Just published in JOSS: 'DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection' https://doi.org/10.21105/joss.09109
14.01.2026 15:10
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Just published in JOSS: 'DART: A GUI Pipeline for Aligning Histological Brain Sections to 3D Atlases and Automating Laser Microdissection' https://doi.org/10.21105/joss.09109
As a longtime fan of cool papers in @currentbiology.bsky.social, I am really thrilled to see this out!
This study sets the stage for understanding the origins of novel (vocal) behaviors.
Big shout out to the main architects of this work @xmikezheng20.bsky.social and @cliffscience.bsky.social
I am recruiting graduate students for the experimental side of my lab @mcgill.ca for admission in Fall 2026!
Get in touch if you're interested in how brain circuits implement distributed computation, including dopamine-based distributed RL and probabilistic representations.
If you are at #SfN2025, don't miss Huihui's poster tomorrow (Sunday) morning at MM6 (PSTR095.13)! He has developed methods for barcoded connectomics across many vertebrates, from frogs to NHPs, and is comparing the single-cell anatomy of the song systems of zebra finches and parrots!
Annoyed at how difficult MAPseq dissections can be? Check out the new preprint from Kebschull undergrad Rishi Koneru and grad student @mmganant.bsky.social: www.biorxiv.org/content/10.1...
Want to learn everything there is to know about barcoded connectomics, brain clearing, and modern neuroanatomy? There is still time to apply for the CSHL High Throughput Neuroanatomy course! Stipends are available. meetings.cshl.edu/courses.aspx...
I hope you all have fun digging into this and using POINTseq and MAPseq2 for your own favorite circuits!
And even when neurons innervate the same kind of regions, they can do so in different ways. VTA and SNc DA neurons projecting to the dorsal striatum project fundamentally differently. SNc neurons innervate more subregions and broadcast randomly to these regions, while VTA neurons are highly specific
This large number of clusters is not an effect of splitting a stochastically wired system. Co-innervation patterns and projection motifs are often far from the null model of independent projection choice.
We find over 30 connectomic cell types, way more than would have been expected from transcriptomic cell types. Overall, our data agrees nicely with what we know, but boy, is there more structure to this system. Maybe easier to see from the dot plots.
To showcase POINTseq's utility, we then applied it to the midbrain dopaminergic system, mapping >3,800 DA neurons in the VTA and SNc.
We validated POINTseq in the mouse motor cortex using two cre lines and AAVretro-cre to define cell types of interest.
This works all over the brain
POINTseq achieves cell type specific barcoding by pseudotyping barcoded Sindbis virus with the structural proteins of Alphavirus CHIKV, and overexpressing CHIKV cellular receptor Mxra8 in target cells. Mxra8 isn't normally expressed in mouse neurons, enabling cell type specific infection.
Finally have time to add some more meat here. MAPseq2 is what it says on the tin. Better and cheaper. Use this going forward for anything involving MAPseq, including BARseq, BRICseq, and ConnectID!
Next-generation of barcoded projection mapping techniques: MAPseq2 and POINTseq! Congratulations @justuskebschull.bsky.social and team.
Excited to share the first 2(!) preprints from the Kebschull Lab. The amazing @hyopilkim.bsky.social developed MAPseq2 & POINTseq and used them to map the dopaminergic cells of VTA and SNc. tl;dr MAPseq2=10x cheaper, 4x better; POINTseq=easy cell type specific barcoding; DA neurons=very cool.
Our work with Pablo Tano, @hyunggoo-kim.bsky.social Athar Malik, Alexandre Pouget and @naoshigeuchida.bsky.social exploring how dopamine neurons could enable multi-timescale reinforcement learning in the brain is out in @nature.com
www.nature.com/articles/s41...
Thank you to @xinjin.bsky.social and @justuskebschull.bsky.social for presenting their research at the recent Klingenstein Fellowship Awards in Neuroscience Conference.
📷 : SimonProPhoto
Fantastic opportunity to move to Europe, and yes, it includes the UK!
But applicants can be from any nationality.
Our team at UCL is still growing. Get in touch if any of our work sounds interesting.
delaslab.com
Welcome to the Bluesky account for Stand Up for Science 2025!
Keep an eye on this space for updates, event information, and ways to get involved. We can't wait to see everyone #standupforscience2025 on March 7th, both in DC and locations nationwide!
#scienceforall #sciencenotsilence
On Friday, Feb 14 ❤️, we will welcome Prof Justus Kebschull @justuskebschull.bsky.social of Johns Hopkins Biomedical Engineering for his talk on “Understanding brain function and evolution with barcodes and sequencing”. Happening at 11am in RW432. See you there!
This is the end of science as we know it if it stands—15% IDCs for all NIH Grants.
grants.nih.gov/grants/guide...
Postdoc (Baltimore, United States)
Viral Phylodynamics & Neuroscience
with @justuskebschull.bsky.social @rezakalhor.bsky.social
More details: http://iddjobs.org/jobs/johns-hopkins-postdoc-position-in-viral-phylodynamics-neuroscience
Bioinformatician (Baltimore, United States)
Viral Phylodynamics & Neuroscience
with @justuskebschull.bsky.social @rezakalhor.bsky.social
More details: http://iddjobs.org/jobs/hopkins-bioinformatician-position-in-viral-phylodynamics-neuroscience
Many academics point to bioRxiv as “the one thing improving science publishing”.
If so, the one thing you all can do is persuade colleagues to submit and make this a norm. 1/2
Hopkins is recruiting 30 Bloomberg Distinguished Professors in AI + X
(X = astrophysics, cancer, neuroscience, genomics, social sciences, etc.)
hub.jhu.edu/2024/12/17/d...
22 of these 30 will be organized in clusters that were selected after rigorous external review.
The list of clusters is:
