Merge branch 'connected_components' into 'master'

Connected components

See merge request !39

_includes/connected_components/activities/connected_components_imagejgui.md

+* Open image: xy_8bit_binary__nuclei.tif
+* Perform connected components analysis
+* Explore multi-color LUTs for object labelling
+* Explore removing and joining labels

_modules/connected_components.md

 ---
 title:     Connected components 
-layout:    page
+layout:    module
+prerequisites:
+  - "[Image binarization](binarization)"
+objectives:
+  - TODO
+motivation: >
+  Very often, one wants to detect objects or specific regions in images. After connected_components, the image is divided in background and foreground pixels. The next step is a connected components analysis, where spatially connected regions of foreground pixels are assigned as being part of one region.
+concept_map: >
+  graph TD
+    BI("Binary image") --> CC("Connected component analysis")
+    CC --> LI("Label image")
+    LI --> PV("Integer pixel values")
+    PV --> BG("0: Background")
+    PV --> R1("1: Region 1")
+    PV --> R2("2: Region 2")
+    PV --> R3("...")
+
+figure: /figures/connected_components.png
+figure_legend: Connected component analysis 
+
+activity_preface: >
+  Open a binary image and conduct a connected components analysis.
+
+activities:
+  "ImageJ GUI": "connected_components/activities/connected_components_imagejgui.md"
+#  "MATLAB": "" 
+
+exercises_preface: >
+
+  Fill in the blanks, using these words: less, more, 8, 255, 4, more.
+  
+  1. In 3D, pixels have _____ neighbors than in 2D.
+  1. 8-connected connectivity results in _____ objects than 4-connected connectivity.
+  1. In 3D, pixels have ____ non-diagonal neighbors.
+  1. In 2D, pixels have ____ non-diagonal neighbors.
+  1. A 8-bit label image can maximally have _____ objects.
+  1. The maximum value in a label image is equal to or _____ than the number of objects.
+
+exercises:
+
+learn_next:
+  - "[Split touching objects](object_splitting)"
+  - "[Measure object shapes](measure_shapes)"
+external_links:
+  - "[Wikipedia: Connected components labeling](https://en.wikipedia.org/wiki/Connected-component_labeling)"
 ---
-
-## Connected components analysis
-
-<img src='https://g.gravizo.com/svg?
- digraph G {
-    shift [fontcolor=white,color=white];
-    "intensity image" -> "connected component analysis" -> "label image";
-    connectivity -> "connected component analysis";
-  }
-'/>
-
-
-### Activity: 2D connected components analysis
-
-* Open image: xy_8bit_binary__nuclei.tif
-* Perform connected components analysis
-* Explore multi-color LUTs for object labelling
-* Explore removing and joining labels
-
-
-### Activity: 3D connected components analysis
-
-Repeat above activity but use a 3D image:
-
-* Open image: xyz_8bit_binary__spots.tif
-
-### Formative assessment
-
-Fill in the blanks, using these words: less, more, 8, 255, 4, more.
-
-1. In 3D, pixels have _____ neighbors than in 2D.
-2. 8-connected connectivity results in _____ objects than 4-connected connectivity.
-3. In 3D, pixels have ____ non-diagonal neighbors.
-4. In 2D, pixels have ____ non-diagonal neighbors.
-5. A 8-bit label image can maximally have _____ objects.
-6. The maximum value in a label image is equal to or _____ than the number of objects.
-
-## Learn next
-
-- shape_measurements.md

module_templates/template.md

+---
+title:     
+layout:    
+prerequisites:
+  - "[some text](module)"
+objectives:
+  - some text
+motivation: >
+  some text
+concept_map: >
+  graph TD
+    BI("Binary image") --> CC("Connected component analysis")
+    CC --> LI("Label image")
+
+figure: /figures/this_module.png
+figure_legend: Connected component analysis 
+
+activity_preface: >
+
+activities:
+#  "ImageJ GUI": "this_module/activities/this_module_ijgui.md"
+#  "ImageJ Macro": "this_module/activities/this_module_ijmacro.md"
+#  "Jython": "this_module/activities/this_module_jython.md"
+#  "MATLAB": "this_module/activities/this_module_matlab.md"
+
+exercises_preface: >
+
+exercises:
+#  "ImageJ GUI": "this_module/exercises/this_module_imagejgui.md"
+#  "ImageJ Macro": "this_module/exercises/this_module_imagejmacro.md"
+#  "Jython": "this_module/exercises/this_module_jython.md"
+#  "MATLAB": "this_module/exercises/this_module_matlab.md"
+
+learn_next:
+  - "[some text](module)"
+external_links:
+
+---