====== 2012 EMBO High-throughput Microscopy Practical Course ======

Dates: 2012.10.15-20
Place: ATC, EMBL Heidelberg

  - Slides for the practical {{:documents:documents:p11_embohtm2012_nucrimdynamics.pdf|"Writing ImageJ macro for analyzing intensity dynamics at nuclear edge"}} 
    - With Andrea Boni @ Ellenberg Lab
    - Abstract: The students will learn basics of image analysis of time lapse data. We will first go through preprocessing steps: filtering, noise reduction and background subtraction. We then move on to image thresholding and segmentation techniques, which allow us to objectively define region of interest (ROI) where the temporal dynamics of signal intensity are measured. Automation is an esseitial aspect in highthroughput imaging. In this session, students will be guided to learn how to automate the imaging processing steps that we went through manually. Scripting is necessary for automation. For this reason, a brief introduction to code ImageJ macro will be provided and students will learn to write a short macro that processes raw data and outputs results automatically. 
  - {{https://github.com/cmci/ijmacros/blob/master/nucRim2.py|Demo script}} (written in Jython)
  - Student ImageJ macro: {{https://gist.github.com/3911066|example}}