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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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Behind the Screen - behind the scenes of setting up a dynamic screening platform

Posted by , on 22 November 2021

The Cell Biophysics lab has focused on FRET (Forster Resonance Energy Transfer) as it is a powerful technique to investigate dynamic protein-protein interactions, along with studying almost every aspect of cellular signaling with biosensors. FRET is detected either by ratioing the  intensities of the FRET donor and acceptor,  or by FLIM (Fluorescence Lifetime Imaging ;
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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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Asymmetric cell divisions in 3 dimension stem cell colonies

Posted by , on 27 September 2021

When looking at the development of a multicellular organism, for example a human, the first striking feature is the progressive increase in cell numbers due to successive divisions, from one single tiny cell 80 mm in diameter to a 3.5 kg ball of organised cells forming a new-born baby. The way cells divide, in particular
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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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