Commit 984bdf41 authored by Christian Tischer's avatar Christian Tischer

EMBL Course

parent ae1e149d
......@@ -322,7 +322,11 @@ True or false? Discuss with your neighbour!
### Learn more
* Especially surface and perimeter measurements are affected by sampling and resolution (see for example: https://en.wikipedia.org/wiki/Coastline_paradox).
* Especially surface and perimeter measurements are affected by sampling and resolution, see for example:
* https://en.wikipedia.org/wiki/Coastline_paradox).
* Results visualisation:
* https://imagej.net/MorphoLibJ#Grayscale_morphological_filters: **Label visualization in 3D viewer**
 
......
......@@ -41,7 +41,9 @@ digraph G {
### Learn more
- https://imagescience.org/meijering/software/featurej/
- https://en.wikipedia.org/wiki/Difference_of_Gaussians
- https://github.com/CellProfiler/CellProfiler/blob/master/cellprofiler/modules/enhanceorsuppressfeatures.py#L4
### Formative Assessment
......
......@@ -6,8 +6,10 @@
digraph G {
shift [fontcolor=white,color=white];
"rank filters" -> awesome [label=" are"];
"rank filters" -> minimum -> erosion [label=" aka"];
"rank filters" -> maximum -> dilation [label=" aka"];
"rank filters" -> minimum;
minimum -> erosion [label=" aka"];
"rank filters" -> maximum;
maximum -> dilation [label=" aka"];
"rank filters" -> median;
"rank filters" -> "size" [label=" have"];
}
......@@ -16,7 +18,7 @@
### Activity: Explore rank filters on binary images
- Open image: xy_8bit_binary__two_spots_different_size.tif
- Explore how the structures grow and shrink when using erosion and dilation
- Explore how structures grow and shrink, using erosion and dilation
### Activity: Explore rank filters on grayscale images
......@@ -51,7 +53,7 @@ Fill in the blanks, using those words: shrinks, increases, decreases, enlarges.
"opening" -> "rank filter sequence" [label=" is"];
"closing" -> "rank filter sequence" [label=" is"];
"opening" -> "removes small structures";
"closing -> "fills small gaps";
"closing" -> "fills small gaps";
}
'/>
......@@ -60,17 +62,17 @@ opening( image ) = dilation( erosion( image ) )
```
```
closing( image ) = erosion( dilation ( image ) )
closing( image ) = erosion( dilation( image ) )
```
### Activity: Explore opening and closing on binary images
- Open image: xy_8bit_binary__for_open_and_close.tif
- Explore the effect of morphological closing and opening
- Closing can fill the hole
- Closing can connect the circle
- Opening can remove thin structures
- Explore effects of morphological closing and opening:
- closing can fill holes
- closing can connect gaps
- opening can remove thin structures
### Formative assessment
......@@ -83,14 +85,14 @@ TODO
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"top hat filter" -> "rank filter sequence" [label=" is"];
"top hat filter" -> "local background subtraction";
"tophat filter" -> "rank filter sequence" [label=" is"];
"tophat filter" -> "local background subtraction";
}
'/>
```
topHat( image ) = image - dilation( erosion( image, r), r )
tophat( image ) = image - dilation( erosion( image, r), r )
```
TODO: Add image from pdf
......@@ -99,16 +101,18 @@ TODO: Add image from pdf
### Activity: Explore tophat filter
- Open image: xy_8bit__spots_local_background.tif
- Use topHat filter to remove local background
- Use a tophat filter to remove local background
## Activity: Implement a tophat filter
- Devise code to implement a tophat filter using basic functions
- Devise code implementing a tophat filter, using minimum and maximum filters
## Activity: Explore tophat filter on biological data
- Open image: xy_16bit__autophagosomes.tif
- Use topHat filter to remove local background
- Appreciate that you cannot readliy segment the spots.
- Use a tophat filter to remove local background.
- Threshold the spots in the tophat filtered image.
## Activity: Explore tophat fiter on noisy data
......@@ -124,7 +128,7 @@ TODO
## Median filter for local background subtraction
<img src='https§://g.gravizo.com/svg?
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"median" -> "local background";
......@@ -160,7 +164,9 @@ TODO
## Learn more
- https://imagej.net/MorphoLibJ#Grayscale_morphological_filters
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment