Announcing AI in Microscopy: A BioImaging Guide

We are pleased to announce the release of AI in Microscopy: A BioImaging Guide!

Advances in AI are rapidly transforming biomedical microscopy, but many end users do not benefit from these advances, in part because of a barrier to entry due to lack of foundational knowledge. Our goal is to inspire microscopists and biologists alike by illustrating how AI can enable their research.

This free, online, interactive textbook features chapters from several leaders in the field:

• Preface by Teng-Leong Chew, Rachel M. Lee, Owen F. Puls (HHMI Janelia Research Campus)
• AI in a Nutshell by Stephan Saalfeld (HHMI Janelia Research Campus)
• Large Language Models and AI Agents by Wei Ouyang & Hanzhao Zhang (SciLifeLab | KTH Royal Institute of Technology)
• Architectures and Loss Functions by Carsen Stringer & Marius Pachitariu (HHMI Janelia Research Campus)
• Collecting Training Data by Martin Weigert (Technische Universität Dresden)
• Image Restoration by Yue Li, Jun Zhu, Mingzhe Wei, Hari Shroff, Min Guo (Zhejiang University & HHMI Janelia Research Campus)
• Object and Event Detection Within Microscopy Images by Victoria Augoustides, Giorgio Tortarolo, Alara Kiris, Suliana Manley, Wesley Legant (University of North Carolina at Chapel Hill & École Polytechnique Fédérale de Lausanne)
• How to Find and Select a Tool by Beth Cimini & Erin Weisbart (Imaging Platform | Broad Institute)
• How to Train and Use Deep Learning Models in Microscopy by Joanna W. Pylvänäinen, Iván Hidalgo-Cenalmor, Guillaume Jacquemet (Åbo Akademi University)
• Output Quality by Morgan Schwartz & Diane Adjavon (HHMI Janelia Research Campus & Biohub)
• Outlook by Anna Kreshuk (EMBL)

Explore the book at bioimagingai.janelia.org. Whether you’re new to AI or already using it, we hope this book gives you the confidence to apply these tools to your own imaging questions.