Trust me I’m a scientist

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

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.

Coffee Break

Coffee and snacks will be served at the venue

Bioimage analysis fundamentals

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.

Lunch break

Lunch will not be provided at the venue. Participants are encouraged to organize their lunch breaks according to their own prefferences.

Common mistakes in bioimage data handling

Intended vs unintended inappropriate image-based data handling, most common mistakes and unethical practices as well as ethical guidelines will be discussed

Making Science More Reliable

Paper mills, research misconduct and what science community is doing to make science more reliable will be discussed

Coffee break

Coffee and snacks will be served at the venue

Artificial intelligence and bioimage data handling

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.

Basic of digital image processing

Dr. Holger Lorenz and Dr. Severina Klaus

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 practiced. Coffee break will be included.

Lunch break

Lunch will not be provided at the venue. Participants are encouraged to organize their lunch breaks according to their own prefferences.

From the raw image to data presentation and publication

Hands-on workshop where raw images will be processed in order to prepare them for presentation and publication. Brightness and contrast adjustment, pseudocolors, scale bar, image annotation etc. will be shown.

Segmenting images with the help of AI

Hands-on workshop where tools for AI-based image segmentation will be presented and applied to microscopy data

Coffee break

Coffee and snacks will be served at the venue

Forensic tools to inspect digital image integrity

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