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Explorative image data science with napari

Posted by , 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
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#GliaMorph - a tool to analyse glial cell morphology in 3D

Posted by , on 17 May 2022

Contents What is #GliaMorph? What can you do and analyse with #GliaMorph? Links to manuscripts and data Contributions and Feedback Thanks to all contributors and people providing feedback References What is GliaMorph? GliaMorph is a toolkit implemented as Fiji Macros to allow modular application to process and analyse Müller glia morphology in the retina. During
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FocalPlane features... Machine Learning

Posted by , on 3 March 2022

In case you missed ‘FocalPlane features…’ last month, here is the recording of the webinar given by Ricardo Henriques (Instituto Gulbenkian de Ciência), Estibaliz Gómez de Mariscal (Instituto Gulbenkian de Ciência) and Martin Weigert (EPFL) on Wednesday 16 February 2022.
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If you can detect it, you can track it - recent TrackMate developments

Posted by , on 17 February 2022

TrackMate is your buddy for your everyday tracking  TrackMate (Tinevez et al., 2017) is an open-source Fiji plugin initially made for tracking single particles imaged with fluorescence microscopes. It has now been updated to include a collection of new detectors and direct implementation of deep-learning models (Ershov, Phan, Pylvänäinen, Rigaud et al., 2021). In addition
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Janelia+EMBL BioImaging Seminar Series: How We Started a Successful Seminar Series during the Pandemic

Posted by , on 25 January 2022

How we started a global BioImaging seminar series in the middle of a global pandemic...
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FocalPlane features... Data Analysis for volume EM

Posted by , on 16 November 2021

In case you missed ‘FocalPlane features…’ this month, here is the recording of the webinar given by Anna Kreshuk (EMBL Heidelberg), Dagmar Kainmueller (MDC Berlin) and Jan Funke (Janelia Research Campus) on Monday 8 November 2021.
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Collaborative bio-image analysis script editing with git

Posted by , on 4 September 2021

TL;DR: I’m a computer scientist who often collaborates with biologists on bio-image analysis scripts. We are using more and more git, a version control program, for working on code collaboratively. When using git, we speak about repositories, commits and pushing to the origin. We also make forks, send pull-requests and merge code. This blog post
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From EUBIAS to NEUBIAS Academy: from trainee to trainer, how to fall in love with a community!

Posted by , on 20 July 2021

During my university time at physics, I specialised in biophysics and started to approach advanced microscopy, but my idea of measurement had always been connected with other instruments’ readouts, not exclusively images. Once obtained my MSc, I started to work in an imaging facility at IFOM (Milan), as a microscopist, becoming later also in charge
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Podcast about Bio-Image Analysis, Microscopy, and Science in General

Posted by , on 7 July 2021

Why a podcast? At my home university, I was formally trained as a chemist. That meant I spent significant amounts of my time in front of the lab bench. I loved lab work, and an important part of the lab’s culture was the radio. There was no successful chemistry without good radio in the background.
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Postdoc in Bioimaging and 3D bioprinting

Posted by , on 20 January 2021

A 2-year postdoc position is available in the Microenvironmental Ecology and Symbiosis group(see https://twitter.com/microsensing) at the Department of Biology, University of Copenhagen Application deadline is February 1, earliest start can be April 1 or later in 2021.Apply via this link: https://employment.ku.dk/faculty/?show=153173 I am looking for talented scientists with a PhD (or in the final phase
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