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Displaying posts in the category: Discussions

LSFM series – Part IV: Data post-processing: Cropping, tailoring, and trimming

Posted by , on 23 January 2021

Elisabeth Kugler 1 and Emmanuel G. Reynaud 2 Contact:kugler.elisabeth@gmail.com; emmanuel.reynaud@ucd.ie There is a very thin sheet of light between gathering data and hoarding. In Science, between pilling up manuscripts on desk, books on shelves and samples in cold freezer, most of us fit in the latter category. It is OK, if you have space available

FocalPlane user survey

Posted by , on 5 January 2021

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“Outreach during a pandemic, it can be done!” – Virtual Microscopy Camp

Posted by , on 1 January 2021

I’ve always believed public outreach and education activities are vital to our role as scientists. While both are familiar concepts to many of us, often they are unappreciated  as important parts of our scientific training and journey. This has become increasingly relevant during this year, where a rise in public mistrust and misunderstanding of the

LSFM series – Part III: Image acquisition: Calibration and acquisition

Posted by , on 17 December 2020

Elisabeth Kugler 1 and Emmanuel G. Reynaud 2 Contact:kugler.elisabeth@gmail.com; emmanuel.reynaud@ucd.ie Now, we are getting closer to the point of setting up our sample in the chamber to image it. Now that we know which microscope we are about to use (Part I) and have mounted it the right way (Part II), we need to trust

A career path to bioimage analysis

Posted by , on 9 December 2020

I am currently working in Heidelberg, Germany, finishing my PhD thesis between the medical university of Heidelberg and the microscopy company ACQUIFER. My research project is dedicated to the development of user-oriented software solutions (Fiji plugins, KNIME workflows…) to facilitate the handling and analysis of large microscopy datasets of 2D images. The project is motivated

Foldscope goes to the Peruvian Amazon!

Posted by , on 18 November 2020

Foldscope Instruments, Inc. is a company that was founded in 2016. We develop low-cost scientific tools with the goal of making science accessible to everyone around the world. In 2018, the Foldscope team visited Peru, Argentina, and Brazil. At the time, I was a Stanford graduate student in Biology and, due to school-related commitments, I

How to use Dragonfly Spinning Disk Microscope for Multiplex In Situ Hybridization

Sponsored by Andor, on 4 November 2020

Multiplexing in cell biology is the unveiling of several (Xn) RNAs in its 2D or 3D biological context. Multiplexing has become a hot topic in neurosciences, oncobiology, disease target diagnostics, development, behavioural studies, etc. Several techniques have been developed to allow multiplex imaging; examples of such are FISSEQ, instaSEQ, osmFISH, STARmap, MERFISH and seqFISH. The advantage of

In-Situ Sequencing and Multiplex Imaging with the Dragonfly High Speed Confocal

Sponsored by Andor, on 27 October 2020

Challenge Background Understanding the molecular basis of development, brain function, neurodegenerative diseases, cancer, and behaviour is an enormous task. Up until recently, RNAs could be sequenced in bulk, or at the single-cell level, but unfortunately, the tissue environment information was lost. With smFISH [1] (single molecule FISH), the spatial information is retained, but this is

Microscopy Open Access collection 2020

Posted by , on 19 October 2020

Here on FocalPlane, Open Access Week is especially close to our hearts as it coincides with the birthday of the father of microscopy, Antonie van Leeuwenhoek (24 October). So every year for Open Access Week, we will be listing all the microscopy-related Open Access articles from The Company of Biologists journals on FocalPlane under the

Bioimage Analysis in FIJI - Resource List

Posted by , on 14 September 2020

If you are on this site, you might be aware of some of the open source image processing and analysis tools are available to you. The toolbox in this space is rapidly expanding. But that doesn’t always mean it’s easy to navigate – it can actually be quite daunting. Luckily the bio-imaging community is friendly