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! ...@@ -322,7 +322,11 @@ True or false? Discuss with your neighbour!
### Learn more ### 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 { ...@@ -41,7 +41,9 @@ digraph G {
### Learn more ### Learn more
- https://imagescience.org/meijering/software/featurej/
- https://en.wikipedia.org/wiki/Difference_of_Gaussians - https://en.wikipedia.org/wiki/Difference_of_Gaussians
- https://github.com/CellProfiler/CellProfiler/blob/master/cellprofiler/modules/enhanceorsuppressfeatures.py#L4
### Formative Assessment ### Formative Assessment
......
...@@ -6,8 +6,10 @@ ...@@ -6,8 +6,10 @@
digraph G { digraph G {
shift [fontcolor=white,color=white]; shift [fontcolor=white,color=white];
"rank filters" -> awesome [label=" are"]; "rank filters" -> awesome [label=" are"];
"rank filters" -> minimum -> erosion [label=" aka"]; "rank filters" -> minimum;
"rank filters" -> maximum -> dilation [label=" aka"]; minimum -> erosion [label=" aka"];
"rank filters" -> maximum;
maximum -> dilation [label=" aka"];
"rank filters" -> median; "rank filters" -> median;
"rank filters" -> "size" [label=" have"]; "rank filters" -> "size" [label=" have"];
} }
...@@ -16,7 +18,7 @@ ...@@ -16,7 +18,7 @@
### Activity: Explore rank filters on binary images ### Activity: Explore rank filters on binary images
- Open image: xy_8bit_binary__two_spots_different_size.tif - 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 ### Activity: Explore rank filters on grayscale images
...@@ -51,7 +53,7 @@ Fill in the blanks, using those words: shrinks, increases, decreases, enlarges. ...@@ -51,7 +53,7 @@ Fill in the blanks, using those words: shrinks, increases, decreases, enlarges.
"opening" -> "rank filter sequence" [label=" is"]; "opening" -> "rank filter sequence" [label=" is"];
"closing" -> "rank filter sequence" [label=" is"]; "closing" -> "rank filter sequence" [label=" is"];
"opening" -> "removes small structures"; "opening" -> "removes small structures";
"closing -> "fills small gaps"; "closing" -> "fills small gaps";
} }
'/> '/>
...@@ -60,17 +62,17 @@ opening( image ) = dilation( erosion( image ) ) ...@@ -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 ### Activity: Explore opening and closing on binary images
- Open image: xy_8bit_binary__for_open_and_close.tif - Open image: xy_8bit_binary__for_open_and_close.tif
- Explore the effect of morphological closing and opening - Explore effects of morphological closing and opening:
- Closing can fill the hole - closing can fill holes
- Closing can connect the circle - closing can connect gaps
- Opening can remove thin structures - opening can remove thin structures
### Formative assessment ### Formative assessment
...@@ -83,14 +85,14 @@ TODO ...@@ -83,14 +85,14 @@ TODO
<img src='https://g.gravizo.com/svg? <img src='https://g.gravizo.com/svg?
digraph G { digraph G {
shift [fontcolor=white,color=white]; shift [fontcolor=white,color=white];
"top hat filter" -> "rank filter sequence" [label=" is"]; "tophat filter" -> "rank filter sequence" [label=" is"];
"top hat filter" -> "local background subtraction"; "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 TODO: Add image from pdf
...@@ -99,16 +101,18 @@ TODO: Add image from pdf ...@@ -99,16 +101,18 @@ TODO: Add image from pdf
### Activity: Explore tophat filter ### Activity: Explore tophat filter
- Open image: xy_8bit__spots_local_background.tif - 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 ## 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 ## Activity: Explore tophat filter on biological data
- Open image: xy_16bit__autophagosomes.tif - 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 ## Activity: Explore tophat fiter on noisy data
...@@ -124,7 +128,7 @@ TODO ...@@ -124,7 +128,7 @@ TODO
## Median filter for local background subtraction ## Median filter for local background subtraction
<img src='https§://g.gravizo.com/svg? <img src='https://g.gravizo.com/svg?
digraph G { digraph G {
shift [fontcolor=white,color=white]; shift [fontcolor=white,color=white];
"median" -> "local background"; "median" -> "local background";
...@@ -160,7 +164,9 @@ TODO ...@@ -160,7 +164,9 @@ TODO
## Learn more
- https://imagej.net/MorphoLibJ#Grayscale_morphological_filters
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