GRANATTraining courses
Image processing and analysis for scientific publications

Editing, Processing and Analysis of Scientific Images - for Academic Publications

Live Online-Workinar

Dr. rer. nat. Jan Brocher (BioVoxxel) will hold an intensive workshop in form of a workinar for doctoral students, scientific staff and postdocs, working or planning to work with digital images and to publish them in scientific journals. The 3.5-day online live-workinar includes a half-day Call4Help session to deal with concrete, topic-specific questions from participants or working groups. It is focused on micrographs and related imaging techniques in life sciences or biology and of general interest for natural scientists working with digital images and respective analyses, e.g. in soil sciences or material sciences. The online live-workinar aims to teach scientists of different research areas how to handle, process and analyze digital images starting from correct image storage, handling and editing until the incorporation into a final publication figure as well as extensive methods regarding automated image analysis.



Important theory will be provided about preserving high quality in digital images, a broad spectrum of methods for scientifically correct image editing and processing as well as specific analytical purposes according to high scientific standards. Participants learn how to extract different types of information from their images and how to quantify objects and intensities. Many hands-on sessions are included and methods to automate repetitive tasks to decrease time investment while reducing user bias.

Do's and don'ts as well as a practical guidelines will be provided regarding publication figure preparation. The workshop content is generally of importance for scientists working with digital images but it has a strong focus on microscopy, image processing and analysis as well as scientific correct image adjustments! Optional topics will be adjusted to meet the participants’ needs as good as possible. Specific participant’s questions will be discussed in the Call4Help session, if communicated beforehand (see below). During the practical parts of the workinar, we exclusively use the professional and free software Fiji. No previous software knowledge required but helpful. All necessary software will be provided (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 prepare

  • LAPTOP / Desktop-PC with stable WLAN-connection (a webcam) and best a second monitor
  • Headset or regular earbuds with a microphone

Central issues and course description

Key Data

  • Course language: English
  • 15 participants
  • Duration: 20 hours, 3.5 days
  • Call4Help-Session on day 4 to solve participant-specific image analysis challenges
  • Lecturer: Dr. Jan Brocher (BioVoxxel)
  • Course number: 80003

 Criteria for the allocation of places


04.07 - 07.07.2023

Deadline for registration: 13.06.2023

Criteria for allocation of course places

As a first priority, the online workinar 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.