Kevin Dean
@kevin-dean.bsky.social
📤 419
📥 154
📝 147
Science, somewhere down in Texas.
https://www.dean-lab.org
https://thedeanlab.github.io
Fun to see photos from the
@mesospim.bsky.social
Symposium this last October.
1 day ago
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Flew over Greenland yesterday, and it is astonishingly beautiful.
11 days ago
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I simply love Dask.
13 days ago
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www.nature.com/articles/s41...
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Isotropic, aberration-corrected light sheet microscopy for rapid high-resolution imaging of cleared tissue - Nature Biotechnology
A light-sheet microscope built from off-the-shelf components enables high-resolution clear tissue imaging.
https://www.nature.com/articles/s41587-025-02882-8
21 days ago
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reposted by
Kevin Dean
Wildtype One
22 days ago
Finally, the love child of AI and microscopy. A major advance. Thanks for sharing
@kevin-dean.bsky.social
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A game changer in our hands...
www.nature.com/articles/s41...
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Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
https://www.nature.com/articles/s41592-025-02887-w
23 days ago
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I am excited to see this resubmitted.
27 days ago
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reposted by
Kevin Dean
James Manton
about 1 month ago
We've now discovered some neat cell culture dishes that feature a 50 micron thick film of a proprietary polymer with refractive index even closer to water than FEP. They work just as well as our homemade FEP assembly and are available in multiwell plate format too!
www.sarstedt.com/en/products/...
add a skeleton here at some point
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www.theregister.com/2025/10/27/p...
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Python Foundation rejects $1.5M grant with no-DEI strings
: Foundation says it won't compromise policy of inclusivity even if that cash would've really helped
https://www.theregister.com/2025/10/27/python_foundation_abandons_15m_nsf/
about 1 month ago
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economist.com/culture/2025...
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The serious reasons for wearing silly costumes to protests
Making an impression on the streets is an art
https://economist.com/culture/2025/10/24/the-serious-reasons-for-wearing-silly-costumes-to-protests?giftId=906aac7a-f829-4eb0-960d-a615ee4df352&utm_campaign=gifted_article
about 1 month ago
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reposted by
Kevin Dean
Real Python
about 1 month ago
Switching From `pip` to `uv` in Python
#python
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Switching From `pip` to `uv` in Python #python
Learn the ins and outs of uv and how to transition from Pip to uv.
https://blog.appsignal.com/2025/09/24/switching-from-pip-to-uv-in-python-a-comprehensive-guide.html
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I finally found it!
about 2 months ago
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reposted by
Kevin Dean
Bede Portz
about 2 months ago
From
@retof.bsky.social
@kevin-dean.bsky.social
et al. As a big proponent of image-based high throughput phenotypic screening and AI-enabled hit calling this looks really cool
www.biorxiv.org/content/10.1...
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Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy
Light-Sheet Fluorescence Microscopy (LSFM) enables gentle, rapid, and efficient volumetric imaging of biological specimens. Despite its potential, LSFM has fragmented into multiple variants, each narr...
https://www.biorxiv.org/content/10.1101/2025.10.04.680473v1
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With miOPM now out on bioRxiv, the future of imaging is super bright.
about 2 months ago
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reposted by
Kevin Dean
Assaf Zaritsky
about 2 months ago
Excited to announce the first
@cshlnews.bsky.social
meeting on Cell Modeling in Space and Time, June 2026 💫
meetings.cshl.edu/meetings.asp...
Bringing together experiments, computation and theory to explore dynamic, multi-scale cellular organization and function! 1/3
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Heidelberg, you disappoint me.
about 2 months ago
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The claim that the spinning disk confocal microscope’s days are limited appears increasingly accurate.
add a skeleton here at some point
about 2 months ago
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An exciting opportunity for recent PhD graduates.
bit.ly/ShanahanFellow
2 months ago
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pubs.acs.org/doi/10.1021/...
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Synthesis and Optical Properties of Unsymmetric Aromatically π-Extended BODIPY
A series of unsymmetrically substituted BODIPY dyes featuring fused benzo- or naphtho-fragments on one pyrrolic unit were synthesized from the corresponding pyrrolic precursors. The synthetic route was optimized using a modular approach based on the condensation of formylpyrroles with alkylpyrroles, enabling the identification of precursor combinations that minimize byproduct formation and improve preparative yields. The resulting benzo- and naphtho-fused BODIPYs display intense fluorescence in the red region, with emission maxima spanning 590–680 nm and fluorescence quantum yields ranging from 0.27 to 0.84. Their two-photon absorption (2PA) properties were studied both experimentally and computationally. An increase in the two-photon absorption cross-section with an increase in the size of the π-conjugated system was observed, reaching 80 GM for the naphthoBODIPY derivative. These findings demonstrate the potential of π-extended BODIPY scaffolds as NIR-active fluorophores with enhanced nonlinear optical properties.
https://pubs.acs.org/doi/10.1021/acs.joc.5c01432
3 months ago
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Look who’s on the cover of Cell Reports Methods!
3 months ago
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Great to hear a seminar from the world famous
@haesleinhuepf.bsky.social
!
3 months ago
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reposted by
Kevin Dean
E11 Bio
4 months ago
E11 seeks a research associate with experience in fluorescence microscopy and tissue sectioning for our sample processing team. Work at a Focused Research Organization with great people, solid benefits, and tons of energy to complete the first mammalian connectome.
jobs.lever.co/convergentre...
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Convergent Research - E11 Bio - Research Assistant, Biological Sample Processing
E11 Bio is on a mission to reach a whole-brain human connectome. We are a collaborative and interdisciplinary team of scientists and engineers engaged in a neuroscience moonshot project to develop a r...
https://jobs.lever.co/convergentresearch/97217ae7-0b4c-4b36-a316-780d1732ea70
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Thrilled to share our new work in Cell Reports Methods: MCT-ASLM, a multiscale light-sheet microscopy platform that captures biology from tissue landscapes down to organelles, revealing rare events like sparse neurons and micrometastases.
www.cell.com/cell-reports...
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Feature-driven whole-tissue imaging with subcellular resolution
Lin et al. present a self-driving light-sheet microscope that integrates whole-organ surveys with automated, high-resolution targeting of either user-specified or autonomously identified features. By ...
https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(25)00184-5
3 months ago
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When your continuous integration pipeline betrays you...
3 months ago
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u-Probe now can be run without a MATLAB license, and exports detection and tracking results in a format that can immediately be visualized with
@napari.org
!
github.com/DanuserLab/u...
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GitHub - DanuserLab/u-probe: Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation...
Processing of raw ratiometric biosensor images (for example based on FRET) into fully corrected "ratio maps" or "activation maps" — images showing the localized activation of th...
https://github.com/DanuserLab/u-probe
3 months ago
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reposted by
Kevin Dean
Virginie Uhlmann
3 months ago
Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
add a skeleton here at some point
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reposted by
Kevin Dean
Denis Wirtz
3 months ago
In our new paper, we use a new 3D single-cell reference map to guide the design and validation of a new multi-compartment assembloid that mimics the function and architecture of the human endometrial tissue, exhibiting stromal decidualization. More here:
www.biorxiv.org/content/10.1...
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reposted by
Kevin Dean
mesoSPIM: Clear Images. Big samples. Open source.
3 months ago
Final program of the 10-year
#mesoSPIM2025
Anniversary Symposium, October 13-15 in Zurich! Amazing lineup of speakers: biologists, physicists, developers, computer scientists and industry experts! Join us to learn, present, and connect! Registration until Sept. 15.
www.adabd.uzh.ch/en/events/me...
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RFK Jr’s attack on mRNA technology endangers the world
economist.com/science-and-...
from The Economist
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RFK Jr’s attack on mRNA technology endangers the world
His cuts will not just hurt vaccines
https://economist.com/science-and-technology/2025/08/20/rfk-jrs-attack-on-mrna-technology-endangers-the-world
4 months ago
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reposted by
Kevin Dean
Rita Strack
4 months ago
There is still time to apply to become part of our team at Nature Biomedical Engineering! Please share!
springernature.wd3.myworkdayjobs.com/SpringerNatu...
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Pan-ASLM: a high-resolution and large field-of-view light sheet microscope for Expansion Microscopy
www.biorxiv.org/content/10.1...
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Pan-ASLM: a high-resolution and large field-of-view light sheet microscope for Expansion Microscopy
Expansion microscopy, a super-resolution fluorescence microscopy technique in which samples are expanded up to ∼8,000 times (after 20-fold expansion) their original volume, places high demands on the ...
https://www.biorxiv.org/content/10.1101/2025.08.06.668765v1
4 months ago
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reposted by
Kevin Dean
mesoSPIM: Clear Images. Big samples. Open source.
4 months ago
We’re excited to welcome
@kevin-dean.bsky.social
to the
#mesoSPIM2025
Symposium! Explore his innovations in Multiscale Cleared-Tissue Axially Swept Light-Sheet Microscopy for imaging from organ to subcellular levels. 🗺️Oct 13–15 | Zurich & hybrid Interested? Register now:
t.uzh.ch/1Ss
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We are launching a new imaging initiative at UT Southwestern Medical Center. The Texas Cancer Cell Imaging Shared Resource will expand high-resolution and quantitative imaging capabilities for cancer research.
www.utsouthwestern.edu/research/cor...
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Texas Cancer Cell Imaging Core
The Cancer Cell Imaging Core (CCIC) at UT Southwestern enables researchers to visualize cancer processes with unprecedented resolution and throughput. CCIC combines state-of-the-art multiscale imaging...
https://www.utsouthwestern.edu/research/core-facilities/texas-cancer-cell-imaging/
4 months ago
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PSA:
@napari.org
continues to grow up, and is pretty damn good.
4 months ago
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reposted by
Kevin Dean
Mueller, She Wrote
4 months ago
Stephen Colbert is going SCORCHED EARTH right now. To RFK Jr: “Fuck you, you roid-addled nepo carnie! Fuck you, you roadkill-munching Luddite human slim jim!”
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Donald Trump’s war on climate science has staggering implications
economist.com/by-invitatio...
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Donald Trump’s war on climate science has staggering implications
Even a policy of “drill, baby, drill” would imply more climate research, not its evisceration, says Ralph Keeling
https://economist.com/by-invitation/2025/07/30/donald-trumps-war-on-climate-science-has-staggering-implications?giftId=1c4127e7-32ca-47b2-ad95-2c86a9ada811
4 months ago
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reposted by
Kevin Dean
DeBerardinis Lab at UT Southwestern Medical Center
4 months ago
1/New paper on peroxisome assembly, reporting the detailed mechanism of PEX39, a new peroxin involved in PTS2 protein transport. Fantastic work by @walterwchen.bsky.social and a dream team of collaborators, as explained below.
www.nature.com/articles/s41...
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PEX39 facilitates the peroxisomal import of PTS2-containing proteins - Nature Cell Biology
Chen et al. show that PEX39 cooperates with PEX7 in the peroxisomal import of proteins containing a PTS2 site and uncover an (R/K)PWE motif in PEX39 and PEX13 that binds to PEX7 and facilitates the im...
https://www.nature.com/articles/s41556-025-01711-z
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The beginning of an era that ends today.
@retof.bsky.social
4 months ago
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Next, we will build a microscope.
5 months ago
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reposted by
Kevin Dean
Denis Wirtz
5 months ago
Grant terminations have grabbed the headlines and have seen legal action, but even more damaging to the US research enterprise has been the massive decrease in number of research grants issued by federal agencies NIH has seen a decrease of 57% in the number of awards & 63% in value compared to FY24
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Forget vibe coding. The future is vibe research.
5 months ago
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reposted by
Kevin Dean
Jon Daniels
5 months ago
Production has started for a new
#Snoutscope
objective, AMS-AGY v3. It has significantly larger FOV and some other tweaks from v1 and v2. Currently accepting pre-orders. The price will need to increase modestly after deliveries start late October.
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To understand America today, study the zero-sum mindset, writes Stefanie Stantcheva
economist.com/by-invitatio...
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To understand America today, study the zero-sum mindset, writes Stefanie Stantcheva
Young people and city-dwellers are among those most likely to see one group’s gain as another’s loss
https://economist.com/by-invitation/2025/07/07/to-understand-america-today-study-the-zero-sum-mindset-writes-stefanie-stantcheva?giftId=d5797515-d1c8-4a56-a020-c931ef1bb53f&utm_campaign=gifted_article
5 months ago
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peps.python.org/pep-0722/
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PEP 722 – Dependency specification for single-file scripts | peps.python.org
This PEP specifies a format for including 3rd-party dependencies in a single-file Python script.
https://peps.python.org/pep-0722/
5 months ago
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The big beautiful bill reveals the hollowness of Trumponomics
economist.com/briefing/202...
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The big beautiful bill reveals the hollowness of Trumponomics
Republicans battle to pass a profligate but insubstantial law
https://economist.com/briefing/2025/07/02/the-big-beautiful-bill-reveals-the-hollowness-of-trumponomics?giftId=47b8b0aa-9bd8-4215-a435-35c099010093
5 months ago
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This looks fun.
realpython.com/micropython/
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MicroPython: An Intro to Programming Hardware in Python – Real Python
Are you interested in the Internet of Things, home automation, and connected devices? If so, then you're in luck! In this tutorial, you'll learn about MicroPython and the world of electronics hardware...
https://realpython.com/micropython/
5 months ago
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A casual North American drive.
5 months ago
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Daughter had tubes put in her ears today. A 10 minute surgery, billed to insurance at $5k, out of pocket $1.5k. This is America.
6 months ago
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What our analysis of 900 firms shows about their values
economist.com/interactive/...
from The Economist
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What our analysis of 900 firms shows about their values
We crunch the numbers on what employees think in 19 industries
https://economist.com/interactive/business/2025/06/16/corporate-culture
6 months ago
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Our reviewed preprint is out!
elifesciences.org/reviewed-pre...
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Altair-LSFM: A High-Resolution, Easy-to-Build Light-Sheet Microscope for Sub-Cellular Imaging
https://elifesciences.org/reviewed-preprints/106910
6 months ago
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