Commit beedb0c8 authored by Christian Tischer's avatar Christian Tischer

Turku

parent c32616b1
Pipeline #10225 passed with stage
in 28 seconds
......@@ -36,20 +36,23 @@ contrast = max - min
* Open image: xy_16bit__nuclei_high_dynamic_range.tif
* Explore different single color LUTs and LUT settings
* Appreciate that LUT settings do not change the pixel values
## Optional activity: Multi color LUTs
* Open image: xy_16bit__nuclei_high_dynamic_range.tif
* Appreciate that a single color LUT does not suffice
* Explore color LUTs
* Add a LUT calibration bar to the image
* Explore multi-color LUT for visualisation of high dynamic range images
* Add a LUT calibration bar to the image
## Formative Assessment
### Fill in the blanks
Fill in the blanks, using those words: decrease, larger than, increase, smaller than
1. Pixels with values _____ `max` will appear saturated.
2. Decreasing `max` while keeping `min` constant will _____ the contrast.
3. Decreasing both `max` and `min` will _____ the overall brightness.
4. Pixels with values _____ the `min` will appear black, when using a grayscale LUT.
### TODO: Comparative image display
Open two images and display with the same LUT settings.
......@@ -14,6 +14,7 @@ layout: page
pixel -> value;
pixel -> indices;
pixel -> voxel [label=" 3D"];
pixel -> size [label=" can have"]
}
'/>
......@@ -24,6 +25,18 @@ layout: page
* Check where the lowest pixel indices are in the displayed image:
* Most commonly: Upper left corner, which is different to conventional coordinate systems.
### Activity: Explore image calibration
* Open image: xyz_8bit_calibrated_anisotropic__mri_head.tif
* Check the calibration of this image
* Explore how image calibration affects spatial measurements, e.g.,
* Measure the distance between two pixels in the image
* Measure the size of an image region
* Appreciate that image calibration might be neccessary, e.g.
* 3D distance measurements
* Appreciate that image calibration can be confusing, e.g.
* not consistently used in image filter parameter specification
## Formative assessment
True or false?
......@@ -31,6 +44,14 @@ True or false?
* The lowest pixel index of a 2D image always is `[1,1]`.
* When looking at a 2D image, the lowest pixel indices are always in the lower left corner.
### Formative assessment
Answer below questions:
* Given a voxel spacing of (100 nm, 100 nm, 300 nm), what is the distance between the voxels at indices [10, 5, 11] and [2, 20, 13]?
## Learn next
- display.md
---
title: Spatial image calibration
layout: page
---
## Voxel size calibration
```mermaid
graph TD
VV(Voxel indices) -->|multiplied by| VS(Voxel spacing)
VS --> |yields|RWC(Calibrated voxel coordinates)
```
### Example
### Activity: Explore image calibration
* Open image: xyz_8bit_calibrated_anisotropic__mri_head.tif
* Check the calibration of this image
* Explore how image calibration affects spatial measurements, e.g.,
* Measure the distance between two pixels in the image
* Measure the size of an image region
* Appreciate that image calibration might be neccessary, e.g.
* 3D distance measurements
* Appreciate that image calibration can be confusing, e.g.
* not consistently used in image filter parameter specification
### Formative assessment
Answer below questions:
* Given a voxel spacing of (100 nm, 100 nm, 300 nm), what is the distance between the voxels at indices [10, 5, 11] and [2, 20, 13]?
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