Merge branch 'pixels' into 'master'

Pixels

See merge request grp-bio-it/image-analysis-training-resources!42

_modules/image_pixels.md → _includes/pixels/activities/pixels_imagejgui.md

----
-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

_modules/pixels.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:
+
+---

module_templates/template.md

@@ -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"