General information

• Target audience: PhD programs (e.g. graduate schools, SFBs, research training groups, etc.)
• 2 days online workinar (via Zoom), daily 9:00 to 15:00 (CET)
• Live, guided by Dr. Jan Brocher and interactive
• up to 12-15 participants (course dependent, see below)
• Group price includes:
  • preparation
  • course material
  • individual participation certificate
• Feedback retrieval (optional)

Scientific Image Editing and Figure Creation

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
• up to 15 participants

Scientific Illustration

Communication of scientific results and research goes beyond tables and graphs.Visual presentation of key concepts can optimally convey your science in an understandable, catchy and attention grabbing way. This Masterclass shows you how.

• Introduction to Inkscape and its workspace
• Proper use of colors and color combinations for scientific communication
• From basic shapes to stunning 3D visuals
• Shading, gradients, image-blending, labeling, and more
• Integrate external data into your design (e.g. PDB protein structures)
• Complete one big design project step-by-step from scratch
• up to 12 participants

Basic Microscopic Image Processing and Analysis

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
• up to 15 participants

ImageJ Macro Scripting for Automatic Image Analysis

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
• up to 15 participants

From Pixels to Patterns: Applying Machine Learning Tools for Advanced Image Analysis

Complex image analysis tasks need next-level software tools and knowledge to extract meaningful data.

This course let’s you leverage the power of AI in image analysis.

• Installing and connecting different software packages
• Key concepts, benefits and limitations of ML in Image Analysis
• Hands-on guided exercises of specific analysis solutions
• Training pixel as well as object classifiers
• Applying pre-trained deep learning (DL) models to images
• Model improvement by customized re-training for non-programmers
• Connecting different Tools via Fiji as hub to streamlined workflows
• up to 12 participants