Program
Day 1 Tuesday, November 28
Trust me I’m a scientist
Dr. Vibor Laketa
The content of the workshop will be introduced. The motivation behind the workshop as well as the current state of scientific affairs will be discussed.
Understanding the Digital Image
Dr. Holger Lorenz
The basic concepts necessary for understanding the digital bioimage data will be introduced. The presentation will be centered around the notion of images as matrix of numbers. Gray levels, 8-bit vs 16-bit vs 32-bit, colours, pixels, histograms, metadata, signal-to-noise ratio etc. will be discussed.
Bioimage analysis fundamentals
Dr. Holger Lorenz
What can typically be quantified/measured in microscopy-derived data? Basic tools to extract the numerical information from the bioimage data. Basic processing (background subtraction, thresholding) and common image processing pitfalls will be discussed in the context of ethical concerns.
Common mistakes in bioimage data handling
Dr. Vibor Laketa
Intended vs unintended inappropriate image-based data handling, most common mistakes and unethical practices as well as ethical guidelines will be discussed
Research misconduct - a journal point of view
Jana Christopher
The unethical manipulation of image data in scientific literature and in society in general will be examined. Case studies of scientific misconduct, consequences and publisher perspective. The current state of the art in data manipulation detection. Paper mills.
Artificial intelligence and bioimage data handling
Dr. Vibor Laketa
The application of machine learning in image processing and analysis is widespread in life sciences. Good scientific practice when using the AI to handle digital images will be discussed.
Day 2 Wednesday, November 29
Basic of digital image processing
Dr. Holger Lorenz
Hands-on workshop where basic tools to extract the numerical information from bioimages will be shown. Mathematical background and utility of various linear and non-linear operations will be discussed and practised. Coffee break will be included.
From the raw image to data presentation and publication
Dr. Vibor Laketa
Hands-on workshop where raw confocal and widefield images will be processed in order to prepare them for presentation and publication. Background subtraction, filtering, brightness and contrast adjustment, pseudocolors, scale bar etc. will be practiced
Forensic tools to inspect digital image integrity
Dr. Holger Lorenz
Automatic workflows and available software applications to check digital image integrity will be introduced.
Open forum
Open questions, discussions on presented topics, comments, concerns, suggestions, closing remarks
