| [Enter] | Interpolate selected contour and start new contour |
| [n] | Start new contour (without interpolating current contour) |
| [u] | Toggle current contour between key/interpolated |
| [;] | Open dialog to change the marking of contours in a selected range from interpolated to key, or vice-versa. The way to get contours drawn with solid lines is to mark them as key. |
| [g] | Find next gap or isolated contour (NOTE: to toggle ghosting, press [ctrl+shift+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 [Ctrl+Z], 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
"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.