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Morphological Segmentation

2,099 bytes added, 01:48, 4 September 2019
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| source = {{GitHub|org=ijpb|repo=MorphoLibJ}}
| released = July 3<sup>rd</sup>, 2014
| latest version = January 12July 23<sup>thrd</sup>, 2016 2019 ([[MorphoLibJ]] v1.14.1)
| status = stable, active
| category = [[:Category:Segmentation|Segmentation]], [[:Category:Mathematical_morphology|Mathematical morphology]]
|style="vertical-align:top" |[[Image:Morphological-Segmentation-animation-blobs.gif|thumb|300px|Visual description of the different steps of the Morphological Segmentation plugin.]]
* '''Tolerance''': dynamic of intensity for the search of regional minima (in the extended-minima transform, which is the regional minima of the H-minima transform, value of h). Increasing the tolerance value reduces the number of segments in the final result, while decreasing its value produces more object splits.
: <b><span style="color:#f80000">Note</span></b>: since the tolerance is an intensity parameter, it is sensitive to the input image type. A tolerance value of 10 is a good starting point for 8-bit images (with 0-255 intensity range) but it should be drastically increased when using image types with larger intensity ranges. For example to ~2000 when working on a 16-bit image (intensity values between 0 and 65535).
* '''Calculate dams''': un-check this option to produce segmentations without watershed lines.
* '''Connectivity''': voxel connectivity (4-8 in 2D, and 6-26 in 3D). Selecting non-diagonal connectivity (4 or 6) usually provides more rounded objects.
[[Image:Morphological-segmentation-result-examples.png|thumb|center|770px|Examples of the 4 different display options]]
=== Post-processing panel ===
[[Image:Morphological-segmentation-post-processing-panel.png|right|thumb|250px|Post-processing panel]]Similarly to the Results panel, this panel only gets enabled after running the segmentation pipeline.
* '''Merge labels''': merge together labels selected by either the '''“freehand” selection too'''l (on a single slice) '''or the point tool''' (on single or multiple slices). The zero-value label belongs to the watershed dams, therefore it will ignored in case of being selected. The first selected label value will be assigned to the rest of selected labels, which will share its color.
: <b><span style="color:#f80000">Note</span></b>: to select labels on different slices, use the point selection tool and keep the SHIFT key pressed each time you click on a new label.
* '''Shuffle colors''': randomly re-assign colors to the labels. This is a very handy option whenever two adjacent labels present a similar color.
== Video tutorials ==
=== Quick start guide ===
This introductory screencast (which needs audio) explains the basic use of the plugin:
=== Segmentation of a 3D image ===
This video tutorial (with audio as well) shows how to use the plugin segment a 3D image (confocal image of an ''Arabidopsis thaliana'' embryo, courtesy of Jean-Christophe Palauqui (INRA-Versailles)):
== Macro language compatibility ==
== Examples ==
|style="vertical-align:top" |[[Image:Arabidopsis-embryo-3d-animation.gif|thumb|300px|3d reconstruction of an ''Arabidopsis Thalianathaliana'' embryo using the Morphological Segmentation plugin. Image courtesy of Jean-Christophe Palauqui (INRA-Versailles)]]
== Citation ==
If you need to cite the plugin, please do so by citing the following paper:
* {{Publication | MorphoLibJ}}
To cite the implementation, [[MorphoLibJ]]'s code repository has its own [ DOI].
== References ==
# Meyer, Fernand, and Serge Beucher. "Morphological segmentation." Journal of visual communication and image representation 1.1 (1990): 21-46.
# Soille, P., "Morphological Image Analysis: Principles and Applications", Springer-Verlag, 1999, pp. 170-171.
== See also ==
* [[Marker-controlled Watershed]], a plugin to perform watershed by flooding from specific seed points or markers.
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