Commit 0ddf1765 authored by Christian Tischer's avatar Christian Tischer

EMBL Course

parent f9d6da52
...@@ -307,14 +307,12 @@ Which statements are true? ...@@ -307,14 +307,12 @@ Which statements are true?
<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];
input_image -> binary_image [label=" threshold"]; intensity_image -> binary_image [label=" threshold"];
binary_image -> label_image [label=" connected components"]; binary_image -> label_image [label=" connected components"];
label_image -> table [label=" measure_shape"]; label_image -> table [label=" measure_shape"];
} }
'/> '/>
### Activity: Segment objects and measure shapes ### Activity: Segment objects and measure shapes
- Open image: `xy_8bit__two_cells.tif` - Open image: `xy_8bit__two_cells.tif`
...@@ -323,37 +321,62 @@ Which statements are true? ...@@ -323,37 +321,62 @@ Which statements are true?
### Formative assessment ### Formative assessment
Which statements are true? Fill in below blanks, using these words:
- a equal_to, larger_than, smaller_than, binary, connected_component_analysis, thresholding
- b
- c
- A label image is the result of _____ .
- The number of pixels in a binary image is typically _____ the number of connected components.
- The number of distinct values in a label image is _____ the number of objects (minus one).
- Converting an intensity image to a _____ image can be achieved by _____ .
- The number of connected components can be _____ the maximal label.
## Intensity measurements
### Activity: Measure DNA intensity
# Automation / Programming - Open image: `xy_float__h2b_bg_corr.tif`
- Measure for both nuclei:
- Maximum intensity
- Average intensity
- Sum intensity
- Discuss the interpretation!
- Discuss where to measure!
## Automated object filtering
<img src='https://g.gravizo.com/svg? ### Activity: Intensity measurements without pixel based background correction
digraph G {
shift [fontcolor=white,color=white]; #### Motivation
label_image -> table [label=" measure_shape"];
table -> filtered_objects;
filtered_objects -> label_image [label=" remove"];
}
'/>
### Activity: Automatically remove objects from label image There are several good reasons not to subtract the background from each pixel in an image:
This activity requires some more advanced programming. - It is a bit tricky to do it right, because one has to convert to float to accomodate floting point and negative values.
- If one has really big image data (TB) one would need (at least) another TB storage for the background corrected version of the image.
#### Workflow
- Open image: `xy_calibrated_8bit__two_nuclei_high_background.tif`
- Measure for both nuclei and a background region:
- Maximum intensity
- Average intensity
- Median intensity
- Sum intensity
- Discuss how to correct the intensities for the background
- Measure the region areas in pixel units
- Watch out: the image is calibrated!
- Use the area for the correction.
### Formative assessment ### Formative assessment
Which statements are true? Fill in below blanks with those 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.
- In an 8-bit image, increasing the size of the measurement region can only _____ the sum intensity.
- In a float image, increasing the size of the measurement region can _____ the sum intensity.
### Formative assessment ### Formative assessment
......
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