Commit c341b09a by Christian Tischer Committed by Aliaksandr Halavatyi

### Pixels

parent 0646dd94
 --- 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
 --- 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: ---

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 ... ... @@ -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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