Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

Dr. Kota Miura is a Freelance Bioimage Analyst and works with various research groups and companies in Europe, for teaching, consulting, and collaborations. He also is affiliated with the Nikon Imaging Center at the University of Heidelberg and is the Vice-Chair of NEUBIAS (the Network of European Bioimage Analysts). Nataša Sladoje is Professor in Computerized Image Processing at the Centre for Image Analysis, Department of Information Technology, Uppsala University, Sweden. She is coordinator of a Master’s programme in Image Analysis and Machine Learning at Uppsala University and has a long experience in education in this field. Her research interests include theoretical development of image analysis methods for robust image processing with high information preservation, robust methods for image comparison and registration, as well as development and applications of machine and deep learning methods particularly suitable for biomedical image analysis.  She is the founder and leader of MIDA – Methods for Image Data Analysis – research group at Department of Information Technology, Uppsala University, and an active member of NEUBIAS – the European Network of Bioimage Analysis.

• Introduction.- Batch Processing Methods in ImageJ.- Python: Data Handling, Analysis and Plotting.- Building a Bioimage Analysis Workflow Using Deep Learning.- GPU-Accelerating ImageJ Macro Image Processing Workflows Using CLIJ.- How to Do the Deconstruction of Bioimage Analysis Workflows: A Case Study with SurfCut.- i.2.i. with the (Fruit) Fly: Quantifying Position Effect Variegation in Drosophila Melanogaster.- A MATLAB Pipeline for Spatiotemporal Quantification of Monolayer Cell Migration.