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In-class problems

In-class problems#

In-class Problems Week 11

../../_images/blobs-homework.png

Preview of the homework image. To work on homework, please download the source of the image from Github-ScopeM-teaching Note: the image appears empty (completely white), but it is only visualisation…#

For the homework, you are required to work on the image shown above (download from Github-ScopeM-teaching - do not use the image above for quantification - your results will be wrong!).

The quiz is posted on Moodle under ‘Quizzes’ and requires answers to the following questions:

  1. Find out how many pixels are in the image blobs-homework.png?

  2. Count the number of ‘blobs’ in blobs-homework.png, following the criteria provided below, and report the number.

  • Segment blobs-homework.png using thresholding (use the Intermodes algorithm to determine the threshold, then configure and run Analyze > Measure Particles).

  • Include partial blobs (i.e. touching the edges)

  • Do not perform any pre-processing on the input image before (e.g. blur) nor post-processing of outputs (e.g. separation of touching blobs)

  • Exclude blobs with area smaller than 100 pixels

  1. Measure some intensity values of the image and report the numbers (in ImageJ/Fiji, use Analyze > Measure, after configuring what is measured in Analyze > Set Measurements…. Feel free to use Python or other software). We allow an error of about 5%, due to the handling of rounding by different software.

  • Mean intensity of image

  • Median intensity of image

  • Standard deviation of intensities of image

  1. Measure the mean gray-scale value of all segmented blobs. We allow 10% error in case your segmentation differs from the “correct” answer in 2.

  2. Measure the average size (number of pixels) of segmented blobs. We allow 10% error in case your segmentation differs from the “correct” answer in 2.