Rosy Favicchio

27 Feb 2025

As the #measles outbreak continues, and has now unfortunately resulted in the death of a child, I see a lot of posts along the lines of: "I had measles as a child and I'm fine". Let me tell you a different version of that story: 🧵1/11 🧪 #medsky

nature.comNeurostimulation protocolsA collection of Protocols covering a wide range of optogenetic and non-genetic procedures that allow the stimulation of neuronal cell populations using ...

Now that #optogenetics has finally been acknowledged by the Nobel committee, it's time to get back to work! Looking to start or improve your neurostimulation experiments? @natprot.nature.com 🧪 🧠 Have a look at our protocols on the topic:

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nature.comSurgical protocols for animalsA compendium of protocols which cover a broad range of surgical procedures to be carried out in experimental animal models of research.

What else is missing to carry out those experiments? Surgical skills! 🧠 🧪 🔬 👨‍⚕️ 👩‍⚕️ www.nature.com/collections/...

nature.comNeural probe protocolsA collection of Protocols and Tutorials covering the fabrication and use of implantable bioelectronic devices which enable the recording of ...

And our collection on neural probes is here: 🧪 🧠 www.nature.com/collections/...

nature.comNeurostimulation protocolsA collection of Protocols covering a wide range of optogenetic and non-genetic procedures that allow the stimulation of neuronal cell populations using ...

nature.comIntravital microscopy protocolsA collection of protocols covering the surgical implantation of imaging windows and the acquisition of intravital imaging data. Updated Oct 2026.

and if you are doing #optogenetics, you are likely going to need some microscopy to go with it: 🧪🔬 www.nature.com/collections/...

Rosy Favicchio reposted

Nobel Prize

@nobelprize.org

BREAKING NEWS The 2026 Nobel Prize in Physiology or Medicine has been awarded to Karl Deisseroth, Peter Hegemann and Georg Nagel “for their discoveries concerning light-gated ion channels and optogenetics.”

nature.comSIMworks—an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy - Nature ProtocolsSIMworks is an integrated software suite for quality-controlled augmented quantitative structured illumination microscopy (SIM), enabling both new learners and experienced users to implement best prac...

A protocol for SIMworks, an integrated software suite for quality-controlled, augmented quantitative structured illumination microscopy (SIM). @natprot.nature.com @fenaochs.bsky.social 🧪 🔬 #imaging www.nature.com/articles/s41...

The protocol includes guidelines for users to understand outputs, decide whether data are suitable for processing and optimize parameters for best results. SIMworks emphasizes reproducibility, interoperability and accessibility, ensuring that new and experienced users implement best practices

Find the readcube link here:

nature.comTissue expansion mass spectrometry imaging (TEMI) for high-spatial-resolution multiomics molecular mapping - Nature ProtocolsTissue expansion mass spectrometry imaging enables the mapping of lipids, metabolites, proteins, peptides and N-glycans at high spatial resolution.

Tissue expansion mass spectrometry imaging enables high-spatial-resolution mapping of lipids, metabolites, proteins/peptides and N-glycans, providing comprehensive molecular multiomics. @natprot.nature.com 🧪 🔬 #imaging #omics

Tissue expansion mass spectrometry imaging (TEMI) preserves molecular integrity while achieving high expansion factors by leveraging a re-embedding strategy and avoiding the harsh conditions typically required in traditional expansion approaches.

Find the readcube link here:

nature.comTrace-n-Seq combines retrograde fluorescent tracing with sorting and single-cell sequencing of innervating peripheral neurons - Nature ProtocolsThis Protocol uses retrograde axonal tracing and fluorescence-activated cell sorting to transcriptionally profile innervating neurons at single-cell resolution.

A Protocol for Trace-n-Seq: a method that combines retrograde tracing with fluorescence-activated cell sorting and single-cell sequencing to molecularly profile individual neurons innervating healthy or diseased tissues. @natprot.nature.com 🧪 🧠

The Protocol allows to selectively profile neurons on the basis of functional tissue connectivity, capture rare tissue-specific neuronal subsets, distinguish disease-associated neuronal states from bulk ganglia signatures and directly compare neuronal remodeling at single-cell resolution.

Find the readcube link here: rdcu.be/QwgNTFq4vwga

@duncanrobertson.bsky.social

Rosy Favicchio reposted

Dr Duncan Robertson

Good luck to all colleagues going into the new university year, persuading students that learning to think isn't the same thing as getting the right answer.

nature.comProteomics protocolsA collection of proteomics protocols from Nature Protocols focussing on our most recent content.

This collection is on proteomics! @natprot.nature.com A collection of proteomics protocols from Nature Protocols focussing on our most recent content. 🧪 #proteomics #MassSpec

nature.comMetabolomics and metabolite analysis protocolsThis Collection from Nature Protocols covers metabolomics and metabolite analysis. The protocols cover key stages of metabolite research, including sample ...

Oh we have been busy! Here another collection: @natprot.nature.com The protocols cover key stages of metabolite research, including sample collection, metabolite extraction, chromatographic separation, mass spectrometric analysis and data processing. 🧪 #metabolomics #chemsky

nature.comProtocols for advanced materialsA collection of articles covering protocols for synthesizing, processing and characterizing advanced materials, with particular emphasis on 2D materials and ...

In this collection we highlight protocols for synthesizing, processing and characterizing advanced materials, with particular emphasis on 2D materials and nanoscale materials. @natprot.nature.com 🧪 #2Dmaterials #materials

nature.comProtocols for sensingSensing technologies provide us with the ability to detect changes in local chemical, biological or physical environments we would otherwise be unaware of. ...

This collection of protocols covers approaches for sensing using molecular, optical or electrochemical materials adopted for applications in imaging, trace analyte detection and organ-on-chip monitoring. @natprot.nature.com 🧪 #sensors #chemsky #materials

nature.comProtocols for bioelectronicsA collection of protocols at the interface of electronic, robotic and living systems to fabricate actuators, circuits, robots, wearables and integrated ...

New collection! @natprot.nature.com covering approaches at the interface of electronics, robotics and biological systems. The protocols cover how to design and fabricate robots, actuators and sensors using biological, magnetic and electronic building tools. 🧪 #bioelectronics

lnkd.in#tech #ai #postdocs #students #juniorpis | Thomas Schwarz-RomondScientific publishing - in times of tremendous #tech acceleration and #AI becomes increasingly complex. Giancarlo Porcella Helmholtz PioneerCampus @ Helmholtz Munich recently hosted an editorial round...

Big thank you to @munichimaging.bsky.social and @helmholtzmunich.bsky.social for the hospitality. I had the opportunity to meet with ECRs and PIs to discuss about careers, research publishing and how to incorporate protocols into their strategy.

nature.comnetneurotools: a trainee-oriented approach to network neuroscience - Nature ProtocolsThis is a Perspective covering a Python toolbox for neuroscience research that enables users to fetch datasets, construct networks and null models, estimate graph metrics, fit statistical models and v...

15 Sept

netneurotools is a Python toolkit that has been continuously developed by lab trainees as a set of tools to navigate the complex informatics ecosystem of brain imaging. @natprot.nature.com @misicbata.bsky.social 🧪 🧠 #imaging

15 Sept

In this Perspective, the authors cover the functions and routines that are often used to integrate the data analyses stages, but that are not part of any established pipeline or package.

nature.comShear-flow-induced assembly of 2D nanosheets for the fabrication of composite films with high tensile strength - Nature ProtocolsWe present a protocol for the fabrication of highly ordered composite films in which 2D nanosheets can be aligned and fixed, yielding high tensile strength and suitability for high-performance wearabl...

15 Sept

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A nanosheet superspreading alignment strategy for fabricating nanocomposite films that uses shear-flow forces between two immiscible phases to induce long-range, high-order alignment of 2D nanosheets to enhance the films’ mechanical properties. @natprot.nature.com 🧪 #materials #chemsky #sensors

The shear-flow-induced alignment strategy bridges the gap between structural precision and scalability that limits alternative methods such as vacuum filtration, layer-by-layer assembly and solution casting.

1 Sept

Find the readcube link here: rdcu.be/hdkmM8vaVqga

The procedure covers two routes for nanosheet alignment via either gelation-assisted superspreading or alignment on hydrophilic solid substrates by crystallization, suitable for the assembly of magnetoelectric sensors.

nature.comSynthesis of radioafterglow nanoprobes for deep-tissue imaging of hydrogen peroxide - Nature ProtocolsThis protocol is for the synthesis of radioafterglow nanoprobes that convert X-ray energy to near-infrared emissions with long half-life and high brightness, detectable from up to 15-cm depth.

1 Sept

Radioafterglow nanoprobes synthesized by co-assembling radioabsorbers, radiosensitizers and radioafterglow substrates into amphiphilic polymers using the film rehydration method. @natprot.nature.com 🧪 🔬 #imaging #chemsky

Radioafterglow probes display long luminescence lifetime, thus facilitating high signal/background ratios. In contrast to photoafterglow or sonoafterglow, radioafterglow imaging uses high-energy X-rays as an excitation source, enabling signal detection from up to 15-cm depth.

1 Sept

Find the readcube link here: rdcu.be/xJ1ssN3XoFza

The protocol includes the synthesis of radioafterglow nanoprobes (RANPs), as well as that of a tumor-specific radioafterglow nanoprobe which is activated in the presence of hydrogen peroxide for the detection and resection of cancer tissue.

rdcu.beUsing MetaboAnalyst 6.0 for exposomics data analysis—from LC–MS2 spectra processing to dose–response modeling and causal inferenceNature Protocols - High-resolution liquid chromatography–tandem mass spectrometry is widely used in exposomics, for example, to study metabolomic responses to environmental exposures. This...

A Protocol for MetaboAnalyst 6.0 which provides instructions for four key tasks in liquid chromatography–tandem mass spectrometry-based exposomics data analysis. @natprot.nature.com 🧪 ⚗️ #chemsky #metabolomics

Find the readcube link here:

nature.comUsing MetaboAnalyst 6.0 for exposomics data analysis—from LC–MS2 spectra processing to dose–response modeling and causal inference - Nature ProtocolsHigh-resolution liquid chromatography–tandem mass spectrometry is widely used in exposomics, for example, to study metabolomic responses to environmental exposures. This Protocol describes spectra pro...

and the link to the article: www.nature.com/articles/s41...

The protocol includes liquid chromatography–tandem mass spectrometry data processing and compound identification, exposomics data processing and exploratory analysis, dose–response modeling and causal inference using known genetic associations.

nature.comCentralized processing of frozen tumor tissues for global cancer genomics - Nature ProtocolsThis Protocol outlines a pathologist-led, centralized workflow for processing frozen tumor tissues to generate high-quality DNA for whole-genome sequencing. It integrates cryosectioning, digital patho...

A Protocol covering the pathological assessment of paired tumor–blood DNA samples, developed by the Mutographs project and suitable for international genomics initiatives @who.int International Agency for Research on Cancer (IARC) @natprot.nature.com 🧪 🔬 #pathology #medsky #genomics

The workflow integrates rigorous pathology evaluation and quality control with molecular processing, enabling high-quality DNA yield from frozen tissues at scale and reducing sequencing failure.

rdcu.beCentralized processing of frozen tumor tissues for global cancer genomicsNature Protocols - This Protocol outlines a pathologist-led, centralized workflow for processing frozen tumor tissues to generate high-quality DNA for whole-genome sequencing. It integrates...

Find the readcube link here: rdcu.be/fA1DF

The Protocol encompasses a centralized, pathologist-driven workflow combining frozen optimal cutting temperature embedding, cryosectioning, hematoxylin and eosin digital pathology, macrodissection, laser-capture microdissection, and automated or manual DNA extraction for whole-genome sequencing.

nature.comONE microscopy - Nature ProtocolsAn approach for combining expansion microscopy with fluctuation-based super-resolution analysis enables the visualization of individual proteins via conventional fluorescence microscopy.

One-step nanoscale expansion microscopy combines #ExM with fluctuation-based super-resolution analysis to enable the direct visualization of individual protein shapes, using conventional fluorescence microscopes. @natprot.nature.com 🧪 🔬 #imaging @alishaib.bsky.social

The protocol details procedures for gel embedding, labeling, expansion, image acquisition and data analysis, as well as a stable, user-friendly software package for efficient fluctuation analysis.

rdcu.beONE microscopyNature Protocols - An approach for combining expansion microscopy with fluctuation-based super-resolution analysis enables the visualization of individual proteins via conventional fluorescence...

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nature.comDirect printing of metasurfaces using formulated optical materials - Nature ProtocolsA printable composite material provides a practical and cost-effective route for fabricating metasurfaces on flexible or curved substrates, scalable from the UV to IR wavelengths and deployable for ph...

Fabrication of optical #metasurfaces via a printable high-index composite material known as nanoparticle-embedded resin (nanoPER) supports real-world applications such as light detection and ranging, compact imaging and integrated #photonics @natprot.nature.com 🧪 #materials #nanotechnology

The fabrication process includes the preparation of the master and soft molds, surface treatment of both molds and target substrates, formulation of the nanoPER material and the nanoimprinting procedure.

Find the readcube here:

Fabrication of optical metasurfaces uses TiO2-based nanoPER formulated by combining an initiator, a monomer, a solvent and high-index nanoparticles. The increased refractive index of the resin to ~1.8 enables the printing of metasurfaces.

nature.comStandardized assays for evaluating superoxide dismutase-like and catalase-like activities of nanozymes - Nature ProtocolsAntioxidant nanozymes are therapeutic candidates for oxidative diseases. Here a standardized protocol is described to characterize superoxide dismutase-like or catalase-like nanozymes and quantify the...

A #protocol for the reliable and reproducible evaluation of antioxidant nanozymes to facilitate direct comparison across materials, elucidating structure–activity relationships and their rational optimization for biomedical applications. @natprot.nature.com 🧪 ⚗️ #chemsky

A xanthine/xanthine oxidase/water-soluble tetrazolium salt-1 system is used to quantitatively determine the catalytic activity and kinetics of superoxide dismutase-like nanozymes in an absorbance-based assay. Catalase-like kinetics are assessed by monitoring the decrease in H2O2 absorbance.

Find the readcube link here: