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Managing Scientific Python environments using Conda, Mamba and friends

Posted by Robert Haase, on 8 December 2022

TL:DR: This blog post gives short instructions and explanations to demystify how some scientific Python programmers, including myself, organize their coding environment for the sake of reproducibility of science. We will see what conda and mamba are, what they are good for, and how to use them properly. We will also take a short excursion

60 years of Fluorescent Proteins

Posted by Joachim Goedhart, on 4 October 2022

In talks about fluorescent proteins I usually include a timeline of events related to Green Fluorescent Protein (GFP). The timeline highlights some of the key moments in the history of fluorescent protein discovery and engineering. I am generally fond of timelines, since they provide a way to pay tribute to the pioneers, and other researchers

First steps for presentation and analysis of calcium imaging data

Posted by Andrey Andreev, on 6 September 2022

Andrey Andreev, Desiderio AscencioCalifornia Institute of Technology, David Prober labaandreev@caltech.edu Calcium imaging is a widely used tool in neuroscience, and our community now has access to multiple computational tools to process and analyze these data. However, a significant portion of work with imaging data relies on much simpler approaches than offered in these software packages.

TrackMate-Oneat: Auto Track correction using deep learning networks

Posted by varun kapoor, 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

Using an autocollimator to align 4f systems

Posted by Brian Patton, 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

If you can detect it, you can track it - recent TrackMate developments

Posted by Joanna Pylvänäinen, 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

Protein micropatterning: beauty standards in cell culture

Posted by Julius Winter, on 16 February 2022

When imaging cells grown on a flat substrate, such as a glass coverslip, we quickly admire the diversity of morphologies different cells can take on. Some cells, such as COS7, will take on a flat “pancake”-like shape, which makes it easy to image its organellar structure in a 2D plane. On the other hand, a

Janelia+EMBL BioImaging Seminar Series: How We Started a Successful Seminar Series during the Pandemic

Posted by Ulrike Boehm, on 25 January 2022

How we started a global BioImaging seminar series in the middle of a global pandemic...

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

Posted by Sravasti Mukherjee, 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 ;

PUMA Open Source Multimodality 3D Printed Microscope

Posted by Paul Tadrous, on 26 October 2021

PUMA is an advanced direct vision 3D printed multimodality microscopy system with fluorescence ,phase contrast, Köhler illumination and augmented reality functions - and more.

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Microscopy-related articles from our journals

HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples Development 2024 151: dev202307
filoVision – using deep learning and tip markers to automate filopodia analysis J Cell Sci 2024 137: jcs261274
C omputational tools for quantifying actin filament numbers, lengths, and bundling Biology Open 2024 13: bio.060267

Microscopy-related preprint highlights

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