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From Click to Code: Reproducibility in Bio-image Analysis

Posted by Mara Lampert, on 5 August 2025

Reproducibility is at the heart of good science. But when it comes to bio-image analysis, it can feel difficult to achieve. Complex datasets, shifting software environments, and countless manual tweaks often make it hard to retrace your own steps and share workflows with others. An aim should be to package the entire analysis, like code, data

Annotating Images in Cellpose

Posted by Lea Kabjesz, on 5 June 2025

In this blog post, I’ll show you how to manually annotate cells in 2D and 3D images using the Cellpose Graphical User Interface (GUI). Manual annotation is a key step in many bioimage analysis workflows. It allows you to create labeled data that can serve as a reference for evaluating segmentation quality – or even

The Foldscope: my portal to another world

Posted by Amy Lowell, on 24 January 2025

Hi, my name is Amy, I’m fifteen years old and I am here to tell you about my Foldscope! What is a Foldscope? A Foldscope is a portable, flat microscope that can fit into your back pocket. It is made of cardboard, cut then folded, and fitted together. The microscope is inspired by origami, hence

Highlighting signalling biosensors 1.

Posted by Greg Redpath, on 16 January 2025

Why there is interest in signalling biosensors, considerations for using biosensors, and the original biosensor, GFP. Why write about signalling biosensors? In my first postdoctoral position, I was introduced to the concept of endosomal signalling- a way for receptor signalling outcomes to be changed by delivering a signal to different regions of the cell. I

Probes 101 – How to choose a fluorescent probe for your imaging experiment

Posted by Lina El Hajji, on 14 December 2024

Fluorescence microscopy is a powerful tool for the visualization of the intricate biological processes occurring within biological organisms. Just like you can make important pieces of information pop up in their notes using colorful highlighters, biologists have at hand a large toolkit of “highlighters” to make their favorite targets stand out in the complex cellular

SAM for Bioimage Analysis: A Comprehensive Guide

Posted by Ranit Karmakar, on 10 December 2024

Image segmentation has always been a cornerstone of image analysis, and in bioimage analysis, its significance cannot be overstated. Precise segmentation of regions of interest is crucial for downstream analysis, yet the inherent complexity of biological data makes this task particularly challenging. While numerous segmentation methods exist, the field has long sought a generalist model

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.

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Microscopy-related articles from our journals

HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples Development 2024 151: dev202307
filoVision – using deep learning and tip markers to automate filopodia analysis J Cell Sci 2024 137: jcs261274
C omputational tools for quantifying actin filament numbers, lengths, and bundling Biology Open 2024 13: bio.060267

Microscopy-related preprint highlights

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