Commit 23b63e17 authored by Christian Tischer's avatar Christian Tischer

EMBL Course

parent 41e02bc1
......@@ -49,28 +49,28 @@ True or false?
LUT -> brightness;
min -> LUT;
max -> LUT;
"pixel value" -> LUT;
value -> LUT;
}
'/>
```
brightness(pixel_value) = ( pixel_value * LUT_min ) / ( LUT_max - LUT_min )
brightness = ( value - min ) / ( max - min )
0 <= brightness <= 1
contrast = LUT_max * LUT_min
contrast = max - min
```
### Activity
* Open image: `xy_8bit__nuclei_noisy_different_intensity.tif`
* Change LUT settings
* Explore different LUTs and LUT settings
* Appreciate that LUT settings do not affect image content.
### Formative Assessment
Fill in the blanks:
decrease, larger_than, increase, smaller_than
Fill in the blanks, using those words: decrease, larger_than, increase, smaller_than
* Pixels with values _____ the `LUT_max` will appear saturated.
* Decreasing `LUT_max` while keeping `LUT_min` constant will _____ the contrast.
......@@ -118,20 +118,20 @@ What are good reasons to change the pixel values in an image?
* Open image: `xy_8bit__nuclei_noisy_different_intensity.tif`
* Appreciate the significant background intensity
* Measure pixel value at `[ 28, 35 ]` and `[ 28, 39 ]`
* Measure background intensity in below region:
* Measure pixel values at `[ 28, 35 ]` and `[ 28, 39 ]`
* Measure the image background intensity in this region:
* upper left corner at `[ 20, 35 ]`
* width = 10
* height = 10
* Subtract the measured background intensity from each pixel.
* Measure pixel values again.
* Measure the pixel values again.
* Observe that the resuls are incorrect.
Repeat above activity, but:
* After opening the image, convert its data type to floating point.
### Activity: Limitations of float
### Activity: Explore the limitations of `float` data type
* Create an empty image
* Set all pixel values to 1000000000.0
......@@ -165,8 +165,8 @@ True or false?
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"pixel_type_conversion" -> "pixel_values" [label=" can change"];
"pixel_type_conversion" -> pixel_value_range [label=" changes"];
"data type conversion" -> "values" [label=" can change"];
"data type conversion" -> "value range" [label=" changes"];
}
'/>
......@@ -219,8 +219,8 @@ In order to find objects in a image, the first step often is to determine whethe
"background value" -> "0";
"foreground value" -> "1";
"foreground value" -> "255";
value -> ">= threshold" -> foreground;
value -> "< threshold" -> background;
"pixel value" -> ">= threshold" -> foreground;
"pixel value" -> "< threshold" -> background;
}
'/>
......@@ -258,7 +258,7 @@ True or false? Discuss with your neighbor!
### Activity: 2D connected components analysis
* Open image: `xy_8bit_binary__nuclei.tif`
* Open image: xy_8bit_binary__nuclei.tif
* Perform connected components analysis
* Explore multi-color LUTs for object labelling
* Explore removing and joining labels
......@@ -268,13 +268,11 @@ True or false? Discuss with your neighbor!
Repeat above activity but use a 3D image:
* Open image: `xyz_8bit_binary__spots.tif`
* Open image: xyz_8bit_binary__spots.tif
### Formative assessment
Fill in the blanks:
less, more, 8, 255, 4, more.
Fill in the blanks, using these words: less, more, 8, 255, 4, more.
* For a given input image there is only one correct connectivity.
* In 3D, pixels have _____ neighbors than in 2D.
......@@ -353,9 +351,7 @@ Which statements are true? Discuss with your neighbor!
### Formative assessment
Fill in below blanks, using these words:
equal_to, larger_than, smaller_than, binary, connected_component_analysis, thresholding
Fill in below blanks, using these words: equal_to, larger_than, smaller_than, binary, connected_component_analysis, thresholding
* A label image is the result of _____ .
* The number of pixels in a binary image is typically _____ the number of connected components.
......@@ -409,9 +405,7 @@ There are several good reasons not to subtract the background from each pixel in
### Formative assessment: Intensity measurements
Fill in below blanks with those words:
integrated, mean, number_of_pixels, decrease, increase, sum
Fill in the blanks, using these words: integrated, mean, number_of_pixels, decrease, increase, sum
* Average intensity is just another word for _____ intensity.
* The _____ intensity is equal to the mean intensity times the _____ in the measured region.
......
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