Image processing and analysis for scientific publications

Live-Webinar: Image Processing and Analysis for Scientific Publications

Dr. rer. nat. Jan Brocher ( will hold an intensive live-webinar for doctoral students, scientific staff and postdocs, working or planning to work with digital images and to publish them in scientific journals. The former 2.5-day workshop has been redesigned into a 3.5-day live webinar including a new half-day Call4Help session to deal with concrete, topic-specific questions from participants or working groups. The webinar 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 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 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 dont's as well as a practical guideline 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 workshop 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 bring

  • 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


01.09.- 04.09.2020

Key Data

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

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.