Allen Institute

Our own Paul Meijer will be presenting a demo at #OSFair2025 on reproducible research from a computing perspective. Catch the talk during the demo parallel presentations happening on Sept. 16 and Sept. 17.

More on this can't-miss @osfair.bsky.social demo: www.opensciencefair.eu/2025/program...

Examine multimodal data from thousands of cells across three mammalian species with the Cell Type Knowledge Explorer, an open science resource developed with BICCN and supported by the BRAIN Initiative Alliance.

🧠📈 Explore the data: knowledge.brain-map.org/celltypes

#BICCN #studyBRAIN

The brain drain puts aging myelin in deep trouble - Nature Neuroscience In this issue, Stamenkovic et al. describe deep in vivo imaging of the brain vasculature to document its evolution during aging, which identifies a unique vulnerability at the site of convergence of c...

When it comes to aging, the health of even the smallest vessels is critical to maintaining cognitive function.

New study in @nature.com finds that deterioration of the brain's drainage system contributes to reduced blood supply in deep white matter: www.nature.com/articles/s41...

Help us bring #OpenScience to @sxsw.com by voting for our panels!

🏃‍♂️ Go to participate.sxsw.com/flow/sxsw/sx...

🌟 Click the yellow “Login” button to create a free account.

🔎 Go to our proposals: participate.sxsw.com/flow/sxsw/sx...

🗳️ Click the little hearts ❤️ next to each one to vote. That's it!

Meet one of the winning teams of our MapMySections challenge! 🧠📈

Daniel Rijsketic, Austen Casey, and @theborislab.bsky.social developed UNRAVEL, a tool that precisely maps fluorescent labels across the mouse brain.

Join us on 8/27 for a webinar and live demo: alleninstitute.org/events/mapmy...

Happy #FluorescenceFriday! Our #CellLineOfTheWeek is MLC-2a - illuminating sarcomeric thick filaments! 💪🧫

Our high-quality stem cell lines & plasmids are available for just the cost of shipping to reduce the barriers to discovery.

📦 Dist. by @coriellinstitute.bsky.social & @addgene.bsky.social.

How does marine life sense and respond to their changing world? The Allen Discovery Center for Neurobiology in Changing Environments is diving (literally) into this #FrontierScience. 🐋🧠

🔗 alleninstitute.org/division/fro...

📸 Dr. David Kline, Erik Jepsen, UCSD, @adc-neuroenv.bsky.social

Get up close with brain cells with the browser-based MICrONS Explorer: www.microns-explorer.org

This #OpenScience data portal contains connectivity and functional imaging data including #ElectronMicroscopy based reconstructions of cortical circuitry from the mouse visual cortex.

Learning how to learn with brains, data and optimization Matthew Storm Bull, a Shanahan Fellow, explores how the brain multitasks and adapts to the world around it.

The Shanahan Fellowship program gave Matthew Storm Bull the freedom and support to explore new ways to study how the brain multitasks and adapts.

🧠📈 alleninstitute.org/news/learnin...

Brain Knowledge Platform The Brain Knowledge Platform is a data platform and website for researchers to access data, explore features and visualizations, and connect data to knowledge. This product is an active area of develo...

Have feedback on this feature or ideas for future updates? We’d love to hear your thoughts on the Brain Map Community Forum: community.brain-map.org/c/how-to/bra...

Scientists search projects using own search terms via Text Search in Brain Knowledge Platform’s Data Catalog The Data Catalog’s new Text Search empowers scientists to search for relevant resources with their own search terms. Text search in Data Catalog Access the Data Catalog’s text search field at https:/...

Learn more about the new feature in the release notes: community.brain-map.org/t/scientists...

We heard you! You can now use text search to browse the Brain Knowledge Platform’s Data Catalog.

Whether you're exploring brain regions, age groups, or specific metadata, this update makes discovery faster and more intuitive.

🧠📈 Try it out: knowledge.brain-map.org/data

First-ever Open Science Quest supports the next generation of scientists Allen Institute's first-ever Open Science Quest immersed students in cutting-edge science and mentorship towards a successful future in STEM

The Education & Engagement program at @alleninstitute.org was delighted to welcome 18 fantastic students from Seattle Public Schools for a brand-new summer intensive program!

alleninstitute.org/news/open-sc...

Open science is opening doors for the next generation.

For two weeks, Seattle students were part of the first-ever Open Science Quest, a summer course featuring hands-on training and exposure to STEM careers.

More in our interactive story: alleninstitute.org/news/open-sc...

#iTeachBio #EduSky

Cell Type Taxonomies A-Z: Webinar Series Webinar series covering everything and anything cell types starting in January 2024. Hosted by the Allen Institute.

Join us for an ABC Atlas office hour! 🧠📈

On Aug. 13 at 10am Pacific, product manager Elysha Fiabane and scientist Rachel Hostetler, PhD will be available to answer all of your questions related to new features and datasets in the Allen Brain Cell Atlas.

RSVP: alleninstitute.org/events/cell_...

Stem cell-derived neural organoids and assembloids are opening new frontiers in neuroscience, but what are the ethical and societal challenges?

Join the discussion at a meeting supported by @danafoundation.bsky.social and @brainorganogenesis.bsky.social.

🎟️ sto.stanfordtickets.org/ethical-and-...

MapMySections - Data Challenge How do firing properties of a cell relate to its molecular cell type? We are seeking tools that can map spikes to brain cell types and visualize the results alongside existing knowledge.

Congrats to all the winners and thank you to everyone who submitted!

Join us on Aug. 27, 10am Pacific for a live demo of these tools. RSVP: alleninstitute.org/events/mapmy...

✨ User-Friendly Tool Award ✨

Nikhil Karthik and Chaitali Khan (APSphysics.bsky.social, NIH) created GT2CT Bayesian Mapper, a tool for spatial probability modeling of genetic tool data: github.com/astronikil/G...

🎯 Algorithm Accuracy Award 🎯

Daniel Ryskamp Rijsketic, Austen Casey, and @theborislab.bsky.social (StanfordMedicine.bsky.social) created UNRAVEL, a Python library for whole-brain fluorescent label mapping: b-heifets.github.io/UNRAVEL/

🧠📈 Announcing the #MapMySections Data Challenge winners!

Congrats to the UNRAVEL (stanfordmedicine.bsky.social) and GT2CT Bayesian Mapper (APSphysics.bsky.social, NIH) teams!

🧵👇 More on their cool #OpenScience tools

Data reuse represents an opportunity to accelerate the pace of science, reduce costs and increase the value of our collective research investments. Data reuse represents an opportunity to accelerate the pace of science, reduce costs and increase the value of our collective research investments. New tools that make open data easier to use—and new…

"The infrastructure is built. The data are waiting. Now it’s time to use them."

#OpenScience is helping people make discoveries faster with less time, money, and resources. @bendichter.com makes the case for data reuse on @thetransmitter.bsky.social.

🧠📈 www.thetransmitter.org/open-neurosc...

Explore how the brain ages with our aging mouse brain data on the Allen Brain Cell Atlas!

Explore the most comprehensive and detailed single-cell dataset of the aged and young adult mouse brain.

🧠📈 knowledge.brain-map.org/abcatlas#AQE...

Our #CellLineOfTheWeek is titin - illuminating the sarcomeres! 🫀🧫

Our high-quality stem cell lines and plasmids are available at-cost to support research and scientific discovery.

📦 Distributed by @coriellinstitute.bsky.social & @addgene.bsky.social.

#OpenScience #CellBio

Needed ASAP: The Partnership Rewiring Neurodegeneration Research Aligning Science Across Parkinson’s (ASAP) and The Allen Institute will examine neurodegenerative disease copathologies to develop precision medicines.

📢 Read this recent feature in Inside Precision Medicine about how we’re teaming up with @alleninstitute.org ‬to power new discoveries in #Parkinsons, #Alzheimers, & beyond.

Learn more: bit.ly/3H8PYLu

I will be presenting in a @aaas.org IUSE Initiative webinar where we investigated impacts of using open science (from @alleninstitute.org) as a teaching tool on student attitudes and knowledge! Register now to join on October 23. aaas-iuse.org/event/embrac...

Chemically active membranes in the generation of cell shape This research project funded by the Allen Distinguised Investigators program challenges the assumption that the cell membrane is a passive material, changing shape only when pushed or pulled.

Using simulations, synthetic cells, and archaeal cell communities, Andela Saric, @kgoepfrich.bsky.social, and @buzzbaum.bsky.social are studying how cell membranes allow cells to change shape, exchange materials, and respond to their environment. #FrontierScience

alleninstitute.org/division/fro...

Scientists used AI to help develop a "digital brain." 🧠📈

In the latest #LabNotes, hear how we used artificial intelligence to stitch together 95 million hi-res images to develop the largest wiring diagram and functional map of a mammalian brain to date.

🎧 alleninstitute.org/news/the-dig...

The MICrONS dataset is public and open access, ready for analysis! But manual edits to the segmentation (“proofreading”) continue to improve data quality. Consider submitting a proofreading request for your cells of interest: www.microns-explorer.org/vortex

The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex - Nature Neuroscience This study maps the connections of layer 5 pyramidal neurons in the mouse cortex, revealing distinct local and intercortical wiring patterns, and provides an open framework for exploring the connectiv...

New electron microscopy study in @nature.com Neuroscience finds that layer 5 ET neurons mostly connect to inhibitory cells locally, esp. those suppressing other excitatory cells, suggesting a "winner-take-all" system.

🧠📈 www.nature.com/articles/s41...

Our #CellLineOfTheWeek is SERCA2 - illuminating the sarcoplasmic/endoplasmic reticulum! 💪🧫

Our high-quality stem cell lines and plasmids are available at-cost to support researchers and accelerate discovery.

📦 Distributed by @coriellinstitute.bsky.social & @addgene.bsky.social