diff --git a/_modules/image_pixels.md b/_includes/pixels/activities/pixels_imagejgui.md similarity index 51% rename from _modules/image_pixels.md rename to _includes/pixels/activities/pixels_imagejgui.md index a33ffdffdbbb7245c721121ec570fd1b17347efc..cc36fbb8e2cff66a27c09d2910ba432cce5bf183 100644 --- a/_modules/image_pixels.md +++ b/_includes/pixels/activities/pixels_imagejgui.md @@ -1,34 +1,14 @@ ---- -title: Image pixels -layout: page ---- - -# Pixels - -## Concept map - - - -## 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 diff --git a/_modules/pixels.md b/_modules/pixels.md new file mode 100644 index 0000000000000000000000000000000000000000..dca976ff405885824c6038c884918a0a2aced2fb --- /dev/null +++ b/_modules/pixels.md @@ -0,0 +1,50 @@ +--- +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: + +--- diff --git a/figures/pixels.png b/figures/pixels.png new file mode 100644 index 0000000000000000000000000000000000000000..30b99142b067f16c7dbc1387eba17898a7939cca Binary files /dev/null and b/figures/pixels.png differ diff --git a/module_templates/template.md b/module_templates/template.md index 2c92f6743ce1bd786adfd4dd56abfed25345c4c2..8cf53af22f5b8e9638e0863ce74d40178e37508f 100644 --- a/module_templates/template.md +++ b/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"