Commit 23b63e17 by Christian Tischer

### EMBL Course

parent 41e02bc1
File deleted
 ... ... @@ -49,28 +49,28 @@ True or false? LUT -> brightness; min -> LUT; max -> LUT; "pixel value" -> LUT; value -> LUT; } '/> ``` brightness(pixel_value) = ( pixel_value * LUT_min ) / ( LUT_max - LUT_min ) brightness = ( value - min ) / ( max - min ) 0 <= brightness <= 1 contrast = LUT_max * LUT_min contrast = max - min ``` ### Activity * Open image: `xy_8bit__nuclei_noisy_different_intensity.tif` * Change LUT settings * Explore different LUTs and LUT settings * Appreciate that LUT settings do not affect image content. ### Formative Assessment Fill in the blanks: decrease, larger_than, increase, smaller_than Fill in the blanks, using those words: decrease, larger_than, increase, smaller_than * Pixels with values _____ the `LUT_max` will appear saturated. * Decreasing `LUT_max` while keeping `LUT_min` constant will _____ the contrast. ... ... @@ -118,20 +118,20 @@ What are good reasons to change the pixel values in an image? * Open image: `xy_8bit__nuclei_noisy_different_intensity.tif` * Appreciate the significant background intensity * Measure pixel value at `[ 28, 35 ]` and `[ 28, 39 ]` * Measure background intensity in below region: * Measure pixel values at `[ 28, 35 ]` and `[ 28, 39 ]` * Measure the image background intensity in this region: * upper left corner at `[ 20, 35 ]` * width = 10 * height = 10 * Subtract the measured background intensity from each pixel. * Measure pixel values again. * Measure the pixel values again. * Observe that the resuls are incorrect. Repeat above activity, but: * After opening the image, convert its data type to floating point. ### Activity: Limitations of float ### Activity: Explore the limitations of `float` data type * Create an empty image * Set all pixel values to 1000000000.0 ... ... @@ -165,8 +165,8 @@ True or false? ... ... @@ -219,8 +219,8 @@ In order to find objects in a image, the first step often is to determine whethe "background value" -> "0"; "foreground value" -> "1"; "foreground value" -> "255"; value -> ">= threshold" -> foreground; value -> "< threshold" -> background; "pixel value" -> ">= threshold" -> foreground; "pixel value" -> "< threshold" -> background; } '/> ... ... @@ -258,7 +258,7 @@ True or false? Discuss with your neighbor! ### Activity: 2D connected components analysis * Open image: `xy_8bit_binary__nuclei.tif` * Open image: xy_8bit_binary__nuclei.tif * Perform connected components analysis * Explore multi-color LUTs for object labelling * Explore removing and joining labels ... ... @@ -268,13 +268,11 @@ True or false? Discuss with your neighbor! Repeat above activity but use a 3D image: * Open image: `xyz_8bit_binary__spots.tif` * Open image: xyz_8bit_binary__spots.tif ### Formative assessment Fill in the blanks: less, more, 8, 255, 4, more. Fill in the blanks, using these words: less, more, 8, 255, 4, more. * For a given input image there is only one correct connectivity. * In 3D, pixels have _____ neighbors than in 2D. ... ... @@ -353,9 +351,7 @@ Which statements are true? Discuss with your neighbor! ### Formative assessment Fill in below blanks, using these words: equal_to, larger_than, smaller_than, binary, connected_component_analysis, thresholding Fill in below blanks, using these words: equal_to, larger_than, smaller_than, binary, connected_component_analysis, thresholding * A label image is the result of _____ . * The number of pixels in a binary image is typically _____ the number of connected components. ... ... @@ -409,9 +405,7 @@ There are several good reasons not to subtract the background from each pixel in ### Formative assessment: Intensity measurements Fill in below blanks with those words: integrated, mean, number_of_pixels, decrease, increase, sum Fill in the blanks, using these words: integrated, mean, number_of_pixels, decrease, increase, sum * Average intensity is just another word for _____ intensity. * The _____ intensity is equal to the mean intensity times the _____ in the measured region. ... ...
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