graph TD (TODO)
Activity: Measure intensities in image regions
- Open image: xy_float__h2b_bg_corr.tif
- Appreciate that this image is already background corrected.
- Measure for both nuclei: * Maximum intensity * Average intensity * Median intensity * Sum intensity
- Discuss the interpretation!
- Discuss where to measure!
Optional activity: Intensity measurements without pixel based background correction
There are several good reasons not to subtract the background from each pixel in an image:
- 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.
- 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 * Appreciate that you also need the region areas for this task * Measure the region areas * Watch out: the image is calibrated! * Use the area for the correction.
Formative assessment: Intensity measurements
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.