Drawing Tools Plugin Help


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This plugin provides a set of drawing tools which allows you to rapidly draw, modify and erase contours. To use these tools make sure 3dmod is on "Model" mode, the "Drawing Tools" plugin window is open and you've selected the "Draw Mode" you wish to use. Notice in the Zap window that many of the tools use a red "sculpt circle", the size of which can be changed using the mouse wheel or the keys [q] and [w].

Click here to see the video tutorial


List of Default Drawing Modes
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  1. Normal - lets you use normal contour drawing behavior.
  2. Warp - allows you to quickly correct bad regions of contour by warping [second_button] or warp-and-smoothing [third_button] the contour points closest to (if you click on a contour) or within (if you click near a contour) the sculpt circle. Holding [shift+third_button] lets you break apart contours.
  3. Sculpt - lets you quickly draw contours by holding the point addition mouse button [second_button] and pushing the contour outwards or inwards with the sculpt circle. Holding down [shift] as well lets you will pinch contours toward the center instead.
  4. Join - is similar to Sculpt, but also allows you to merge two contours by pushing one contour over another or split a contour by pushing a gap through the middle. Using [third_button] lets you join or split contours using a rectangle.
  5. LiveWire - an edge detection tool to help you quickly trace around dark membranes [second_button], similar to the "magnetic lasso" tool in Photoshop. For more details, see the Tips section below. *
  6. The Wand - an adaptive flood filling algorithm where you can click and drag [second_button] to rapidly fill in an area of similar greyscale. Using the [third_button] you can use the little scuplt circle to make minor touchups to the selected contour.
  7. Eraser - allows you to delete contours [second_button] or points [third_button] touching the sculpt circle. Holding [shift+second_button] lets you break apart contours.
  8. Measure - allows you to draw a straight line between any two points [second_button] and displays the distance between these points in the relevant units.

* With the LiveWire tool be warned that it doesn't work on certain images. Either it works brilliantly or not at all. It should crash much less than it used to; if it crashes for you, be sure to save regularly and please report the problem.

Extra Drawing Modes
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NOTE: The list above shows the default order of drawing tools, but by clicking any of the numbers (to the right of the tools) it's possible to change the order and/or add to the list one of these other modes:

 


Hot Key Summary
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[1]-[9] Select corresponding draw mode (see above)
[w] Increase size of sculpt circle (hold shift to go faster)
[q] Decrease size of point painter circle.
   
[r] Reduce current contour
[e] Smooth current contour by moving points
[E] Smooth current contour without moving existing points
   
[a] Find next intersecting contour edge
[i] Invert points in current contour
[I] Reorder points in current contour to start at selected point
   
[y] Go to next largest value using find property (see: More Actions - find points/contours)
[Y] Go to next smallest value using find property
[l] Recalculate values of contours/points using find property and select the smallest
[L] Recalculate values of contours/points using find property and select the largest
   
[ctrl+x] Cut current contour
[ctrl+c] Copy current contour
[ctrl+v] Paste contour into current slice and object, centered on mouse
[ctrl+V] Paste contour into current slice and object in same XY position
   
[space] Copy current contour to current slice (use also [?])
[shift] Hold Shift down to alter the behavior of certain draw modes





Tips
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Holding and dragging [shift+first_button] allows you to quickly scroll up and down through the slices.

Be warned that the sculpt and join tool were designed for 2D closed contours and so I would not recommend using these tools with open or scattered contours which span multiple slices.

To use the Livewire, click to add the first point of a contour, move the mouse to another point along the membrane, and click to add the segment if it follows the membrane well enough. You can finish the contour by clicking close enough to the starting point; or, if the line forward to the starting point follows the membrane from the last point added, you can just click again near that last point to complete the contour. Smoothing occurs after the contour is finished.
If you select a contour using the "transform" tool, you can copy it to nearby slices by simply scrolling to a different slice and mouse clicking [second_button]. In this way transform can be useful to quickly mark-up simple shapes.
The join tool and, to a lesser extent, the sculpt tool 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.

Another way to improve performance can be to reduce contours. Use 'Reduce Contour' to reduce the current contours, by selectively removing points, or 'Reduce Object' to reduce ALL contours in the current object. Use 'Smooth Contour' to smooth the current contours, by adding points, or 'Smooth Object' to smooth ALL contours in the current object.
Reducing objects can often substantially reduce the number of points in the model, but be very careful you don't lose information in the process.

Under More Actions are a number of other options to sort, transform, move, copy, expand and modify contours. These have been listed in more detail below and it's recommended you read about them all - especially the 'crop contours' feature.

In 3dmod (without the drawing tool plugin) there are several useful drawing tools you might not know about:

  1. You can select multiple contours by holding [ctrl+first_button].
  2. You can delete points by holding [shift+third_button].
  3. You can transform selected contour(s) by toggling the Zap "contour transform mode" with [P] - this mode is similar to the "transform" drawing tool.

More Actions
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In addition to the options on the plugin you can see, a large number of additional tools are available when you click the "More Actions" button. A small description of each is written below. Note that most of these tools allow you to specify a range of contours and/or apply the action to only dotted or solid contours.

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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. Jeffrey Bush at the The National Center for Microscopy and Imaging Research (www.ncmir.ucsd.edu) for helping me add the amazing LiveWire code, and Mark Ellisman for encouraging us to give back to IMOD. 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.