Commit 97ad7ab4 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi

Merge branch 'pixels' into 'master'

Pixels

See merge request !42
parents 0646dd94 c341b09a
Pipeline #10619 passed with stage
in 1 minute and 12 seconds
---
title: Image pixels
layout: page
---
# Pixels
## Concept map
<img src='https://g.gravizo.com/svg?
digraph G {
shift [fontcolor=white,color=white];
image -> pixel [label=" has many"];
pixel -> value;
pixel -> indices;
pixel -> voxel [label=" 3D"];
pixel -> size [label=" can have"]
}
'/>
## Activity: Explore pixel values and indices
## 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.
## Activity: Explore image calibration
## Explore pixel sizes
* Open image: xyz_8bit_calibrated_anisotropic__mri_head.tif
* Check the calibration of this image
* Check the pixel sizes (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
......@@ -36,14 +16,3 @@ layout: page
* 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?
* 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.
## Learn next
- display.md
---
title: Pixels
layout: module
prerequisites:
objectives:
- Examine the values of pixels in an image.
motivation: >
Images are very often composed of pixels. Pixel stands for "picture element". In 3-D, a pixel is sometimes also called a voxel, which stands for "volume element".
To analyse images it is very important to know how to examine the pixels (voxels) in an image.
concept_map: >
graph TD
Im("Image") -->|has many| P("Pixel")
P -->|has| V("Value")
P -->|has| I("Indices")
P -->|aka| V("Voxel")
P -->|can have| S("Size")
figure: /figures/pixels.png
figure_legend:
activity_preface: >
Explore the values, indices (and sizes) of pixels in an image.
activities:
"ImageJ GUI": "pixels/activities/pixels_imagejgui.md"
# "ImageJ Macro": "pixels/activities/pixels_ijmacro.md"
# "Jython": "pixels/activities/pixels_jython.md"
# "MATLAB": "pixels/activities/pixels_matlab.md"
exercises_preface: >
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.
exercises:
# "ImageJ GUI": "pixels/exercises/pixels_imagejgui.md"
# "ImageJ Macro": "pixels/exercises/pixels_imagejmacro.md"
# "Jython": "pixels/exercises/pixels_jython.md"
# "MATLAB": "pixels/exercises/pixels_matlab.md"
learn_next:
- "[Image display](image_display)"
external_links:
---
......@@ -18,8 +18,8 @@ figure_legend: Connected component analysis
activity_preface: >
activities:
# "ImageJ GUI": "this_module/activities/this_module_ijgui.md"
# "ImageJ Macro": "this_module/activities/this_module_ijmacro.md"
# "ImageJ GUI": "this_module/activities/this_module_imagejgui.md"
# "ImageJ Macro": "this_module/activities/this_module_imagejmacro.md"
# "Jython": "this_module/activities/this_module_jython.md"
# "MATLAB": "this_module/activities/this_module_matlab.md"
......
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