diff --git a/workshops/bioimage-analysis-fundamentals.md b/workshops/bioimage-analysis-fundamentals.md index 676b157c064a02bdc471b19160314aa6dde0209f..d10897e4a660d037bbd85fb7f92934099198da9f 100644 --- a/workshops/bioimage-analysis-fundamentals.md +++ b/workshops/bioimage-analysis-fundamentals.md @@ -72,12 +72,12 @@ contrast = max - min ### Formative Assessment -Fill in the blanks, using those words: decrease, larger_than, increase, smaller_than +Fill in the blanks, using those words: decrease, larger than, increase, smaller than -* Pixels with values _____ `max` will appear saturated. -* Decreasing `max` while keeping `min` constant will _____ the contrast. -* Decreasing both `max` and `min` will _____ the overall brightness. -* Pixels with values _____ the `min` will appear black, when using a grayscale LUT. +1. Pixels with values _____ `max` will appear saturated. +2. Decreasing `max` while keeping `min` constant will _____ the contrast. +3. Decreasing both `max` and `min` will _____ the overall brightness. +4. Pixels with values _____ the `min` will appear black, when using a grayscale LUT.   @@ -254,13 +254,12 @@ Repeat above activity but use a 3D image: 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. -* 8-connected connectivity results in _____ objects than 4-connected connectivity. -* In 3D, pixels have ____ non-diagonal neighbors. -* In 2D, pixels have ____ non-diagonal neighbors. -* A 8-bit label image can maximally have _____ objects. -* The maximum value in a label image is equal to or _____ than the number of objects. +1. In 3D, pixels have _____ neighbors than in 2D. +2. 8-connected connectivity results in _____ objects than 4-connected connectivity. +3. In 3D, pixels have ____ non-diagonal neighbors. +4. In 2D, pixels have ____ non-diagonal neighbors. +5. A 8-bit label image can maximally have _____ objects. +6. The maximum value in a label image is equal to or _____ than the number of objects.   @@ -338,11 +337,11 @@ True or false? Discuss with your neighbour! 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. -* The number of distinct values in a label image is _____ the number of objects (minus one). -* Converting an intensity image to a _____ image can be achieved by _____ . -* The number of connected components can be _____ the maximal label. +1. A label image is the result of _____ . +2. The number of pixels in a binary image is typically _____ the number of connected components. +3. The number of distinct values in a label image is _____ the number of objects (minus one). +4. Converting an intensity image to a _____ image can be achieved by _____ . +5. The number of connected components can be _____ the maximal label.   @@ -392,10 +391,10 @@ There are several good reasons not to subtract the background from each pixel in 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. -* In an 8-bit image, increasing the size of the measurement region can only _____ the sum intensity. -* In a float image, increasing the size of the measurement region can _____ the sum intensity. +1. Average intensity is just another word for _____ intensity. +2. The _____ intensity is equal to the mean intensity times the _____ in the measured region. +3. In an 8-bit image, increasing the size of the measurement region can only _____ the sum intensity. +4. In a float image, increasing the size of the measurement region can _____ the sum intensity.   diff --git a/workshops/rank-filters.md b/workshops/rank-filters.md index fc03b61532a5623998fec3545c50135b6d82c7c7..c3ffefa0f4a10acad64c9209515f942a9ecd3dec 100644 --- a/workshops/rank-filters.md +++ b/workshops/rank-filters.md @@ -58,11 +58,11 @@ Fill in the blanks, using those words: shrinks, increases, decreases, enlarges. '/> ``` -opening( image ) = dilation( erosion( image ) ) +opening( image, r ) = dilation( erosion( image, r ), r ) ``` ``` -closing( image ) = erosion( dilation( image ) ) +closing( image, r ) = erosion( dilation( image, r ), r ) ``` @@ -72,13 +72,16 @@ closing( image ) = erosion( dilation( image ) ) - Explore effects of morphological closing and opening: - closing can fill holes - closing can connect gaps - - opening can remove thin structures + - opening can remove thin structures ### Formative assessment -TODO +True of false? Discuss with your neighbour! +1. Morphological openings on binary images can decrease the number of foreground pixels. +2. Morphological closings on binary images never decreases the number of foreground pixels. +3. Performing a morphological closing a twice in a row does not make sense, because the second closing does not further change the image. ## Top hat filter for local background subtraction @@ -149,7 +152,11 @@ median_based_background_correction = image - median( image, r) ### Formative assessment -TODO +Answer below questions. Discuss with your neighbour! + +1. What could one do to close small gaps in a binary image? +2. What could one do to remove small objects in a image? +3. What could you use for local background subtraction in a very noisy image? ## Learn more diff --git a/workshops/recap.md b/workshops/recap.md index b8028d135fb455fa29c5f734541bab652c0b6269..8dd19aa72cf3aca806b631cb947de7d97db0613f 100644 --- a/workshops/recap.md +++ b/workshops/recap.md @@ -4,12 +4,13 @@ Take few sheets of empty (A4) paper. Work in pairs of two. * Draw a typical image analysis workflow: From intensity image to objects shape table. -* Write down few (e.g., two) noteworthy facts about: +* Write down a few (e.g., two) noteworthy facts about: * Pixel data types * Label images * Intensity measurements * Object shape measurements -* Answer below questions: +* Write down answers to below questions (there can be multiple answers for some questions): * How can you split touching objects? * What can you use a distance map for? * What can you do to segment spots in prescence of uneven background signal? + * What can you do to remove small objects from a binary image?