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Workshop: Scientific Image Processing and Analysis

IRTG Workshops SFB1116 Seminars

Workshop Description

The workshop – “Scientific Image Processing and Analysis” aims to teach natural scientists from different areas of life science how to handle and process digital images starting from microscopic image acquisition on until the incorporation into the final publication figure. This includes important theory about high quality digital images in general as well as a broad spectrum of methods for correct image processing and specific analytical purposes according to high scientific standards. You will learn how to extract most information from your images and how to quantify regions of interest. Additionally, the workshop includes a lot of hands-on sessions and explains how to save time during repetitive image processing steps You will be able to revisit the learned material using the provided exercises and script also later on. The workshop content is generally of importance for scientists working with digital images and their analysis.


Specific Topics (among others)

  • Basics about correct image acquisition 
    • Image formats - which formats serve scientific images and which should be avoided
    • Metadata - information saved beyond the visible image
    • Information content of images - learn about bit-depth, color spaces and different image types (or: how much information can be saved in and retrieved from an image).
  • Correct image adjustments avoiding alterations - contrast and brightness, image rotation, size changes, background subtraction methods.
  • Use of different image filters to improve extractability and preparation for further analysis
  • Image segmentation - How to extract specific objects of interest (e.g. cells positive for a certain marker stain)
  • Automated object counting
  • Image Quantifications (selected topics depending on participants field of interest): 
    • Measurements of areas, area fractions, shapes, intensities…)
  • Dimension scaling of images
  • Labeling of (scale bars, calibration bars,…)
  • Ethics in image handling, processing and publication - where are the limits?!
  • Process automation using macro recording and batch processing. 



The workshop should give scientists a better understanding about the Do's and Don'ts during digital image processing and insight in the methodology of extracting a multiplicity of information from their images. The participants will gain extensive knowledge about the possibilities they have to analyze their imaging data.


Target Group

PhD Students and PostDocs working or planning to work with digital images. The workshop has a focus on microscopic images but all the content is applicable for digital images of different origin in general. No previous software knowledge required, but of advantage.



During the practical parts of the workshop we will use the professional software Fiji (customized ImageJ bundle). The software is free and installation instructions will be given in advance.


Workshop language: English

Trainer: Dr. rer. nat. Jan Brocher (www.biovoxxel.de)

Registration link



Beginn: 01.09.2021, 09:00 Uhr
Ende: 03.09.2021, 15:00 Uhr
Ort: Online Workshop