#PhysicsFactlet A Shack-Hartmann sensor is a simple and widely used device to measure the phase profile of a wavefront (aka "where the light is coming from"). A mini 🧵 1/ #Optics #Physics

New blog at "Engineering {X}," where X = serendipity, understanding, or existence! @clairebookworm.bsky.social, Nina Khera, and I are co-editors. Our first post, "The Dropout Curriculum," asks: what should you learn, to disrupt fields from the outside? engineeringx.substack.com/p/the-dropou...

The Dropout Curriculum

How do you plan what to learn, to solve the problems you care about?

engineeringx.substack.com

Light-microscopy-based connectomic reconstruction of mammalian brain tissue rdcu.be/ek8GG Wow! 😍

Light-microscopy-based connectomic reconstruction of mammalian brain tissue

Nature - A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling...

rdcu.be

How can organs regenerate fast? Bioelectricity helps -- by coupling sub-second electrical injury signals to regenerative proliferation. First preprint from my potsdoc :D with @liujinghui.bsky.social @ritamateus.bsky.social @mpi-cbg.de and collaborators @mpipks.bsky.social @csbdresden.bsky.social

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

Injury-induced electrochemical coupling triggers regenerative cell proliferation https://www.biorxiv.org/content/10.1101/2025.04.03.647033v1

We have a new review out! In this Microscopy & Microanalysis piece, Louisa Mezache and I survey some of the latest commercially available microscope technologies: Nikon NSPARC, Re-scan Gaia, CSR Biotech MI-SIM, refinements to STED, SMLM from Bruker and Abbelight… Check it out with free access:

Advancing Super-Resolution Microscopy: Recent Innovations in Commercial Instruments

Abstract. Super-resolution microscopy techniques have accelerated scientific progress, enabling researchers to explore cellular structures and dynamics wit

academic.oup.com

It feels a bit strange having such a watery liquid behave optically like glass... www.biorxiv.org/content/10.1...

Published in final form, Feb 12, 2025: Shin et al., "Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues." Journal link: www.nature.com/articles/s41... PDF link: synthneuro.org/publications... News story: mcgovern.mit.edu/2025/02/18/s...

⚡️ Excited to introduce ZAPBench, our #ICLR2025 spotlight: The Zebrafish Activity Prediction Benchmark measures progress in predicting neural activity within an entire vertebrate brain (70k+ neurons!) Explore interactive visualizations, datasets, code + paper: google-research.github.io/zapbench 🧠🧪

ZAPBench

ZAPBench evaluates how well different models can predict the activity of over 70,000 neurons in a novel larval zebrafish dataset.

google-research.github.io

Just a start! Who's missing? go.bsky.app/LAA7Sdx

Clinical applications of human organoids - a new review article in Nature Medicine 🧪 #MedSky @natureportfolio.nature.com www.nature.com/articles/s41...

Clinical applications of human organoids - Nature Medicine

Organoid research is moving beyond developmental and disease biology, driving insights into current and emerging health threats and enabling personalized and regenerative medicine applications.

nature.com

Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues Ultrastructural membrane expansion microscopy enables imaging of membranes and proteins in brain slices at a resolution of ~60 nm on a confocal microscope www.nature.com/articles/s41...

Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues - Nature Communications

Lipid membranes are hard to visualise in tissues with nanoscale precision. The authors report ultrastructural membrane expansion microscopy (umExM), a tool that enables dense membrane labelling for na...

nature.com

So much happening in the segmentation space for bioimage analysis. These two papers that were published online today really stood out to me as noteworthy (a thread).

The self-driving multiscale microscope from @daetwylerstephan.bsky.social is out. It can image an entire zebrafish embryo longitudinally and follow a volume of interest over time with high resolution. We used it to study cancer-immune cell interactions. www.nature.com/articles/s41...

Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy

Nature Methods - A self-driving multiresolution light-sheet microscope enables the simultaneous observation and quantification of cellular and subcellular dynamics in the context of intact and...

nature.com

We present: Direct-view oblique plane microscopy www.biorxiv.org/content/10.1...

Direct-view oblique plane microscopy

The ability to rapidly image mesoscopic samples is critically important for many areas of biological research. Owing to its high throughput and gentle, volumetric imaging nature, light-sheet fluoresce...

biorxiv.org

My favorite quote from Nature's 10 year retrospective on expansion microscopy (ExM): “It’s so easy, even my nine-year-old can do it,” [CMU professor, SynthNeuro group alum, and ExM innovator, Yongxin] Zhao says. Happy 10th birthday, expansion microscopy!

Nature@nature.com · 2y ago

A decade in, expansion microscopy is unlocking insights across biology and medicine https://go.nature.com/4adlNgg

Looking to inject some fishy goodness into your timeline? Check out our exhaustive lists (x3) of Group Leaders and Senior Scientists in the #zebrafish community! 🧪 Version 1: go.bsky.app/2cHYybY Version 2: go.bsky.app/4zBuxAF Version 3: go.bsky.app/JvjuSZg

We hope other labs find it as useful as we do! Given that it's free, we also hope it can be used in teaching labs, which are often low resourced. Congratulations to all authors! #zebrafish 🧠🧪🧬 bmcbioinformatics.biomedcentral.com/articles/10....

Marigold: a machine learning-based web app for zebrafish pose tracking - BMC Bioinformatics

Background High-throughput behavioral analysis is important for drug discovery, toxicological studies, and the modeling of neurological disorders such as autism and epilepsy. Zebrafish embryos and lar...

bmcbioinformatics.biomedcentral.com

Köcher et al. report that concussion severity impacts zebrafish larvae escape behavior through opposing effects: habituation deficits at lower forces and fatigue at higher forces. Insights could advance concussion research. Read at: https://buff.ly/40jXYPo

A Sensitive Soma-localized Red Fluorescent Calcium Indicator for Multi-Modality Imaging of Neuronal Populations In Vivo. It works well with wide-field imaging, two-photon microscopy, and fiber photometry biorxiv.org/content/10.1...

@e11bio.bsky.social needs help to scale optical connectomics to humans and other mammals! Huge opportunity to have an impact on brain science as part of a world-class, mission-driven team. #hiring computational scientists at all levels to build data pipelines for brain microscopy images! 🧪

Johan Winnubst@johanwinn.bsky.social · last yr.

🚀 We are looking for Image Data Scientists to join our mission to advance connectomics towards whole brain scale for humans and other mammals (1/3) 🚀

"Imagine a DAPI-like stain, but for the extracellular matrix." That's basically how this work was pitched to me by Kayvon and Antonio a year or so ago. Now the final product really delivers. Read about their versatile label for ECM in living tissues here: www.nature.com/articles/s41...

Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits Zebrafish larvae can learn to perceive a stationary object as a threat, via noradrenergic and forebrain circuits, after being chased by the object for ∼1 min www.cell.com/current-biol...

Days-old zebrafish rapidly learn to recognize threatening agents through noradrenergic and forebrain circuits

Zocchi et al. utilize a robotic predator-learning assay to show that larval zebrafish as young as 5 days post-fertilization rapidly learn to avoid robots following predatory-like experiences. Whole-brain imaging of neural activity implicates the noradrenergic system and forebrain populations in this “conditioned robot avoidance” learning.

cell.com

An integrative data-driven model simulating C. elegans brain, body and environment interactions www.nature.com/articles/s43...

An integrative data-driven model simulating C. elegans brain, body and environment interactions - Nature Computational Science

BAAIWorm is an integrative data-driven model of C. elegans that simulates interactions between the brain, body and environment. The biophysically detailed neuronal model is capable of replicating the ...

nature.com

🍾Our small #UExM adventure is only starting! #ProtistsOnSky We are happy to announce that the Moore Foundation will be funding our efforts in creating an Expansion Microscopy atlas of #Microbial #Eukaryotes with @gautamdey.bsky.social @UNIGE @embl.org LINK: www.unige.ch/sciences/chi... 1/4

In our recent preprint, we address this question - combining smart microscopy with optogenetics to present a platform for 'outcome-driven' microscopy, precisely controlling cells to bring them to the same outcome, despite all the variation. www.biorxiv.org/content/10.1...

The birth of fruit fly's central nervous system imaged with multicolor #adaptive #lightsheet microscopy. The microscope self-aligns to a signal that appears during imaging. www.nature.com/articles/nbt...

SERVICE UPDATE We normally don't ask you to "share like and subscribe" but please distribute this. You are now able to delete the link after it embeds on your post so you can get those precious extra characters, and we will catch your post mentioning research. #AcademicSky #Medsky #HigherEd

10,000 times faster than traditional methods: new computational framework discovers experimental designs in microscopy For human researchers, it takes many years of work to discover new super-resolution microscopy techniques. The number of possi... weiterlesen

Working on a #StarterPack to collect researchers using human biology-based tools ( #organoids, #microphysiologicalsystems, other human-derived #invitro tools) + computational models & the orgs & accounts that promote non-animal science. Small so far, but I'm new here. Msg to add. go.bsky.app/SVWGwgu

High-speed 3D random access two-photon imaging at ≥ 300 kHz – with SPARCLS: opg.optica.org/optica/fullt... By the outstanding @carolineberlage.bsky.social and team, including @urslucasboehm.bsky.social, @andrewplested.bsky.social et al.