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Displaying posts in the category: How to

Teaching co-localisation analysis from lecture to leisure

Posted by Romain Guiet, on 20 October 2024

The origin There was one thing I was always skeptical about: colocalization analysis. When I started out as a BioImage Analyst, it was one of the first things I had to help users with in the BIOP at EPFL. I started learning more about it (and still continue to do so), tried with my own

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,

FocalPlane features... data management

Posted by FocalPlane, on 23 September 2024

The fourth webinar in the latest series of FocalPlane features… was on data management. Caterina Strambio De Castillia introduced us to the topic of research data management, while Tom discussed how to use OMERO from the perspective of a group leader, a microscopist and an image analyst. We wrapped up the webinar with a short

MicroList and FocalPlane join forces

Posted by FocalPlane, on 2 September 2024

MicroList’s database of resources are now available on FocalPlane. The resources, which have been created by the global imaging community, are presented as cards that are divided into community resources, education resources and tools. The database is fully searchable using our search bar or can be filtered using a variety of categories.

BioImage.IO Chatbot: Ready to use and discover!

Posted by Caterina Fuster-Barceló, on 21 August 2024

We are delighted to announce the publication of the BioImage.IO Chatbot in Nature Methods this August and its immediate availability for the bioimaging community. This milestone signifies academic recognition and marks the chatbot’s readiness for everyday use in streamlining complex bioimage analysis tasks. Broadening Access to Advanced Bioimage Analysis The BioImage.IO Chatbot, equipped with state-of-the-art

DL4MicEverywhere - Overcoming reproducibility challenges in deep learning microscopy imaging

Posted by Iván Hidalgo-Cenalmor, on 29 July 2024

DL4MicEverywhere is out! Learn about it and how you can apply deep learning workflows on microscopy imaging in reproducible research and in a user-friendly manner across different systems.

Prompt Engineering in Bio-image Analysis

Posted by Mara Lampert, on 18 July 2024

Prompt engineering and its importance Communication is key. This saying is not only true in day-to-day life, but also when interacting with Generative Artificial Intelligence, a system able to generate text, images or other output types in response to prompts. In prompt engineering, we use natural language to describe the task that a Large Language

How to write a bug report

Posted by Mara Lampert, on 3 April 2024

Imagine you try out a software tool for the analysis of your data and for some reason it is not working in the way you expected. Neither the user documentation, nor forums like image.sc or stack overflow can provide answers. Then it is likely that you either found a bug in the software tool or

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.

New FocalPlane features... webinar series

Posted by FocalPlane, on 22 February 2024

We are excited to announce a new series of FocalPlane features… webinars. Our first webinar, on 7 March at 15:00 GMT (10:00 PET) focusses on outreach projects using microscopy, with talks from Paola Moreno-Roman, Alexander Strachan and Martin Jones.

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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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