From 0ddf1765421e92ad9193f82a4f717f9f3bbc138f Mon Sep 17 00:00:00 2001 From: Christian Tischer Date: Mon, 1 Apr 2019 18:23:38 +0200 Subject: [PATCH] EMBL Course --- workshops/bioimage-analysis-fundamentals.md | 63 ++++++++++++++------- 1 file changed, 43 insertions(+), 20 deletions(-) diff --git a/workshops/bioimage-analysis-fundamentals.md b/workshops/bioimage-analysis-fundamentals.md index f2d5628..6366c5a 100644 --- a/workshops/bioimage-analysis-fundamentals.md +++ b/workshops/bioimage-analysis-fundamentals.md @@ -307,14 +307,12 @@ Which statements are true? - - ### Activity: Segment objects and measure shapes - Open image: `xy_8bit__two_cells.tif` @@ -323,37 +321,62 @@ Which statements are true? ### Formative assessment -Which statements are true? +Fill in below blanks, using these words: -- a -- b -- c +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. +## 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: Intensity measurements without pixel based background correction + +#### Motivation -### 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 -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 -- 2.26.2