Cody Slater
@codyslater.bsky.social
Curious | Lover of art | M4-in-waiting @Columbia VPS | PhD student for now | Building tools to converge RNA biology, neural computation, and control theory | Trying to decide if I surpass my brain's physical state
Reposted by Cody Slater
📢Alain Destexhe and colleagues from @neuropsi.bsky.social introduce a computational framework to study how molecular changes impact brain activity. #compneurosky #Neuroskyence www.nature.com/articles/s43...
A computational approach to evaluate how molecular mechanisms impact large-scale brain activity - Nature Computational Science
A computational framework is introduced to study how molecular changes impact brain activity, using biophysically grounded mean-field models to evaluate how drugs acting on synaptic receptors lead to ...
www.nature.com
May 28, 2025 at 3:58 PM
📢Alain Destexhe and colleagues from @neuropsi.bsky.social introduce a computational framework to study how molecular changes impact brain activity. #compneurosky #Neuroskyence www.nature.com/articles/s43...
Reposted by Cody Slater
🧠📈 Announcing the MapMySections data challenge! Deadline May 30.
The challenge:
📈 create an algorithm that matches fluorescent images of genetic tools to the most likely spatial transcriptomic cell types
💻 present it as part of a user-friendly tool
The challenge:
📈 create an algorithm that matches fluorescent images of genetic tools to the most likely spatial transcriptomic cell types
💻 present it as part of a user-friendly tool
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.
alleninstitute.org
April 8, 2025 at 5:57 PM
🧠📈 Announcing the MapMySections data challenge! Deadline May 30.
The challenge:
📈 create an algorithm that matches fluorescent images of genetic tools to the most likely spatial transcriptomic cell types
💻 present it as part of a user-friendly tool
The challenge:
📈 create an algorithm that matches fluorescent images of genetic tools to the most likely spatial transcriptomic cell types
💻 present it as part of a user-friendly tool
Looking forward to trying this!
🥳Alrighty - end-of-year push to get the final version of #CellSeg3D out!
👩💻 pip install napari-cellseg3d==0.2.2
📚 biorxiv.org/content/10.1...
We extended benchmarking, new videos, extended text, and a demo on cFOS 👋
👩💻 pip install napari-cellseg3d==0.2.2
📚 biorxiv.org/content/10.1...
We extended benchmarking, new videos, extended text, and a demo on cFOS 👋
December 23, 2024 at 5:31 PM
Looking forward to trying this!
Reposted by Cody Slater
Meet ACE - a new tool for comparing annotations across Allen Institute transcriptomic taxonomies!
Join us for a webinar on how to use it in your #neuroscience research, incl. studies using our Alzheimer's datasets.
📆 Dec. 18, 9:30am PT
💻 Webinar
🎟️ alleninstitute.org/events/cell_...
#neuroskyence
Join us for a webinar on how to use it in your #neuroscience research, incl. studies using our Alzheimer's datasets.
📆 Dec. 18, 9:30am PT
💻 Webinar
🎟️ alleninstitute.org/events/cell_...
#neuroskyence
Cell Type Taxonomies A-Z: Webinar Series
Webinar series covering everything and anything cell types starting in January 2024. Hosted by the Allen Institute.
alleninstitute.org
December 12, 2024 at 10:30 PM
Meet ACE - a new tool for comparing annotations across Allen Institute transcriptomic taxonomies!
Join us for a webinar on how to use it in your #neuroscience research, incl. studies using our Alzheimer's datasets.
📆 Dec. 18, 9:30am PT
💻 Webinar
🎟️ alleninstitute.org/events/cell_...
#neuroskyence
Join us for a webinar on how to use it in your #neuroscience research, incl. studies using our Alzheimer's datasets.
📆 Dec. 18, 9:30am PT
💻 Webinar
🎟️ alleninstitute.org/events/cell_...
#neuroskyence
Reposted by Cody Slater
So excited to share our work developing a new class of modular synthetic GPCRs, out today @Nature! Check it out nature.com/articles/s41...
December 5, 2024 at 8:10 AM
So excited to share our work developing a new class of modular synthetic GPCRs, out today @Nature! Check it out nature.com/articles/s41...
Reposted by Cody Slater
𝗕𝗶𝗼𝗹𝗼𝗴𝗶𝗰𝗮𝗹 𝗢𝗿𝗴𝗮𝗻𝗶𝘇𝗮𝘁𝗶𝗼𝗻
By none other than one of my favorite theoretical biologists. Jumps all the way to the top of the reading list!
And free access for 2 weeks (??), so get it right away.
#biology
www.cambridge.org/core/element...
By none other than one of my favorite theoretical biologists. Jumps all the way to the top of the reading list!
And free access for 2 weeks (??), so get it right away.
#biology
www.cambridge.org/core/element...
December 4, 2024 at 4:57 PM
𝗕𝗶𝗼𝗹𝗼𝗴𝗶𝗰𝗮𝗹 𝗢𝗿𝗴𝗮𝗻𝗶𝘇𝗮𝘁𝗶𝗼𝗻
By none other than one of my favorite theoretical biologists. Jumps all the way to the top of the reading list!
And free access for 2 weeks (??), so get it right away.
#biology
www.cambridge.org/core/element...
By none other than one of my favorite theoretical biologists. Jumps all the way to the top of the reading list!
And free access for 2 weeks (??), so get it right away.
#biology
www.cambridge.org/core/element...
Reposted by Cody Slater
Very promising paper bundle on single cell genomics in #neuroscience! 🧠 🖥️ 🧬
Big day for single cell and neuroscience. Trio of single cell perspective pieces discussing applications, opportunities, challenges, and validation of single cell and spatial genomics in neuroscience are out now in Nature Neuroscience. Links in thread below.👇 1/n
December 3, 2024 at 8:17 PM
Very promising paper bundle on single cell genomics in #neuroscience! 🧠 🖥️ 🧬
Reposted by Cody Slater
Good news everyone! A new version of graph-tool is just out! @graph-tool.skewed.de
graph-tool.skewed.de
Graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N
#networkscience
graph-tool.skewed.de
Graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N
#networkscience
December 2, 2024 at 12:55 PM
Good news everyone! A new version of graph-tool is just out! @graph-tool.skewed.de
graph-tool.skewed.de
Graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N
#networkscience
graph-tool.skewed.de
Graph-tool is a comprehensive and efficient Python library to work with networks, including structural, dynamical, and statistical algorithms, as well as visualization. 1/N
#networkscience
Hooray!
If you love browsing our AAV plasmids, but dread the thought of making the viral vectors, we have good news: Addgene will soon be offering Packaged on Request viral vectors!
Can't wait? Sign up for email updates below!
info.addgene.org/pac...
Can't wait? Sign up for email updates below!
info.addgene.org/pac...
December 3, 2024 at 5:02 PM
Hooray!
Very excited to see this. Direct, real-time interfaces with neural systems will drive neuroscience forward. Now to extend with integrated photo-activation for perturbation of targeted neural activity in real-time?
Together with some friends we built an optical Brain Machine Interface to see if cortical activity (PPC) can control behaviour in real time, without animals having to learn to use it. Here's what happened:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
December 3, 2024 at 4:14 PM
Very excited to see this. Direct, real-time interfaces with neural systems will drive neuroscience forward. Now to extend with integrated photo-activation for perturbation of targeted neural activity in real-time?
Reposted by Cody Slater
8/ Trainees at different career stages proposed 7 actions that academic institutions and departments can take to improve their science training.
https://buff.ly/3VbDo1X
https://buff.ly/3VbDo1X
Research Culture: Actionable recommendations from trainees to improve science training
Early-career researchers propose seven actions that can be taken by research institutions and departments to improve science training.
buff.ly
November 26, 2024 at 3:42 PM
8/ Trainees at different career stages proposed 7 actions that academic institutions and departments can take to improve their science training.
https://buff.ly/3VbDo1X
https://buff.ly/3VbDo1X
Reposted by Cody Slater
If you think Bluesky is cool now, just wait until we start getting sophisticated feeds that curate cool papers, data, or code based on intelligent custom algorithms. This will become a second layer of scholarly communication.
November 25, 2024 at 1:49 PM
If you think Bluesky is cool now, just wait until we start getting sophisticated feeds that curate cool papers, data, or code based on intelligent custom algorithms. This will become a second layer of scholarly communication.
After watching users slowly trickle in for the past year, it finally feels like a lot of communities are hitting critical mass
November 25, 2024 at 2:05 AM
After watching users slowly trickle in for the past year, it finally feels like a lot of communities are hitting critical mass
Reposted by Cody Slater
🎉Ach, calretinin+, and more (-) expression in Rh🐒means we can start to connect functional cell groups like here doi.org/10.1016/j.ce... to “omics” cell types, and selectively manipulate circuits! It’s a big deal for understanding population dynamics. Thanks to authors and funders: Brain Initiative!
November 24, 2024 at 3:58 PM
🎉Ach, calretinin+, and more (-) expression in Rh🐒means we can start to connect functional cell groups like here doi.org/10.1016/j.ce... to “omics” cell types, and selectively manipulate circuits! It’s a big deal for understanding population dynamics. Thanks to authors and funders: Brain Initiative!
Reposted by Cody Slater
Optogenetic stimulation of a cortical biohybrid implant guides goal directed behavior https://www.biorxiv.org/content/10.1101/2024.11.22.624907v1
Optogenetic stimulation of a cortical biohybrid implant guides goal directed behavior https://www.biorxiv.org/content/10.1101/2024.11.22.624907v1
Brain-computer interfaces (BCIs) hold exciting therapeutic potential, but tissue damage caused by pr
www.biorxiv.org
November 23, 2024 at 9:15 PM
Optogenetic stimulation of a cortical biohybrid implant guides goal directed behavior https://www.biorxiv.org/content/10.1101/2024.11.22.624907v1
Reposted by Cody Slater
Lately we’ve noticed that while PIs and senior researchers know and use our resources, they are not quite reaching the same proportion of graduate student researchers. 🧪🧵
November 15, 2024 at 5:36 PM
Lately we’ve noticed that while PIs and senior researchers know and use our resources, they are not quite reaching the same proportion of graduate student researchers. 🧪🧵
Reposted by Cody Slater
Activity-dependent Sonic hedgehog signaling promotes astrocyte modulation of synaptic plasticity https://www.biorxiv.org/content/10.1101/2024.04.05.588352v1
Activity-dependent Sonic hedgehog signaling promotes astrocyte modulation of synaptic plasticity https://www.biorxiv.org/content/10.1101/2024.04.05.588352v1
The influence of neural activity on astrocytes and their reciprocal interactions with neurons has em
www.biorxiv.org
April 7, 2024 at 10:14 AM
Activity-dependent Sonic hedgehog signaling promotes astrocyte modulation of synaptic plasticity https://www.biorxiv.org/content/10.1101/2024.04.05.588352v1
Reposted by Cody Slater
Molecular insights into G protein specificity and biased agonism at the β2-adrenergic receptor https://www.biorxiv.org/content/10.1101/2024.03.28.587240v1
Molecular insights into G protein specificity and biased agonism at the β2-adrenergic receptor https://www.biorxiv.org/content/10.1101/2024.03.28.587240v1
G protein coupled receptors (GPCRs) activated by their native hormone or neurotransmitter exhibit va
www.biorxiv.org
March 30, 2024 at 5:16 AM
Molecular insights into G protein specificity and biased agonism at the β2-adrenergic receptor https://www.biorxiv.org/content/10.1101/2024.03.28.587240v1
I'm being dramatic, but vscode feels like a turning point for civilization
November 7, 2023 at 12:30 AM
I'm being dramatic, but vscode feels like a turning point for civilization