AI in Microscopy: A BioImaging Guide
Welcome
AI in Microscopy is an interactive online textbook intended to introduce biologists and microscopists to the fundamentals of artificial intelligence and machine learning.
The table of contents on the left can be used to navigate the book. Subsections of each chapter appear as a clickable menu on the right side of each chapter page. Key terms in each chapter are highlighted as links to the Glossary page. The upper left menu contains a toggle for using the website in dark mode.
A free PDF of the textbook can be downloaded from the upper left menu. Note that this PDF lacks some of the functionality of the online interactive book.
The source code for this textbook is available on GitHub. All content is licensed under BSD 3-Clause, except where noted otherwise.
Contributors
Teng-Leong Chew, Rachel M. Lee, Owen F. Puls
HHMI Janelia Research Campus
2 AI in a Nutshell
Stephan Saalfeld
HHMI Janelia Research Campus
3 Large Language Models and AI Agents
Wei Ouyang & Hanzhao Zhang
SciLifeLab | KTH Royal Institute of Technology
4 Architectures and Loss Functions
Carsen Stringer & Marius Pachitariu
HHMI Janelia Research Campus
5 Collecting Training Data
Martin Weigert
Technische Universität Dresden
6 Image Restoration
Yue Li, Jun Zhu, Mingzhe Wei, Hari Shroff, Min Guo
Zhejiang University & HHMI Janelia Research Campus
7 Adding AI to Hardware
Victoria Augoustides, Giorgio Tortarolo, Alara Kiris, Suliana Manley, Wesley Legant
University of North Carolina at Chapel Hill & École Polytechnique Fédérale de Lausanne
8 How to Find and Select a Tool
Beth Cimini & Erin Weisbart
Imaging Platform, Broad Institute
9 How to Train and Use Deep Learning Models in Microscopy
Joanna W. Pylvänäinen, Iván Hidalgo-Cenalmor, Guillaume Jacquemet
Åbo Akademi University
10 Output Quality
Morgan Schwartz & Diane Adjavon
HHMI Janelia Research Campus & Biohub
11 Outlook
Anna Kreshuk
European Molecular Biology Laboratory
AI Disclosure
Anthropic’s Claude (Sonnet 5 and Sonnet 5.5) assisted in identifying broken links, proof reading, and developing formatting solutions for this book. All content was reviewed, revised, and verified by the human editors and authors, who take full responsibility for the final text.