'More Settings' button. Note also you can force linear interpolation between the current contour and the last contour you interpolated with [shift+enter], regardless of Z Bridge.

For more information on what each button/option does hover your mouse over it.

---------------------

This plugin was created by Andrew Noske (andrew.noske<at>gmail<dot>com).
If you encounter bugs please e-mail me before e-mailing the IMOD group (to reduce traffic).
In your e-mail please tell me exactly how and when the problem occurred and attach the model file you were using with enough information that I can replicate the error/crash.

NOTE: Maintaining this plugin is part of the is part of the "SLASH segmententation" initiative. Please contact me for citation information.


Acknowledgements: Brad Marsh at the Institute for Molecular Bioscience (www.imb.uq.edu.au) for helping encourage this work - without this nor any of my other plugins would exist. Mark Ellisman and the The National Center for Microscopy and Imaging Research (www.ncmir.ucsd.edu) for ongoing support and funding of these expedited segmentation tools. David Mastronarde and the team at The Boulder Lab for 3-D Electron Microscopy (bio3d.colorado.edu) for their wonderful support of all my plugins.