12-16 April 2021
Digital
Europe/Berlin timezone

Exercise

Those attendees who would like to receive the credit points for this course will need to submit their homework by Thursday evening and they need to pass the 50% threshold both in the "Microscopy and Imaging" block (to take place on Monday) and the "Image Analysis" block (Tuesday).

To solve this exercise, you will need to install JIPipe, Icy, and KNIME. Please follow the installation instructions provided here.

The image analysis exercise contains a part where you will fill out a mandatory survey. You will not recieve any credit points if you do not fill out the survey.

While attendees who will not receive credit points are not required to fill out the home work, we invite them to at least do the image analysis exercise and fill out the survey, as this will provide helpful data for evaluating the ease-of-use of image analysis software.

The homework will be made available on this page.

Download Description
MicroscopyExc Exercise "Microscopy and Imaging"
ImageAnalysisExc Exercise "Image Analysis"
12-39-10_Kontrolle 1a zoom063 z5 647_UltraII_C00_xyz-Table Z0311.ome.tif Image slice to be analyzed in this exercise
12-39-10_Kontrolle 1a zoom063 z5 647_UltraII_C00_xyz-Table Z0311_cutout.tif Image slice (cut-out). Use this if KNIME is slow with extracting glomeruli.
Glomeruli_exercise.jip JIPipe project file
Glomeruli_exercise.knwf KNIME project file
Glomeruli_exercise.protocol Icy project file
Glomeruli_solution.jip Solution: JIPipe project file
Glomeruli_solution.knwf Solution: KNIME
Glomeruli_solution.protocol Solution: Icy