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Annotating 3D images in napari

Posted by Mara Lampert, on 30 March 2023

This blog post revolves around generating ground truth in 3D images for segmentation. Therefore, we will define what ground truth is and how we can generate it using napari in a time-efficient way. We will also learn about difficulties of annotating alone or in groups and address possible solutions for both. Challenges of image segmentation

Rescaling images and pixel (an)isotropy

Posted by Mara Lampert, on 2 March 2023

This blog post shows the importance of rescaling 3D image data and what anisotropy of pixels/voxels has to do with it. We will see which different options exist to rescale an image as well as their advantages and limitations. We will also apply a commonly used segmentation algorithm, Voronoi-Otsu-Labeling, on the original and the rescaled

VollSeg and its extension Napari plugins

Posted by varun kapoor, on 15 January 2023

In this article we present the Napari plugin VollSeg and its ongoing extension plugins that we are creating as a part of the CZI grant awarded successively to the non-profit company KapoorLabs, Paris. VollSeg is a Napari plugin for performing semantic, instance segmentation and denoising using the seed pooling approach that requires StarDist and either

Job Opportunity: Scientific Officer on Smart Microscopy at the Centre for Cellular Imaging of Gothenburg University

Posted by Rafael Camacho, on 9 January 2023

We are looking for a new colleague (Scientific Officer) at the Centre for Cellular Imaging of Gothenburg University (CCI). The CCI, in operation since 2003, is a national research infrastructure and one of the leading academic imaging facilities in Sweden providing expertise and access to advanced microscopy to the research community, both locally and at other Swedish

PhD Studentship: Engineering the properties of coherent light sources for in situ diagnostic and intervention in surgical robotics 2023

Posted by Rodrigo Aviles, on 19 December 2022

The Robotics and Mechatronic Systems research group is currently looking for a highly motivated person aiming to obtain a PhD in photonics at the University of Sussex . This PhD project will focus on studying the light tissue interaction using novel laser technologies. Through the implementation of microscopy and photonic technologies the candidate will develop

Crick BioImage Analysis Symposium (CBIAS) 2022 - a review

Posted by Stefania Marcotti, on 14 December 2022

Did you want to participate in the Crick BioImage Analysis Symposium (CBIAS) but missed it? Are you planning to join us next year for CBIAS2023 but unsure if it would be relevant for you? We’ve asked three of this year’s participants to tell us about their experience and collated their reports here! We’ll hear from

Microscopy in Africa – an interview with Michael Reiche

Posted by Helen Robertson, on 29 July 2022

We talk with Michael Reiche about the recently launched African Microscopy Inititiative and two other imaging-related programmes in Africa that he is overseeing

Imaging Specialist - University of Warwick

Posted by Claire Mitchell, on 28 June 2022

Permanent Position, Full time – 36.5 hours per week The postholder will provide expert-level hands-on technical and user support for optical microscopy. The appointee will need to combine enthusiasm and careful attention to detail with adaptability. The post would suit an individual with a background in physics who wants to apply their skills to advance

Explorative image data science with napari

Posted by Robert Haase, on 23 May 2022

When analysing microscopy image data of biological systems, a major bottleneck is to identify image-based features that describe the phenotype we observe. For example when characterising phenotypes of nuclei in 2D images, often questions come up such as “Shall we use circularity, solidity, extend, elongation, aspect radio, roundness or Feret’s diameter to describe the shape

ELMI/FocalPlane image contest - deadline extended!

Posted by FocalPlane, on 20 May 2022

Does your work involve capturing stunning images on a microscope? Enter your image to our joint contest with ELMI (https://elmi2022.eu/) for a chance to win €250 and have your image featured on the cover of Journal of Cell Science. Competition details: The ELMI/FocalPlane image contest is open to anyone (not only participants of the ELMI

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Microscopy-related articles from our journals

Dynamics of intracellular cGMP during chemotaxis in Dictyostelium cells Journal of Cell Science 2023 136: jcs.260591
GliaMorph: a modular image analysis toolkit to quantify Müller glial cell morphology Development 2023 150: dev.201008
A novel class of sulphonamides potently block malaria transmission by targeting a Plasmodium vacuole membrane protein Disease Models & Mechanisms 2023 16: dmm.049950

Microscopy-related preprint highlights

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Microscopy-related articles from our journals

Microscopy-related preprint highlights

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