Commit af5e72cf authored by Christian Tischer's avatar Christian Tischer

EMBL course

parent 17bf6fbb
Monday: Basic concepts (Fiji)
Tuesday: Basic concepts (Fiji)
Wednesday: Repeat basic concepts (Workflows in KNIME)
9:30 - 16:30
lunch: 12:30 - 13:30
Communication:
chat.embl.org
https://chat.embl.org/embl/channels/image-analysis
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# Bioimage analysis fundamentals
## Pixel values, coordinates, and data types
## Pixel values and indices
<img src='https://g.gravizo.com/svg?
digraph G {
......@@ -8,31 +8,54 @@
image -> pixel [label=" has many"];
pixel -> value;
pixel -> indices;
pixel -> voxel [label=" 3D"];
}
'/>
### Activity: Explore pixel values and indices
* Open image: xy_8bit__nuclei_noisy_different_intensity.tif
* Explore different ways to inspect pixel values and indices
* Check where the lowest pixel indices are in the displayed image:
* Most commonly: Upper left corner, which is different to conventional coordinate systems.
## Image calibration
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
pixel -> indices;
pixel -> coordinates;
indices -> calibration;
calibration -> coordinates;
calibration -> anisotropic [label=" can be"];
image -> calibration [label=" can have"];
pixel -> voxel [label=" 3D"];
}
'/>
### Activity
### Activity: Explore image calibration
* Open image: xy_8bit__nuclei_noisy_different_intensity.tif
* Explore different ways to inspect pixel values and indices
* Add image calibration
* Check where the calibration is visible
* Add image calibration
* Explore whether and how this affects image display and measurements (e.g. distance between two points)
### Activity: Explore anisotropic 3D image data
* Open image: xy_8bit_calibrated_anisotropic__mri_stack.tif
* Appreciate that the pixels are anisotropic
### Formative assessment
True or false?
* 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.
* The lowest pixel index of a 2D image always is `[1,1]`.
* When looking at a 2D image, the lowest pixel index is in the lower left corner.
* When looking at a 2D image, the lowest pixel indices are always in the lower left corner.
&nbsp;
......
# Teaching recommendations
- Try to use white-board whenever possible.
- Make sure there is (at least) one whiteboard with sufficient paper.
# Neighborhood filters
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"neighbourhood filter" -> "central neighbourhood pixel" [label=" replaces"];
"neighbourhood filter" -> "size" [label=" has"];
"neighbourhood filter" -> "shape" [label=" has"];
"neighbourhood filter" -> "convolution filters";
"neighbourhood filter" -> "rank filters";
}
'/>
| | | | | | | | |
|---|---|---|---|---|---|---|---|
| NC | NC | NC | | | | | |
| NC | C, NC | NC | | | | | |
| NC | NC | NC | | | | | |
| | | | | NB | NB | NB | |
| | | | | NB | B, NB| NB | |
| | | | | NB | NB | NB | |
| | | | | | | | |
# Rank filters
## Basic rank filters
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
"rank filters" -> awesome [label=" are"];
"rank filters" -> "neighbourhood filters" [label=" are"];
"rank filters" -> minimum;
minimum -> erosion [label=" aka"];
"rank filters" -> maximum;
......@@ -15,6 +42,8 @@
}
'/>
### Activity: Explore rank filters on binary images
- Open image: xy_8bit_binary__two_spots_different_size.tif
......
# Teaching tips
## White-boards
- Try to frequently use white-board, because:
- It makes teaching more interactive.
- It slows down teaching, because you have to draw.
- Make sure you have good pens with high contrast.
- Have two white-boards:
- One for tidy concept maps.
- One for messy notes.
## Stand
- Try not to sit, because:
- Teaching will be more dynamic.
- People can see and hear you better.
- Construct something to have your computer up, such that you can stand in front of it.
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