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Mathew Summers

@summersathome.bsky.social
217 followers 334 following 40 posts

Thalamic hodologist, formerly retina surfer. Scientist @AllenInstitute

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Mathew Summers @summersathome.bsky.social · 16/09/2026
Busy day - our work on the organization of norepinephrine neurons in the locus coeruleus is out today in Nature too. If you're interested in digging deeper, the data and analyses supporting all of our work is hosted in a public CodeOcean collection: codeocean.allenneuraldynamics.org/collections/...
codeocean.allenneuraldynamics.org
Code Ocean
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Mathew Summers @summersathome.bsky.social · 16/09/2026
If you are interested in deploying 3D-MAESTRO, either in your lab or at your core imaging facility, please reach out! We're happy to help you get the pipeline running.
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Mathew Summers @summersathome.bsky.social · 16/09/2026
We built 3D-MAESTRO using Nextflow, supporting interoperability on local machines, high-performance compute clusters, or in the cloud. Processing stages produce standardized outputs, & fused volumes + intermediate results are viewable via Neuroglancer in web browsers (e.g. tinyurl.com/48229vfp)
tinyurl.com
neuroglancer
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Mathew Summers @summersathome.bsky.social · 16/09/2026
In the preprint we showcase the utility of 3D-MAESTRO with several whole mouse brain experiments including characterization of genetic tools, tracing anatomical connectivity, and localizing neural activity based on immediate early gene activation as well as reconstructed Neuropixels probe tracks.
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Mathew Summers @summersathome.bsky.social · 16/09/2026
We also developed a new 3D template of aqueous-cleared mouse brains, enabling accurate registration to the Allen Common Coordinate Framework (CCF). Accurate registration between samples is key to integrating between data modalities and to doing biology at scale.
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Mathew Summers @summersathome.bsky.social · 16/09/2026
We've used 3D-MAESTRO to process thousands of whole mouse-brain samples. The modular design of the pipeline allows us to benchmark and swap out competing algorithms for individual processing steps. Check out the preprint for our head-to-head comparison of stitching and cell detection algorithms!
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Mathew Summers @summersathome.bsky.social · 16/09/2026
3D-MAESTRO "orchestrates" the steps that transform your raw imaging data into quantitative biological insight. Steps such as optical artifact correction, stitching and volume fusion, atlas registration, and object detection are all organized under a single modular framework.
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Mathew Summers @summersathome.bsky.social · 16/09/2026
Acquiring terabyte sized light-sheet datasets has become increasingly common, but processing large scale volumetric microscopy data remains hard. I've spoken to scientists with hard won data that has sat for years on hard drives due to the challenges of processing and analyzing that data.
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Mathew Summers @summersathome.bsky.social · 16/09/2026
Proud to announce our latest preprint introducing 3D-MAESTRO: an automated pipeline that makes processing volumetric imaging data routine and reproducible. Out now on BioRxiv: www.biorxiv.org/content/10.6...
biorxiv.org
3D-MAESTRO: A scalable, modular, portable pipeline for automated processing of large-scale volumetric brain microscopy data
Light microscopy is routinely used to explore the cellular and molecular structure of tissues, but the scale and complexity of data remains a bottleneck for discovery. We introduce 3D-MAESTRO (3D-Micr...
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Fix the L8 @fixthel8.bsky.social · 17/08/2026
Bus lanes on Denny are getting painted THIS WEEKEND! Join us and Mayor Wilson to celebrate with another Race the L8 on Tuesday, September 8th at 5 PM at Denny Park! Lets prove that she Fixed the L8 and that it's finally faster than walking!
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Mathew Summers @summersathome.bsky.social · 08/08/2026
Cool work! www.nature.com/articles/s41...
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Mathew Summers @summersathome.bsky.social · 13/04/2026
reposting with non-transparent figure backgrounds!
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Mathew Summers @summersathome.bsky.social · 13/04/2026
reposting with non-transparent figure backgrounds!
Correlation matrix of LC axonal projections
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Mathew Summers @summersathome.bsky.social · 13/04/2026
Check out the rest of the manuscript to see how the LC's anatomical connectivity beautifully corresponds to transcriptomic and functional structure! www.biorxiv.org/content/10.6...
biorxiv.org
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Mathew Summers @summersathome.bsky.social · 13/04/2026
Finally, with the effort invested in these reconstructions, it's important that the data live beyond an individual project. We've created a portal for perusing, visualizing, and downloading our single neuron morphologies, and we'll upload reconstructions from future projects here as well.
morphology.allenneuraldynamics.org
Neuron Morphology Community Portal
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Mathew Summers @summersathome.bsky.social · 13/04/2026
We went to great lengths (pun intended) to make this work as reproducible as possible. Data is stored on public S3 buckets, and all of the figure panels can be re-generated via CodeOcean capsules (mine is linked in this post). You can also find our analysis code on Github: github.com/AllenNeuralD...
codeocean.allenneuraldynamics.org
Code Ocean
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Mathew Summers @summersathome.bsky.social · 13/04/2026
What about fine-scale projection structure? We looked at co-innervation along the cortical surface. Axons seemed to sample areas near to one another in space - but we didn't see compelling evidence for spatially distant "functional specificity". We compared to cerebellum as well (see supplement).
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Mathew Summers @summersathome.bsky.social · 13/04/2026
Projection targets were related to the position of the soma within LC. Dorsal neurons were more likely to project to the forebrain, while ventral neurons projected to hindbrain and spinal cord. Coloring axons by soma position beautifully highlights this relationship!
LC axons color coded by dorsal/ventral soma position.
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Mathew Summers @summersathome.bsky.social · 13/04/2026
How do these LC neurons wire in space? Individual neurons have diverse projections, but clear structure emerges across the population. Length in forebrain areas is correlated, and anticorrelated with length in the hindbrain. Cerebellum and midbrain were mostly uncorrelated with forebrain & hindbrain
Axonal length correlation matrix
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Mathew Summers @summersathome.bsky.social · 13/04/2026
LC neurons are long, and branch relatively little. Compared to 1200+ neurons from the MouseLight database, LC neurons had significantly fewer branches per cm of length. For this reason, we chose to quantify connectivity via axonal length in a brain region (though axon terminus counts look similar).
Scatterplot of axon length vs branch count
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Mathew Summers @summersathome.bsky.social · 13/04/2026
This was a hard-won dataset, with our tracers reconstructing over 37 meters(!) of LC axons. The average neuron took about 48 hours to trace, and the entire dataset represents >250 days of continuous tracing effort (more to come in the future about machine learning work to speed reconstructions).
Mouse brain with three example LC neuron reconstructions.
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Mathew Summers @summersathome.bsky.social · 13/04/2026
Check out our latest work on the structure and function of locus coeruleus (LC)! My own contribution to this project was investigating the anatomical projections of individually reconstructed LC neurons from our ExA-SPIM pipeline (see: elifesciences.org/reviewed-pre...). A few more notes:
elifesciences.org
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues
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Mathew Summers @summersathome.bsky.social · 18/02/2026
All the more reason to be excited by the latest generation of glutamate indicators: www.nature.com/articles/s41...
nature.com
Glutamate indicators with increased sensitivity and tailored deactivation rates - Nature Methods
iGluSnFR4f and iGluSnFR4s are the latest generation of genetically encoded glutamate sensors. They are advantageous for detecting rapid dynamics and large population activity, respectively, as demonst...
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Andrew Straw @andrewstraw.bsky.social · 16/02/2026
Using our bee-tracking drone, we discovered that honey bees 🐝 have highly precise and individual routes. Now published at @currentbiology.bsky.social : doi.org/10.1016/j.cu...
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Mathew Summers @summersathome.bsky.social · 06/02/2026
Retinal waves are known to be important for proper wiring at the retina's downstream targets: but their role in the development of microcircuits -within the retina itself- is less understood. Some nice work on this topic by @miah-pitcher.bsky.social!
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Annie G. Bryant @anniegbryant.bsky.social · 27/01/2026
The extended version of my thesis procrastination project/subcortex visualization package is out now in both Python and R, now that I’ve graduated 🤠 This figure shows the 9 atlases included (and counting)! Preprint: www.biorxiv.org/content/10.6... Website: anniegbryant.github.io/subcortex_vi...
Nine subcortical/cerebellar atlases included in the subcortex_visualization Python package (and subcortexVisualizationR package in R). The atlases are depicted in two-dimensional vector graphic format.
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Mathew Summers @summersathome.bsky.social · 08/01/2026
We've got a great lineup of speakers for our Thalamocortical Interactions GRS! Only a few spots remaining for poster presenters - apply soon!
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adamezracohen.bsky.social @adamezracohen.bsky.social · 04/01/2026
What is the computational role of dendritic excitations? Byung Hun Lee and team mapped voltage dynamics throughout the dendritic trees of CA1 pyramidal neurons in mice navigating in virtual reality. www.biorxiv.org/content/10.6...
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Ben Sivyer @bensivyer.bsky.social · 04/11/2025
We’re hiring! Join the Sivyer Lab at The University of Sydney as a Postdoctoral Research Fellow in Neurodegeneration within the Snow Vision Accelerator, a $50M initiative tackling glaucoma and optic nerve disease. iPSCs, electrophysiology, drug discovery, and gene therapy.
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Mathew Summers @summersathome.bsky.social · 15/12/2025
i think people are just upset about the chiefs
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John Ball @john-m-ball.bsky.social · 03/12/2025
Extremely proud to share our publication on S-cone circuitry in the ground squirrel, newly available this week in PNAS. We've been staring at these reconstructions for a long time, and I'm excited for others to see the results. 1/n www.pnas.org/doi/10.1073/...
pnas.org
S-cone-specific circuitry in the outer plexiform layer of a cone-dominant mammal | PNAS
In the vertebrate retina, short wavelength-sensitive S-cones and their downstream interneurons play unique roles in both image forming and non-imag...
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Mathew Summers @summersathome.bsky.social · 16/11/2025
Come check out my poster this morning (FF9) to learn about thalamic innervation of frontal cortex! We've got a lot of cool data for ya #sfn2025 #sfn25
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Matteo Carandini @carandinilab.net · 12/11/2025
Our lab is looking for a postdoc! We have interesting projects and cutting-edge techniques such as Neuropixels Opto, Light Beads Microscopy and more. We would be delighted to receive your application. Deadline is 25 November 2025. More info here: www.ucl.ac.uk/cortexlab/po...
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Mathew Summers @summersathome.bsky.social · 06/11/2025
10 days left to be considered for a speaking slot at the Thalamocortical Interactions GRS! If you're a trainee at the NIH and unable to submit an application due to furlough, shoot me a DM and we'll figure something out.
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Washington State Democrats @wadems.org · 03/11/2025
Can’t always trust everyone. Drop your ballot in an official drop box, not in someone’s hands. To find your nearest drop box, visit: www.sos.wa.gov/elections/vo...
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Kevin Bender @neurobender.bsky.social · 15/10/2025
Fresh off the press! @selinsch.bsky.social discovered some really cool features of mouse frontal cortex pyramidal cells that co-vary with dopamine receptor expression. D3R+ cells appear very responsive to AP bursts, producing Ca transients across dendritic arbors. www.jneurosci.org/content/earl...
jneurosci.org
Intrinsic dendritic integration features of prefrontal layer 5 pyramidal cell subclasses
Prefrontal cortex (PFC) is an associative center in the brain and integrates various inputs to support cognition. Layer 5 pyramidal cells are themselves associative centers, as their dendrites span al...
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Mathew Summers @summersathome.bsky.social · 09/10/2025
well deserved!
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BWJones @bwjones.bsky.social · 09/10/2025
YEEEEEAAAAAAAHHHH, Teresa!!!
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The Transmitter @thetransmitter.bsky.social · 07/10/2025
To celebrate the first anniversary of the release of FlyWire, we asked nine neuroscientists to share how they are using connectome data in their research and what they hope is in store for the future of fly connectomics. By @franciscorr25.bsky.social #neuroskyence bit.ly/3Wx5nt3
bit.ly
How FlyWire is redefining Drosophila research, one year in
Nine Drosophila researchers share how the connectome transformed the field and what additional new tools they would like to see.
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Congresswoman Pramila Jayapal @jayapal.house.gov · 06/10/2025
A huge congrats to Seattle scientist Mary E. Brunkow for winning the Nobel Prize in medicine! This is exactly the kind of groundbreaking work that we should be leading on — and it’s exactly why I’ll continue to fight Trump’s cuts to the NIH and research. www.seattletimes.com/seattle-news...
seattletimes.com
A Seattle scientist won a Nobel Prize. She thought the call was spam
Mary E. Brunkow, Fred Ramsdell and Dr. Shimon Sakaguchi won the Nobel Prize in medicine on Monday for their discoveries concerning peripheral immune tolerance.
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Mathew Summers @summersathome.bsky.social · 03/10/2025
Check out our resource for navigating and analyzing spatial transcriptomics data in the thalamus, which we fondly call "the THALMANAC" (𝐓𝐇𝐀𝐋amus 𝐌ERFISH 𝐀𝐍alysis and 𝐀𝐂cess), now live on bioRxiv: www.biorxiv.org/content/10.1...
biorxiv.org
Exploring the correspondence between gene expression and thalamic nuclei using the THALMANAC resource
The thalamus connects the sensory organs and major subcortical brain regions with the neocortex. The thalamus has long been divided into multiple discrete nuclei, based on cytoarchitecture, histochemi...
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Mathew Summers @summersathome.bsky.social · 18/09/2025
Sensitivity is one thing, but do you think a single light sensitive ion channel will ever have sufficient dynamic range for natural-ish vision? After all, the retina uses tiered adaptation systems even for just photopic vision. www.nature.com/articles/nat...
nature.com
Light adaptation in cone vision involves switching between receptor and post-receptor sites - Nature
Humans can see in conditions from darkened cinemas to bright sun because cone photoreceptors adapt their mean output to the current light conditions; here, a second site of adaptation is identified, i...
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Mathew Summers @summersathome.bsky.social · 18/09/2025
Cool stuff! I had a similar "headlamp test" when troubleshooting retina recordings.
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Mathew Summers @summersathome.bsky.social · 10/09/2025
If you're a trainee studying the thalamus, consider checking out our GRS on Thalamocortical Networks in Sensation, Behavior, and Disease: www.grc.org/thalamocorti.... Apply by Nov 16th to be considered for a talk!
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Nigel Goldenfeld @nigelgoldenfeld.bsky.social · 29/08/2025
Very few PhD students finish within 4 years. But international students will need to do that if US proposed visa rules change go through. Sound reasonable to you? Fed register is accepting comments for next month. Details at the link & comment button www.federalregister.gov/documents/20...
federalregister.gov
Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media
Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...
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Dr. Lucky Tran @luckytran.com · 22/08/2025
The ideological cancellation of $800 million of scientific research grants because they supposedly focused on DEI was just backed by the Supreme Court. This is horrific on so many levels.
npr.org
Supreme Court allows NIH to stop making nearly $800M in research grants for now
But the court, in its emergency docket order, also left in place by a 5-4 order a lower court ruling that threw out NIH memos that enforced the administration's policies.
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Mathew Summers @summersathome.bsky.social · 20/08/2025
A great environment!
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RoordaLab @roordalab.bsky.social · 17/07/2025
6+6 = 12 reasons to move to Waterloo, Canada. First 6..... 6 job openings in the University of Waterloo School of Optometry & Vision Science/Waterloo Eye Institute. lnkd.in/d3QD5wFA see thread for the next 6.
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Max Kozlov @maxkozlov.bsky.social · 15/07/2025
NEW: In an unprecedented move, the NIH will soon disinvite dozens of scientists about to take positions on advisory councils that make final decisions on grant funding. NIH staff were told to select others aligned with the Trump administration and told to expect placements by political appointees.
nature.com
Exclusive: NIH to dismiss dozens of grant reviewers to align with Trump priorities
The move would undo years of work, leaving advisory councils understaffed, and without the full expertise needed for reviews.
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Chuck Taylor | Seattle @chcktylr.bsky.social · 15/07/2025
CCTV comes to Seattle.
seattletimes.com
Seattle police cameras, now up and running, draw constitutional concerns
Seattle's newly revamped Real Time Crime Center is operational, with analysts monitoring dozens of surveillance cameras placed in areas with high crime rates.
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