Commit 45f75824 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi

Merge branch 'connected_components' into 'master'

Connected components

See merge request grp-bio-it/image-analysis-training-resources!39
parents 714ff3d0 acc4f3eb
Pipeline #10610 passed with stage
in 1 minute and 15 seconds
* Open image: xy_8bit_binary__nuclei.tif
* Perform connected components analysis
* Explore multi-color LUTs for object labelling
* Explore removing and joining labels
---
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
---
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:
---
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