Add image data

_includes/image_inspection_and_presentation/inspect_collagen_data.md

@@ -4,7 +4,7 @@ In this workflow we inspect the content of images of tissue culture cells expres
 
 - [Inspect the image pixel values](/pixels/index.html#inspect_collagen) 
 - [Adjust the image display](/lut/index.html#configure)
-- Inspect image metadata
+- [Inspect image metadata and datatype](/datatypes/index.html#metadata_and_datatype)
 - Inspect and display spatial calibration
 - Create line profiles
 - Create magnified insets

_includes/spatial_calibration/scale_bar.md

@@ -0,0 +1,7 @@
+<h4 id='scale_bar'><a href="#scale_bar>Inspect spatial calibration metadata and add a scale bar</a></h4>
+  - Open an image and inspect the spatial calibration metadata 
+  - Add a scale bar to the image  
+
+##### Image data
+
+- [TODO: MD Collagen](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyz_8bit__mitotic_plate_calibrated.tif)

_includes/spatial_calibration/scale_bar_imagej_gui.md

@@ -0,0 +1,17 @@
+* Open image:  [xyz_8bit__mitotic_plate_calibrated.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyz_8bit__mitotic_plate_calibrated.tif)
+* Check the pixel sizes (calibration) of this image
+* Where to see the calibration?
+  * Next to the pixel indices in the ImageJ menu bar
+  * Properties of the image **[Image > Properties]** or **[Shift-Ctrl-P]**
+* How to check whether the calibration makes sense?
+  * Explore the typical size of objects in 3D. 
+     * Orthogonal view **[Image > Stacks > Orthogonal Views]** or **[Ctrl-Shift-H]**
+  * An example of a wrong calibration: [xyz_8bit__mitotic_plate_badZcalibrated.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyz_8bit__mitotic_plate_badZcalibrated.tif)
+* Appreciate that image calibration might be necessary, e.g.
+  * 2D distance measurement between two pixels
+    * One can use the Line tool
+  * 3D distance measurement between two voxels
+    * One cannot use the Line tool but needs to measure manually: `sqrt( (x0-x1)^2 + (y0-y1)^2 + (z0-z1)^2 )`
+      * Note: It is critical to use the calibrated voxel positions and not the voxel indices in above formula!
+* Appreciate that image calibration can be confusing, e.g.
+  * It is not consistently used in image filter parameter specification

_modules/datatypes.md

@@ -1,6 +1,7 @@
 ---
 title:     Data types
 layout:    module
+permalink: /datatypes/
 
 prerequisites:
   - "[Digital image basics](../pixels)"
@@ -24,6 +25,7 @@ figure_legend: Examples for data types of different bit depths.
 
 multiactivities:
   - ["datatypes/datatypes_act1.md", [["skimage napari", "datatypes/datatypes_act1_skimage_napari.py"], ["ImageJ GUI", "datatypes/datatypes_act1_imagej_gui.md"]]]
+  - ["datatypes/metadata_and_datatype.md", [["ImageJ GUI", "datatypes/metadata_and_datatype_imagej_gui.md"]]] 
 
 exercises:
 

_modules/spatial_calibration.md

@@ -1,6 +1,7 @@
 ---
 title:  Spatial calibration
 layout: module
+permalink: /spatial_calibration/
 
 prerequisites:
   - "[Basics properties of images and pixels](../pixels)"
@@ -31,6 +32,7 @@ figure: /figures/spatial_calibration.png
 figure_legend: Spatial calibration and size measurements
 
 multiactivities:
+  - ["spatial_calibration/scale_bar.md", [["ImageJ GUI", "spatial_calibration/scale_bar_imagej_gui.md"],["ImageJ Macro", "spatial_calibration/scale_bar_imagej_macro.md"]]]
   - ["spatial_calibration/spatial_calibration_act1.md", [["ImageJ GUI", "spatial_calibration/spatial_calibration_act1_imagejgui.md", "markdown"], 
   ["skimage napari", "spatial_calibration/spatial_calibration_act1_skimage_napari.py", "python"]]]
   - ["spatial_calibration/spatial_calibration_act2.md", [["ImageJ GUI", "spatial_calibration/spatial_calibration_act2_imagejgui.md"], ["skimage napari", "spatial_calibration/spatial_calibration_act2_skimage_napari.py", "python"]]]