Commit 8c6db746 authored by Christian Tischer's avatar Christian Tischer

Turku

parent c87a021f
......@@ -81,4 +81,5 @@ True of false? Discuss with your neighbour!
## Learn more
- https://en.wikipedia.org/wiki/Morphological_gradient
- https://imagej.net/MorphoLibJ#Grayscale_morphological_filters
<h1 id="pixels">Pixels</h1>
<h2 id="concept-map">Concept map</h2>
<p><img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
image -> pixel [label=" has many"]; pixel -&gt; value; pixel -&gt; indices; pixel -&gt; voxel [label=" 3D"]; } ’/&gt;</p>
<h2 id="activity-explore-pixel-values-and-indices">Activity: Explore pixel values and indices</h2>
<ul>
<li>Open image: xy_8bit__nuclei_noisy_different_intensity.tif</li>
<li>Explore different ways to inspect pixel values and indices</li>
<li>Check where the lowest pixel indices are in the displayed image: * Most commonly: Upper left corner, which is different to conventional coordinate systems.</li>
</ul>
<h2 id="formative-assessment">Formative assessment</h2>
<p>True or false?</p>
<ul>
<li>The lowest pixel index of a 2D image always is <code>[1,1]</code>.</li>
<li>When looking at a 2D image, the lowest pixel indices are always in the lower left corner.</li>
</ul>
<h2 id="learn-next">Learn next</h2>
<ul>
<li>display.md</li>
</ul>
......@@ -3,13 +3,13 @@ title: Spatial image calibration
layout: page
---
## Image calibration
## Voxel size calibration
```mermaid
graphTD
graph TD
VV(Voxel indices) -->|multiplied by| VS(Voxel spacing)
VS --> |yields|RWC(Calibrated voxel coordinates)
'/>
```
### Example
......
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