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How do I get started with image analysis?

Posted by Rachel Lee, on 15 December 2025

Given the abundance of image analysis tools, it can be difficult to know where to get started with analyzing microscopy images. In this post, we provide a framework for getting started with image analysis that focuses on experimental design and the extraction of informative biological results.

A new version of TrackMate with improved integration of key AI algorithms and track edition improvements

Posted by Jean-Yves Tinevez, on 12 December 2025

We’re excited to announce TrackMate v8.1, the latest version of Fiji’s powerful cell and organelle tracking plugin. This release combines all the major features from v8 with important usability improvements, making TrackMate more useful and easier to use than ever before. What is TrackMate? TrackMate is an extensible, open-source tracking software designed for biologists and

Register for Journal of Cell Science Meeting on Imaging Cell Dynamics

Posted by FocalPlane, on 15 September 2025

Registration is open for Journal of Cell Science Meeting on Imaging Cell Dynamics. The meeting will bring together experts working at the interface between cell biology and imaging, with a focus on researchers who use advanced light and electron microscopy approaches, and novel image analysis tools.

Connecting Researchers Through Bioimaging: Reflections from UCL’s BioImage Interest Group

Posted by Courtney Lancaster, on 11 August 2025

Bioimaging: A bridge across scales and disciplines Bioimaging has become a cornerstone in modern biological research, allowing scientists to visualise the intricate structures of cells and organisms. It also allows us to bridge biological scales — from whole organisms down to molecules. Beyond its beautiful images, bioimaging provides crucial quantitative insights into a whole host

Structural Repetition Detector (SReD): quantitative mapping of molecular complexes through microscopy

Posted by Afonso Mendes, on 23 September 2024

Unbiased, multi-dimensional, multi-scale and GPU-accelerated analysis of structural patterns across all microscopy modalities From biomolecules to larger assemblies and cellular architectures, molecular structures govern biological processes. Identifying these repetitive patterns is essential to understand their functions and the underlying biological mechanisms. While microscopy offers molecular-level detail, manually detecting structural motifs is labor-intensive, susceptible to bias,

QuPath and scripting - why isn't it easier?

Posted by Laura Nicolas-Saenz, on 29 March 2024

As I explained in my previous post, this journey began because I needed to learn how to master QuPath. I turned it into a vlogging affair to be held accountable, help others, and use it to find common user problems. For the last six weeks I have explored all the ways QuPath can easily help

From Zero to QuPath Hero - A journey unveiled

Posted by Laura Nicolas-Saenz, on 22 March 2024

Laura, a postdoc researcher in biomedical image analysis and artificial intelligence, embarked on her journey with a dedication to improving image analysis tools after completing her PhD at Universidad Carlos III, Madrid. Joining the QuPath team in June 2023, she found an ideal environment to contribute her expertise and innovate in the field. Despite facing

“Image analysis workshop” in Dublin (Ireland) - 24-25/04/2024

Posted by Stefania Marcotti, on 14 March 2024

This two-day workshop on April 24th-25th 2024 is designed to empower microscopists and researchers with the necessary skills and tools to confidently analyse their data. Under the instruction of experienced core facility staff from the Francis Crick Institute and King’s College London, participants will be introduced to open-source tools such as FIJI and napari, and

FocalPlane features... microscopy-based outreach

Posted by FocalPlane, on 11 March 2024

The first webinar of our new series of FocalPlane features... focussed on microscopy-based outreach. We hosted fantastic talks from Paola Moreno-Roman from Foldscope Instruments and Martin Jones from The Francis Crick Institute and we share the recordings here.

Need Deep Learning support for your image analysis project?

Posted by Marianna Poli, on 5 February 2024

The Second AI4Life Open Call, tailored to offer Deep Learning support to life scientists dealing with image analysis challenges, is open.

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Microscopy-related articles from our journals

Toggle-Untoggle – a cell segmentation tool with an interactive user verification interface J Cell Sci 2025 138: jcs264154
The ratio of Wnt signaling activity to Sox2 transcription factor levels predicts neuromesodermal fate potential Development 2025 152: dev204661
The short isoform of Tango1 is dispensable for zebrafish survival but is required for skeletal patterning and integrity Biology Open 2025 14: bio062117

Microscopy-related preprint highlights

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Microscopy-related articles from our journals

Microscopy-related preprint highlights

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