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--- eyes:interactive:contouring [2017/06/12 09:44]
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+++ eyes:interactive:contouring [2017/06/12 17:56] (current)
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 ====== Contouring (Interactive) ======
-The interactive contouring logic can be used to contour the particle of interest within a stack of 2D images or a 3D model. The logic can also be used to design a mask suitable to the specific shape of the particle.
+The interactive contouring logic can be used to manually contour 2D particle images and class averages or 3D volume(s) in a shape-specific manner.
 ===== Usage =====
-As input data a stack of 2D images or a 3D model is required. In order import the data of interest into the contouring logic the PLAY button hast to be pushed once until a blue hourglass appears. By clicking the notepad a new window for the contouring process will be opened.
+Contouring defines the boundary between particle and unwanted particle regions or background-noise - an important step to increase the signal-to-noise ratio and/or to focus image processing on a certain region.
-In the preset //Bezier//-mode or by choosing the //Polyline//-mode single images of the dataset can be contoured using the cursor. With the //Drawing//-mode the area that should be excluded can be marked. The contoured area appears clear whereas the excluded area is shaded. With //Invert-Mask// the whole selection within one image can be inverted.
-At the bottom the current image plus a preview of the previous and the following image are shown. By using the mouse-wheel or clicking the on the previous/next image each image of the stack can be contoured. 3D models are subdivided into single images corresponding to the box size (in pixel).
+As input data a stack of 2D images or a 3D volume is required. Push the PLAY button once to import the data resulting in a blue hourglass. Then click the notepad to start the contouring process in a new window. In the main area, the current slice of the 2D/3D stack to be contoured is shown. At the bottom the current slice and previews of the previous and the following image are shown. Areas to be excluded are overlaid with a mesh, areas to be included are clear. To apply the selection of contoured images the process has to be saved by clicking the SAVE button and then executed with the RUN button.
-To apply the selection of contoured images the process has to be saved by clicking the SAVE button and then executed with the RUN button. For further applications three different output datasets can be selected.
+Different masks ("layers") can be defined to obtain more flexible masks, which may be combined in different ways, also with masks from other contouring sessions.
-  * **Bezier-Mode:** The area of interest can be chosen by using the cursor. By pressing SHIFT while contouring independent areas within one image can be contoured. With CTRL areas which should be excluded can be selected.
+==== Contouring Modes ====
-  * **Poly-Line:** By single mouse clicks the contouring area is connected by lines. By double-clicking the right mouse button inside the selected area the mode can be finished resulting in a clear contoured and a shaded non-contoured area.
+Three different modes are available for contouring, which all act on the slice of the 2D/3D stack shown in the main window:
-  * **Drawing-Mode:** By holding the left mouse button areas that should be excluded can be marked.
+|< 100% 30% >|
+^ Parameters                 ^ Description     ^
+| Bezier-Mode  | A continuous line can be drawn with the cursor by keeping the left mouse button pressed, thereby defining the boundary between particle and background-noise. |
+| Poly-Line | By single mouse clicks the contouring area is connected by lines. By double-clicking the right mouse button inside the selected area the mode can be finished resulting in a clear contoured and a shaded non-contoured area.|
+| Drawing-Mode | By holding the left mouse button areas that should be excluded can be marked. |
+| Invert-Mask | Invert the definition of areas to be included or excluded for the current slice. |
+==== Layers ====
+Use the plus (+) button on the bottom left to add separate masks ("layers"), the minus (-) button to delete selected masks. Overlapping areas of different selected masks can be combined in three different ways: //Union// (all areas of all selected masks are combined), //Intersection// (only overlaps of masks are combined) and //Difference// (only none overlapping parts are combined).  Only masks with checked boxes will be later applied for contouring of the respective slice.
 ===== Shortcuts =====
@@ Line 26: / Line 33: @@
   * excluding specific areas from contouring: CTRL + selection in //Bezier//-mode
+===== Input =====
+|< 100% 30% >|
+^ Input   ^ Description ^
+| Io::in  | Input stack of 2D images/3D volume to be contoured |
+| //Io::input::layer// | Masks (layers) from previous Contouring run |
+===== Output =====
+|< 100% 30% >|
+^ Output   ^ Description ^
+| Io::layer | All masks created as separate layers to be used in another Contouring run |
+| Io::mask | Mask as applied to the image stack  |
+| Io::out | Stack of 2D images/3D volume contoured with selected mask/combination of masks |