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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.

Imaging spotlight: Volumetric Imaging via Photochemical Sectioning (VIPS)

Posted by FocalPlane, on 2 December 2025

In this paper highlight, we learn more about VIPS, a method developed by Srigokul Upadhyayula, Ruixuan Gao and colleagues.

Africa Microscopy Initiative redistributes research-grade light microscopes to four African institutions

Posted by Africa Microscopy Initiative, on 7 October 2025

Four research institutions in Senegal, Nigeria, Cameroon, and Ethiopia have been selected to each receive a microscope for advancing scientific research in Africa.

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

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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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