Mathew Summers
@summersathome.bsky.social
Thalamic hodologist, formerly retina surfer. Scientist @AllenInstitute
Pinned
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...
www.biorxiv.org
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...
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/...
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/...
September 16, 2026 at 8:07 PM
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/...
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/...
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...
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...
www.biorxiv.org
September 16, 2026 at 6:18 PM
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...
Reposted by Mathew Summers
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!
August 17, 2026 at 5:29 PM
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!
Cool work! www.nature.com/articles/s41...
August 8, 2026 at 2:47 PM
Cool work! www.nature.com/articles/s41...
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:
April 13, 2026 at 6:55 PM
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:
All the more reason to be excited by the latest generation of glutamate indicators:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 18, 2026 at 12:48 AM
All the more reason to be excited by the latest generation of glutamate indicators:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Mathew Summers
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...
Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too!
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
preprint (with videos!) + thread 🧵
Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking
www.biorxiv.org/content/10.6...
1/9
February 16, 2026 at 4:22 PM
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...
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!
Before mice open their eyes at two weeks old, the retina exhibits spontaneous retinal waves. Waves at the start of the second postnatal week show a bias to propagate in the nasal direction (or right to left in the movie below). (2/11)
February 6, 2026 at 6:01 PM
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!
Reposted by Mathew Summers
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...
Preprint: www.biorxiv.org/content/10.6...
Website: anniegbryant.github.io/subcortex_vi...
January 27, 2026 at 3:04 AM
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...
Preprint: www.biorxiv.org/content/10.6...
Website: anniegbryant.github.io/subcortex_vi...
We've got a great lineup of speakers for our Thalamocortical Interactions GRS! Only a few spots remaining for poster presenters - apply soon!
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!
January 8, 2026 at 7:40 PM
We've got a great lineup of speakers for our Thalamocortical Interactions GRS! Only a few spots remaining for poster presenters - apply soon!
Reposted by Mathew Summers
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...
January 4, 2026 at 6:17 AM
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...
Reposted by Mathew Summers
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.
November 4, 2025 at 10:20 AM
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.
Reposted by Mathew Summers
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/...
www.pnas.org/doi/10.1073/...
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...
www.pnas.org
December 3, 2025 at 3:36 PM
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/...
www.pnas.org/doi/10.1073/...
Reposted by Mathew Summers
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...
www.ucl.ac.uk/cortexlab/po...
November 12, 2025 at 3:41 PM
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...
www.ucl.ac.uk/cortexlab/po...
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.
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.
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!
November 6, 2025 at 9:42 PM
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.
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.
Reposted by Mathew Summers
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...
To find your nearest drop box, visit: www.sos.wa.gov/elections/vo...
November 3, 2025 at 10:10 PM
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...
To find your nearest drop box, visit: www.sos.wa.gov/elections/vo...
Reposted by Mathew Summers
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...
www.jneurosci.org/content/earl...
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...
www.jneurosci.org
October 15, 2025 at 7:55 PM
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...
www.jneurosci.org/content/earl...
Reposted by Mathew Summers
YEEEEEAAAAAAAHHHH, Teresa!!!
Teresa Puthussery, a UC Berkeley vision scientist whose insights into the retina could one day help those with vision loss regain their sight, has been named a 2025 MacArthur “genius” Fellow. news.berkeley.edu/2025/10/08/v...
Vision scientist Teresa Puthussery receives MacArthur ‘genius’ award - Berkeley News
Puthussery’s discoveries about the retina are paving the way for new treatments for eye disease and vision loss
news.berkeley.edu
October 8, 2025 at 11:26 PM
YEEEEEAAAAAAAHHHH, Teresa!!!
Reposted by Mathew Summers
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
By @franciscorr25.bsky.social
#neuroskyence
bit.ly/3Wx5nt3
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.
bit.ly
October 7, 2025 at 1:55 PM
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
By @franciscorr25.bsky.social
#neuroskyence
bit.ly/3Wx5nt3
Reposted by Mathew Summers
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...
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...
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.
www.seattletimes.com
October 6, 2025 at 8:05 PM
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...
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...
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 3, 2025 at 1:46 AM
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...
www.biorxiv.org/content/10.1...
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!
September 10, 2025 at 4:16 PM
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!
Reposted by Mathew Summers
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...
Sound reasonable to you?
Fed register is accepting comments for next month. Details at the link & comment button
www.federalregister.gov/documents/20...
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...
www.federalregister.gov
August 29, 2025 at 6:32 AM
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...
Sound reasonable to you?
Fed register is accepting comments for next month. Details at the link & comment button
www.federalregister.gov/documents/20...
Reposted by Mathew Summers
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.
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.
www.npr.org
August 21, 2025 at 11:11 PM
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.