Commit 0ddf1765 by Christian Tischer

EMBL Course

parent f9d6da52
 ... @@ -307,14 +307,12 @@ Which statements are true? ... @@ -307,14 +307,12 @@ Which statements are true? binary_image [label=" threshold"]; intensity_image -> binary_image [label=" threshold"]; binary_image -> label_image [label=" connected components"]; binary_image -> label_image [label=" connected components"]; label_image -> table [label=" measure_shape"]; label_image -> table [label=" measure_shape"]; } } '/> '/> ### Activity: Segment objects and measure shapes ### Activity: Segment objects and measure shapes - Open image: `xy_8bit__two_cells.tif` - Open image: `xy_8bit__two_cells.tif` ... @@ -323,37 +321,62 @@ Which statements are true? ... @@ -323,37 +321,62 @@ Which statements are true? ### Formative assessment ### Formative assessment Which statements are true? Fill in below blanks, using these words: - a equal_to, larger_than, smaller_than, binary, connected_component_analysis, thresholding - b - c - 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. ## Intensity measurements ### Activity: Measure DNA intensity # Automation / Programming - Open image: `xy_float__h2b_bg_corr.tif` - Measure for both nuclei: - Maximum intensity - Average intensity - Sum intensity - Discuss the interpretation! - Discuss where to measure! ## Automated object filtering ### Activity: Automatically remove objects from label image There are several good reasons not to subtract the background from each pixel in an image: This activity requires some more advanced programming. - It is a bit tricky to do it right, because one has to convert to float to accomodate floting point and negative values. - If one has really big image data (TB) one would need (at least) another TB storage for the background corrected version of the image. #### Workflow - Open image: `xy_calibrated_8bit__two_nuclei_high_background.tif` - Measure for both nuclei and a background region: - Maximum intensity - Average intensity - Median intensity - Sum intensity - Discuss how to correct the intensities for the background - Measure the region areas in pixel units - Watch out: the image is calibrated! - Use the area for the correction. ### Formative assessment ### Formative assessment Which statements are true? Fill in below blanks with those 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. ### Formative assessment ### Formative assessment ... ...
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