Commit fda9ae85 by Christian Tischer

### EMBL course

parent 899bf55d
 ... @@ -32,6 +32,7 @@ True or false? ... @@ -32,6 +32,7 @@ True or false? * Pixel coordinates depend on image calibration. * Pixel coordinates depend on image calibration. * Pixel indices are always positive integer values. * Pixel indices are always positive integer values. * The lowest pixel index of a 2D image always is `[1,1]`. * The lowest pixel index of a 2D image always is `[1,1]`. * When looking at a 2D image, the lowest pixel index is in the lower left corner.     ... @@ -39,6 +40,7 @@ True or false? ... @@ -39,6 +40,7 @@ True or false?     \pagebreak ## Image display ## Image display ... @@ -100,20 +102,6 @@ Fill in the blanks, using those words: decrease, larger_than, increase, smaller_ ... @@ -100,20 +102,6 @@ Fill in the blanks, using those words: decrease, larger_than, increase, smaller_ } } '/> '/> ### Motivation It sometimes is necessary to change the numeric content of images. It is important to understand how to do this properly in order to avoid uncontrolled artifacts. What are good reasons to change the pixel values in an image? 1. For intensity measurements, the image background (e.g. camera based offset) should be subtracted from all pixels. 2. For threshold based image segmentation (object detection), it helps to first filter noise in the image. 3. For intensity measurements, it helps to filter noise in the image. 4. The image appears to dark, multiplication of all pixels by a constant number is a means to make it brighter. 5. For uneven illumination (e.g. occuring in wide-field microscopy with large camera chips), one should do flat-field correction, which makes the intensity values even across the image. 6. Our microscope was broken. We took images on a replacement microscope. The pixel values were consistently higher than on our usual microscope. We multiplied the pixels on all images from the replacement microscope by a constant factor to make them comparable to our usual data. ### Activity: Pixel based background subtraction ### Activity: Pixel based background subtraction * Open image: xy_8bit__nuclei_noisy_different_intensity.tif * Open image: xy_8bit__nuclei_noisy_different_intensity.tif ... @@ -170,13 +158,6 @@ True or false? ... @@ -170,13 +158,6 @@ True or false? } } '/> '/> ### Motivation What are good reasons to change the pixel data type of an image? * TODO * TODO ### Activity: 16-bit to 8-bit conversion ### Activity: 16-bit to 8-bit conversion * Open image: xy_16bit__two_values.tif * Open image: xy_16bit__two_values.tif ... @@ -209,16 +190,17 @@ In order to find objects in a image, the first step often is to determine whethe ... @@ -209,16 +190,17 @@ In order to find objects in a image, the first step often is to determine whethe threshold; "intensity image" -> threshold; threshold -> "binary image"; threshold -> "binary image"; "binary image" -> "background value"; "binary image" -> "mask" [label=" aka"]; "binary image" -> "foreground value"; "binary image" -> "background value"; "background value" -> "0"; "binary image" -> "foreground value"; "foreground value" -> "1"; "background value" -> "0"; "foreground value" -> "255"; "foreground value" -> "1"; "pixel value" -> ">= threshold" -> foreground; "foreground value" -> "255"; "pixel value" -> "< threshold" -> background; "pixel value" -> ">= threshold" -> foreground; "pixel value" -> "< threshold" -> background; } } '/> '/> ... ...
 ... @@ -112,18 +112,12 @@ tophat( image ) = image - opening( image, r ) = image - dilation( erosion( imag ... @@ -112,18 +112,12 @@ tophat( image ) = image - opening( image, r ) = image - dilation( erosion( imag - Use a tophat filter to remove local background. - Use a tophat filter to remove local background. - Threshold the spots in the tophat filtered image. - Threshold the spots in the tophat filtered image. ## Activity: Explore tophat fiter on noisy data ## Activity: Explore tophat filter on noisy data - Open image: xy_8bit__spots_local_background_with_noise.tif - Open image: xy_8bit__spots_local_background_with_noise.tif - Use topHat filter to remove local background - Use topHat filter to remove local background - Appreciate that noise poses a challenge to the tophat filter - Appreciate that noise poses a challenge to the tophat filter ### Formative assessment TODO ## Median filter for local background subtraction ## Median filter for local background subtraction
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