Editing, Processing and Analysis of Scientific Images

BioVoxxel Workshops – “Processing and Analysis of Scientific Images”

The course consists of different basic hands-on modules which deal with scientifically correct image editing, basic image processing methods as well as standard image analyses (counting, size and shape measurements, selection creation and intensity measurements). The course content has a focus on micrographs and fluorescent microscopical images. It is constantly reviewed and updated to keep up with the rapidly changing data acquisition and analysis necessities as well as scientific ethics guideline suggestions.

Course 1 (basic): Scientific Image Editing and Figure Creation (2-day course), 12.-13.03.2026

Best practice in handling and editing of scientific images for publications and efficient figure creation methods according to highest ethical standards.

• Proper and efficient image editing for publications
• Handling channels, colors, calibration and sale bars
• Good scientific principles for publication figures
• Diverse image correction methods (lighting, background,…)
• Correct contrast adjustment for publications
• Prevent data-loss at each step towards your figure!
• Efficient figure creation in Inkscape

 

Course 2 (intermediate): Basic Microscopic Image Processing and Analysis (2-day-course), 16.-17.04.2026

Learn all necessary basics to understand and perform image analysis and feature extraction step-by-step. Build the foundation for more advanced techniques.

• Introduction to Fiji / ImageJ and basic functions
• Proper scientific image file formats, metadata, and a lot more
• Understand and successfully use image pre- and post-processing
• Object detection and segmentation techniques
• Automatic ROI (region of interest) creation
• Basic insight into user friendly machine learning in Fiji
• Quality control of segmentation results
• Different basic automatic analyses such as object counting, measurements, shapes, intensities, and more
• Info on how to extend the course knowledge to 3D data
• Introduction to macro recording for analysis automation

 

Course 3 (advanced): ImageJ Macro Scripting for Automatic Image Analysis (2-day-course), 11.-12.05.2026

Bring image analysis to the next level with automated processing, feature extraction, analysis as well as file and data handling with ImageJ macro programming.

• Basic ImageJ macro recording of a general image analysis pipeline
• How to use variables and macro commands
• Looping over image files, table data, ROIs
• Interaction between user and macro
• Customized measurements and objects classification
• Interacting with customized tables
• Handle folder structures and flexibly saving all data
• Testing conditions and integrate automatic decision making
• Write reusable functions and customized dialogs
• Making your own ImageJ menu with your own macros
• Recommended: If you do not have prior experience, visit first the Basic Microscopic Image Processing and Analysis course

Find more information on the website: BioVoxxel

For more infortmation and registration, please write the IRTG coordinator (laura.ambrosius@med.uni-muenchen.de).

Location:

Online (Zoom)