Commit 045f9546 authored by Christian Tischer's avatar Christian Tischer

Course

parent 0df5560d
# Bioimage analysis fundamentals
## Image content
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
image -> pixel [label=" has many"];
pixel -> value;
pixel -> indices;
pixel -> coordinates;
indices -> calibration;
calibration -> coordinates;
image -> calibration;
image -> data_type;
data_type -> value [label=" restricts"];
pixel -> voxel [label=" 3D"];
}
'/>
### Activity
- Open image: *_8bit_*
- Explore pixel values and pixels indices
- Add image calibration
- Explore pixel coordinates
- Check whether the sofware changed indices to coordinates
- Open image: *_float_*
- Explore pixel values
### Formative assessment
Which statements about images are true (multiple answers)?
- Pixel coordinates are always integer values.
- Changing the image calibration changes the pixel values.
- Pixel coordinates depend on image calibration.
- Pixel indices are always positive integer values.
- Image data type affects the possible range of pixel coordinates.
- A pixel can take any value.
- The lowest pixel index of a 2D image always is `[1,1]`.
## Image display
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
lookup_table__LUT -> color;
lookup_table__LUT -> brightness;
lookup_table__LUT -> LUT_min;
lookup_table__LUT -> LUT_max;
pixel_value -> brightness;
LUT_min -> brightness;
LUT_max -> brightness;
}
'/>
```
brightness( pixel_value ) = ( pixel_value - LUT_min ) / ( LUT_max - LUT_min )
0 <= brightness <= 1
contrast = LUT_max - LUT_min
```
### Activity
- Open image:
- Change LUT settings
- Appreciate that LUT settings do not affect image content.
###
...@@ -165,7 +165,7 @@ What can you do to show images with a high dynamic range (multiple answers)? ...@@ -165,7 +165,7 @@ What can you do to show images with a high dynamic range (multiple answers)?
4. Never use multi color LUTs, they are confusing. 4. Never use multi color LUTs, they are confusing.
5. Already on the microscope change the settings such that only relevant structures are visible, e.g. lower the gain such that dark irrelevant objects have zero pixel values. 5. Already on the microscope change the settings such that only relevant structures are visible, e.g. lower the gain such that dark irrelevant objects have zero pixel values.
6. Adjust LUT settings such that background noise is not visible, because this is distracting. 6. Adjust LUT settings such that background noise is not visible, because this is distracting.
G. Add a LUT calibration to the image, such that readers can see that not all information might be visible. 7. Add a LUT calibration to the image, such that readers can see that not all information might be visible.
## Image math ## Image math
......
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