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DL4MicEverywhere - Overcoming reproducibility challenges in deep learning microscopy imaging

Posted by Iván Hidalgo-Cenalmor, on 29 July 2024

DL4MicEverywhere is out! Learn about it and how you can apply deep learning workflows on microscopy imaging in reproducible research and in a user-friendly manner across different systems.

Prompt Engineering in Bio-image Analysis

Posted by Mara Lampert, on 18 July 2024

Prompt engineering and its importance Communication is key. This saying is not only true in day-to-day life, but also when interacting with Generative Artificial Intelligence, a system able to generate text, images or other output types in response to prompts. In prompt engineering, we use natural language to describe the task that a Large Language

How to write a bug report

Posted by Mara Lampert, on 3 April 2024

Imagine you try out a software tool for the analysis of your data and for some reason it is not working in the way you expected. Neither the user documentation, nor forums like image.sc or stack overflow can provide answers. Then it is likely that you either found a bug in the software tool or

FocalPlane features... microscopy-based outreach

Posted by FocalPlane, on 11 March 2024

The first webinar of our new series of FocalPlane features... focussed on microscopy-based outreach. We hosted fantastic talks from Paola Moreno-Roman from Foldscope Instruments and Martin Jones from The Francis Crick Institute and we share the recordings here.

New FocalPlane features... webinar series

Posted by FocalPlane, on 22 February 2024

We are excited to announce a new series of FocalPlane features… webinars. Our first webinar, on 7 March at 15:00 GMT (10:00 PET) focusses on outreach projects using microscopy, with talks from Paola Moreno-Roman, Alexander Strachan and Martin Jones.

How to Minimise Photodamage with LED illumination

Sponsored by CoolLED, on 15 November 2023

Both fixed and live samples are susceptible to photodamage during fluorescence microscopy, which can shorten time-lapse experiments and cast doubt on observations. LED illumination for widefield fluorescence has the potential to counter this serious problem, whether running a complete experiment or simply finding the region of interest prior to confocal microscopy. Exposing biological samples to

Creating a Research Data Management Plan using chatGPT

Posted by Robert Haase, on 6 November 2023

TL;DR: Data Management Plans (DMPs) are documents which describe what happens to data in a [research] project. More and more funding agencies require these documents when scientists apply for funding. However, different funding agencies may require different information in DMPs. In this blog post I will demonstrate how chatGPT can be used to combine a

Analyzing calcium imaging data using Python

Posted by Andrey Andreev, on 27 October 2023

Andrey AndreevCalifornia Institute of Technology, David Prober labaandreev@caltech.edu Calcium imaging allows tracking neural activity in time with single-cell resolution. There are many questions you might be interested in answering using this technique: which cells are tuned to the stimuli? is there periodic activity present in the data? which cells act together? how complex is the activity

behind DeXtrusion: an automated pipeline to detect epithelial cell extrusion through machine learning

Posted by alvillars, on 6 October 2023

The problem In animals, epithelial tissue covers most of our organs. In order to create the very intricate and complex shapes of these organs, these tissues are drastically remodelled during embryogenesis through growth and shape changes. Once they achieve these final shapes, they maintain their cell number in a dynamic equilibrium. Both of these mechanisms,

How to… Publish Images blog series

Posted by FocalPlane, on 27 September 2023

by Helena Jambor In biology, images document appearances or structures of animals, issues, or cells, and increasingly are a source of quantitative insights of biological processes. Many papers are published every single day with images (Lee, 2018).Not all of these images are truthful or insightful. Some images are manipulated to mislead audiences (Bik et al.,

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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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