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VollSeg and its extension Napari plugins

Posted by , 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
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TrackMate-Oneat: Auto Track correction using deep learning networks

Posted by , on 4 July 2022

During the tracking of motile cells, solving the problem of linking objects between two consecutive timepoints becomes even more complicated, if the cells divide or undergo cell death. In the terms of trajectories, this means the addition of trajectory branches and terminations. However, dividing and dying cells are characteristic in their shape, and leveraging this
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Using an autocollimator to align 4f systems

Posted by , on 29 June 2022

Graeme Johnstone, Brian Patton, Department of Physics and SUPA, University of Strathclyde, Glasgow G4 0NG, United Kingdom Modern microscope systems comprise many optical elements with precise alignment tolerances. As such, as the complexity of the system increases, the challenge to align them rapidly becomes a major hurdle to implementing home-built designs. One recurring problem is
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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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Using the Dragonfly Spinning Disk Confocal to Understand the Molecular Basis of Epigenetics

Sponsored by Andor, on 28 March 2022

Silviya Dimova: Uncovering the Epigenetic Role of PRC2 in the Meehan Laboratory Epigenetics is the study of transmissible modifications in gene expression that are not encrypted in the genomic DNA, and for this reason, are named (Epi)genetic – (Above)genetics.  Epigenetics is linked with chemical modifications to DNA or chromatin proteins. A common epigenetic modification is DNA
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The Third Euro-BioImaging User Forum: “At the Forefront of Neuroscience”

Posted by , on 17 March 2022

Euro-BioImaging is organizing a third online User Forum on Tuesday, April 5, 2022 from 14:00-17:00 CEST. The topic is “At the Forefront of Neuroscience.” This event will highlight the importance of cutting-edge imaging technologies in support of brain research and showcase the specific expertise available at our Nodes across Europe through case studies presented in tandem with the research community.  Program:
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Imaging nuclear dynamics and chromatin organization in a live intact organism: the design of the minimal constraint device

Posted by , on 9 March 2022

To visualize the response of the nucleus and chromatin to mechanical signals, I developed a device that enables their imaging in a live intact Drosophila larva.   Together with genetically encoded fluorescent markers, we can track muscle contraction and nuclear dynamics, as shown in Movie 1.  While the muscle is at rest, we can image chromatin
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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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Revealing the spatial regulation of the transcriptome using Split-FISH

Sponsored by Andor, on 9 February 2022

Featured Lab: The Chen Lab, Genome Institute of Singapore  As cells develop and function in tissues, many changes occur not just at the level of RNA transcription, but also at the larger level of spatial organisation of cellular gene expression within the tissue. Studying these changes to RNA profiles at the single-cell level can thus provide
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DeepImageJ: Deep learning in bioimage analysis for dummies

Posted by , on 2 December 2021

Written by Estibaliz Gómez-de-Mariscal, Cristina de-la-Torre-Gutiérrez, Arrate Muñoz-Barrutia, and Daniel Sage Do you invest significant time looking for tools to analyze your microscopy images? Probably you have already heard about the extraordinary capabilities of deep learning (DL) to reveal complex visual structures in images. If you are a biologist practicing daily ImageJ, you may look
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