U2OS cells transfected with an Mx1-GFP plasmid (signal enhanced using Alexa Fluor 488-conjugared anti-GFP antibody) and co-stained for nuclear DNA (Hoechst 33342), microtubules (Alexa 555) and F-actin (ATTO 643). Image was captured on Mateo FL.

Microscopy and AI Solutions for 2D Cell Culture

A practical guide to enhancing 2D Cell Culture through imaging and automation

U2OS cells transfected with an Mx1-GFP plasmid (signal enhanced using Alexa Fluor 488-conjugared anti-GFP antibody) and co-stained for nuclear DNA (Hoechst 33342), microtubules (Alexa 555) and F-actin (ATTO 643). Image was captured on Mateo FL. U2OS_cells_enhanced_co-stained_for_DNA_microtubules_F-actin.jpg

This eBook explores the integration of microscopy and AI technologies in 2D cell culture workflows. It highlights how traditional imaging methods—such as brightfield, phase contrast, and fluorescence—support routine cell monitoring, while digital platforms like the Mateo TL and FL enhance reproducibility through automated confluency checks, cell counting, and transfection analysis. It also shows how integrated data management, audit trails, and sample tracking improve documentation and research integrity. The book concludes with a look at future trends, including microfluidics and hybrid 2D–3D systems, emphasizing the growing need for advanced imaging tools to meet evolving research demands.

What you’ll learn from this ebook?

  • How to optimize 2D cell culture workflows using digital microscopy and AI for greater consistency and reproducibility.
  • How to boost confluency checks, cell counts and transfection analysis with automated tools that reduce human error.
  • How to improve data management and tracking through integrated audit trails, user management, and barcode-enabled traceability
  • How to stay ahead of emerging trends like microfluidics and hybrid 2D–3D systems with adaptable imaging platforms.

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"This resource is a result of a collaboration between Leica Microsystems and Bitesize Bio, created to help you understand the intersection of 2D cell culture and modern imaging technologies. We hope you find it both accessible and applicable to your research.

Our aim is to share practical knowledge that helps scientists overcome real-life challenges at the bench.


2D cell culture may be familiar, but getting the most out of your cultures increasingly depends on understanding microscopy and imaging—areas that can feel like someone else’s specialty.

However, you may find that by learning just a little more about microscopy technologies, you can expand what’s possible in your experiments. The right imaging approach can help you answer new biological questions, generate more reliable data, and improve the efficiency of routine steps you already perform, such as checking confluency, monitoring transfections, or counting cells.

We wrote this eBook to provide you with the tools to bring microscopy and AI analysis to your 2D cell culture with confidence. In the chapters ahead, we explore both traditional and digital imaging techniques,alongside AI-powered tools that simplify complex analysis tasks, and improve data documentation. By combining these technologies with your existing cell culture expertise, you can bring greater consistency,reproducibility, and confidence to your work."

Skye Marshall and Thomas Warwick
Editors, Bitesize Bio 

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