12-16 April 2021
Europe/Berlin timezone


Here you will find the slides. We will release them after the lecture for the day has concluded.

Download link Description
FSU_OIAC_2021_April_Day1_part1.pdf Microscopy and Imaging, part 1.
FSU_OIAC_2021_April_Day1_part2.pdf Microscopy and Imaging, part 2.
FSU_OIAC_2021_April_Day1_part3.pdf Microscopy and Imaging, part 3.
FSU_OIAC_2021_April_Day1_part4.pdf Microscopy and Imaging, part 4.
FSU_OIAC_2021_April_Day2_Image_Analysis_Basics.pdf Image analysis: Basics
FSU_OIAC_2021_April_Day2_Analysis_Blobs.pdf Blobs example in Fiji/JIPipe/Icy/KNIME
FSU_OIAC_2021_April_Day2_Analysis_Glomeruli_ImageJ.pdf Glomeruli example in Fiji
FSU_OIAC_2021_April_Day3.pdf Homework discussion


As mentioned in the microscopy lecture, here you can find a very nice video about the quantum mechanics behind light bending, explained in a very easily understandable way: https://www.youtube.com/watch?v=cep6eECGtw4

Excellent interview with Stefan Hell about MINFLUX and MINSTED: https://www.youtube.com/watch?v=G5cdAmo6so4


Here are the Icy, KNIME, and JIPipe workflows that we worked on in the lecture:

Download link Description
blobs-icy.protocol Icy protocol
blobs-jipipe.jip JIPipe project file
blobs-knime.knwf KNIME workflow (import it via File -> Import KNIME workflow)


Here you will find recordings of the lectures. Unfortunately we accidentally did not record the ImageJ session, so we provide you with the recording from 2020. If you cannot play these files, try to use software like VLC.

Download link Description
OIAC_Microscopy_Part1.mp4 Microscopy part 1
OIAC_Microscopy_Part2.mp4 Microscopy part 2
OIAC_Microscopy_Part3.mp4 Microscopy part 3
OIAC_Microscopy_Part4.mp4 Microscopy part 4
OIAC_Image_Analysis_Basics.mp4 Image analysis basics
OIAC_2020_Image_Analysis_ImageJ.mp4 Image analysis: ImageJ (2020)
OIAC_Image_Analysis_JIPipe.mp4 Image analysis: JIPipe
OIAC_Image_Analysis_Icy.mp4 Image analysis: Icy
OIAC_Image_Analysis_KNIME.mp4 Image analysis: KNIME


Here you will find recordings of the homework session. Please use 7-zip to unpack the multi-part ZIP files (*.zip.001 - 004). You need to download all parts into the same folder. Unpack the *.001 file - 7-zip will automatically pick up the other files. We had to split it due to a file size limit.

Download link Description
OIAC_Homework_Microscopy.mp4 Microscopy homework
OIAC_Homework_Image_Analysis.zip.001 Image analysis homework
OIAC_Homework_Image_Analysis.zip.002 Image analysis homework
OIAC_Homework_Image_Analysis.zip.003 Image analysis homework
OIAC_Homework_Image_Analysis.zip.004 Image analysis homework