Commit 229cd4fb authored by Christian Tischer's avatar Christian Tischer

Update bioimage-analysis-fundamentals.md

parent 8faed5db
......@@ -70,17 +70,16 @@ decrease, larger_than, increase, smaller_than
- Decreasing both `LUT_max` and `LUT_min` will _____ the overall brightness.
- Pixels with values _____ the `LUT_min` will appear black, when using a grayscale LUT.
   
## Image math and pixel data types
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"data type" -> "pixel values" [label=" restricts"];
"data type" -> "pixel values" [label=" restricts"];
"image math" -> "pixel values" [label=" changes"];
"N-bit unsigned integer" -> "0, 1, ..., 2^N-1";
"data type" -> float -> "..., -1031.111, ..., 10.5, ...";
"data type" -> "...";
"data type" -> float -> "e.g., -1031.111, 10.5";
"data type" -> "N-bit unsigned integer";
}
'/>
......@@ -101,20 +100,20 @@ What are good reasons to change the pixel values in an image?
### Activity: Pixel based background subtraction
- 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:
- upper left corner at `[ 20, 35 ]`
- width = 10
- height = 10
- Subtract the measured background intensity from each pixel
- Measure pixel values again at above coordinates ( `[ 28, 35 ]` and `[ 28, 39 ]` )
- Discuss how the pixel values changed during background subtraction
* 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:
* upper left corner at `[ 20, 35 ]`
* width = 10
* height = 10
* Subtract the measured background intensity from each pixel
* Measure pixel values again at above coordinates ( `[ 28, 35 ]` and `[ 28, 39 ]` )
* Discuss how the pixel values changed during background subtraction
Repeat above activity, but:
- After opening the image, convert its pixel data type to floating point
* After opening the image, convert its pixel data type to floating point
### Activity: Limitations of float
......@@ -139,13 +138,13 @@ True or false?
- [Limitations of float](https://randomascii.wordpress.com/2012/02/13/dont-store-that-in-a-float/)
## Data type conversion
## Pixel data type conversions
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"data type conversion" -> "values" [label=" can change"];
"data type conversion" -> "value range" [label=" changes"];
"pixel_type_conversion" -> "pixel_values" [label=" can change"];
"pixel_type_conversion" -> pixel_value_range [label=" changes"];
}
'/>
......@@ -153,8 +152,6 @@ True or false?
What are good reasons to change the pixel data type of an image?
TODO
- a
- b
- c
......@@ -162,14 +159,13 @@ TODO
### Activity: 16-bit to 8-bit conversion
* Open image: `xy_16bit__two_values.tif`
* Convert to 8-bit
* Understand the mathematics of the conversion
- Open image: `xy_16bit__two_values.tif`
- Convert to 8-bit
### Activity: 16-bit to float conversion
* Open image: `xy_16bit__two_values.tif`
* Convert to float
- Open image: `xy_16bit__two_values.tif`
- Convert to float
### Formative Assessment
......@@ -182,6 +178,7 @@ True or false?
## Image segmentation overview
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
......@@ -432,7 +429,7 @@ Which statements are true?
- Intensity measurements
- Object shape measurements
- Label image
- Data types
- Pixel data types
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