diff --git a/doc/MorphoLibJ-manual/MorphoLibJ-manual.lyx b/doc/MorphoLibJ-manual/MorphoLibJ-manual.lyx index 0ac77707..294f1844 100644 --- a/doc/MorphoLibJ-manual/MorphoLibJ-manual.lyx +++ b/doc/MorphoLibJ-manual/MorphoLibJ-manual.lyx @@ -15264,7 +15264,15 @@ label maps each pixel or voxel of a label image corresponds to the integer index of the particle it belongs to. By convention, the value 0 corresponds to the background. - Label images are typically computed from binary images by connected component algorithms (section + +\end_layout + +\begin_layout Standard +Label images are typically computed from binary images by +\series bold +connected component algorithms +\series default + (section \begin_inset CommandInset ref LatexCommand ref reference "sec:Connected-Components-Labeling" @@ -15281,7 +15289,7 @@ status open \backslash -hyperref[sec:Morphological-Segmentation-Plugin]{Watershed} +hyperref[sec:Morphological-Segmentation-Plugin]{watershed} \end_layout \end_inset @@ -15289,6 +15297,16 @@ hyperref[sec:Morphological-Segmentation-Plugin]{Watershed} may also return their result as a label image. \end_layout +\begin_layout Standard +This chapter presents several utilities for managing label maps, + in particular for facilitating their visualisation, + to convert them into ROI, + or to visualize the result of region features. + Several plugins allows for selecting or filtering label maps, + some of them being implemented into the Label Edition Plugin. + +\end_layout + \begin_layout Standard \begin_inset ERT status open @@ -15732,7 +15750,7 @@ status open \begin_layout Plain Layout GlasbeyBright, - White + Black \end_layout \end_inset @@ -15952,7 +15970,36 @@ Conversion to ROI \begin_layout Standard When working with label maps, it is often convenient to convert one or several regions into a Region Of Interest (ROI) that can be managed by the ROI Manager from ImageJ. - Several macros and plugins have been developed for this. + Several macros and plugins have been developed for this, + see for example the BIOP plugin +\begin_inset Quotes eld +\end_inset + +Label image to ROIs +\begin_inset Quotes erd +\end_inset + + +\begin_inset Foot +status collapsed + +\begin_layout Plain Layout +\begin_inset Flex URL +status collapsed + +\begin_layout Plain Layout + +https://github.com/BIOP/ijp-LaRoMe +\end_layout + +\end_inset + + +\end_layout + +\end_inset + +. MorphoLibJ also provides a plugin \begin_inset Quotes eld \end_inset @@ -16015,7 +16062,7 @@ nolink "false" \begin_layout Description Name_Pattern the string pattern used to name each ROI. - When a boundary of a region is composed of several polygons, + When the boundary of a region is composed of several polygons, they are identified by a trailing dash and index. Example: @@ -16035,7 +16082,7 @@ placement document alignment document wide false sideways false -status open +status collapsed \begin_layout Plain Layout \align center @@ -16044,7 +16091,7 @@ placement document alignment document wide false sideways false -status collapsed +status open \begin_layout Plain Layout \align center @@ -16077,7 +16124,7 @@ placement document alignment document wide false sideways false -status collapsed +status open \begin_layout Plain Layout \align center @@ -16110,7 +16157,7 @@ placement document alignment document wide false sideways false -status collapsed +status open \begin_layout Plain Layout \align center