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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
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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
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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
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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
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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
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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
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SRRF-Stream+ Super-Resolution Microscopy Accessible to All

Sponsored by Andor, on 12 August 2020

Fast, reliable & live-cell compatible Super-Resolution Science has limits imposed by the laws of physics that constrain discoveries and the advance of knowledge. In microscopy, up until the beginning of the XXI century, the diffraction limit of light was an unbreakable barrier. This law of physics imposes that two points could not be resolved (clearly
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Science and Art – the not so odd couple?

Posted by , on 31 July 2020

At a first, superficial glance, you could be forgiven for placing scientists and artists at the opposite ends of the career spectrum. Scientists need to be accurate and methodical. They must generate highly reproducible data while adhering to strict regulations. On the other hand, artists are often stereotyped as disorganized, free spirits, ungoverned by rules,
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“openFrame” for modular, extensible, easily maintained, open-source microscopy

Posted by , on 23 July 2020

The openFrame [1] is an open-source microscopy hardware project initiated by the Photonics Group in the Physics Department at Imperial College London that is intended to provide access to a modular, upgradable, easily maintained and modifiable microscope frame that can be implemented at relatively low cost compared to existing commercial instruments. openFrame is a component
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Electron microscopy: from the dark ages to a bright future

Posted by , on 21 July 2020

Good sample preparation is, as every microscopist knows, the key to delivering sound results from an imaging experiment. In the digital age, and with the advent of big data, image analysis is also critical to extract meaningful quantitative results from image data. Indeed nowadays, the microscope itself is often the most well-developed and user-friendly part
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