GRANATTraining Courses
Image Processing and Analysis for Scientific Publications

Workshop: Image Processing and Analysis for Scientific Publications

Dr. rer. nat. Jan Brocher ( will hold an intensive workshop for doctoral students, scientific staff and postdocs, working or planning to work with digital images and to publish them in scientific journals. The workshop is focused on micrographs and related imaging techniques in life sciences or biology. However, it is also of general interest for all natural scientists working with digital images and respective analyses, e.g. in soil sciences or material sciences.  The workshop aims to teach scientists of different research areas how to handle, process and analyze digital images starting from correct image acquisition until the incorporation into the final publication figure.


Important theory will be included about high quality digital images in general, information beyond the obvious pixels as well as a broad spectrum of methods for correct image processing and specific analytical purposes according to high scientific standards. The workshop aims to impart a better understanding about the Do's and Don'ts during digital image processing for publication figures (contrast, brightness, rotations, size changes, etc.). Methodological insights will be provided on how to extract a wide range of information from scientific images. The limits of image processing and analyses will be pinpointed. Participants will gain extensive knowledge about the possibilities they have to analyze imaging data. Using the scientific open source software Fiji/ImageJ in hands-on sessions the following questions will be answered: How to extract a maximum of information from images (e.g. with respect to numbers of objects or areas of interest)? How to quantify intensities correctly? How to automate tedious and repetitive processing tasks?

Helpful advices will be presented how to build figures for scientific publications in a manner preserving image quality and storing processing data. Participants will be able to revisit the information gained during the course using the provided exercises and the course script. To meet participants’ needs potential optional topics will be adjusted. Furthermore, specific participants’ questions regarding image processing or solutions for analysis issues can be discussed individually, if communicated in advance with example images. During the workshop’s practical sessions, the Fiji/ImageJ professional software will be used. No previous software knowledge required. All necessary software will be provided and installed during the course (open source).

Central Issues

  • Basics in microscopy and imaging acquisition (theory)
  • File types, digital images, metadata, bit-depth and the image histogram
  • Scaling of images, scale bars and labeling
  • Uneven lighting correction and diverse background correction methods
  • Correct image adjustments (contrast, brightness, size and rotations)
  • DOs and DON'Ts during publication figure creation
  • Image segmentation – data extraction from scientific images

Please Bring

  • Your own laptop

Central Issues and Course Description


01.09.- 03.09.2020

Key Data

  • Course language: English
  • 15 participants
  • Duration: 20 hours, 2.5 days
  • NEW: Call4Help-Session on day 3 to solve participant-specific image analysis challenges
  • Lecturer: Dr. J. Brocher
  • Course number: 80003

Registration possible from 06.04.2020

Deadline for registration: 16.07.2020
* Criteria for the allocation of places

*Criteria for Allocation of Course Places

As a first priority, the workshop places will be awarded to doctoral students, postdocs and scientific staff of the Faculty of Natural Sciences at Leibniz University Hannover (LUH). However, registrations from other faculties of the LUH and of Hannover Medical School (MHH) are also considered. Participation fees see fee list! Basically, the places are awarded in each case in the order of registration. The participants and rejected applicants receive a notification by e-mail.