Kevin Dean
@kevin-dean.bsky.social
📤 443
📥 160
📝 168
Science, somewhere down in Texas.
https://www.dean-lab.org
https://thedeanlab.github.io
In
@elife.bsky.social
: A high-resolution, easy-to-build light-sheet microscope for subcellular imaging
doi.org/10.7554/eLif...
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A high-resolution, easy-to-build light-sheet microscope for subcellular imaging
An accessible light-sheet microscope delivers subcellular-resolution, multicolor volumetric, and live-cell imaging, lowering barriers to state-of-the-art performance.
https://doi.org/10.7554/eLife.106910
1 day ago
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Kevin Dean
Reto Fiolka
11 days ago
We have two funded postdoctoral positions available. Topics encompass: -Next gen light-sheet fluorescence microscopy instrumentation -Structured illumination microscopy and other approaches to extend the resolution limit. -Nonlinear microscopy combined with adaptive optics / phase conjugation
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You know a grant is due shortly when your children stop sleeping through the night, and school gets closed for multiple days.
12 days ago
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DNA PAINT in a drosophila embryo. I'm impressed.
www.cell.com/biophysj/ful...
18 days ago
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Navigate can now run entirely with ASI's Tiger Controller, eliminating the NI data acquisition board altogether, simplifying the optoelectronics, and providing deterministic frame-to-frame operation. Documentation coming soon...
github.com/TheDeanLab/n...
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GitHub - TheDeanLab/navigate: navigate - open source light-sheet microscope controls
navigate - open source light-sheet microscope controls - TheDeanLab/navigate
https://github.com/TheDeanLab/navigate
18 days ago
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My favorite conferences are always at Janelia. I cannot recommend enough...
www.janelia.org/you-janelia/...
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Imaging Mouse Development
Organizers Isabel Espinosa Medina, HHMI/Janelia Research Campus Kate McDole, MRC Laboratory of Molecular Biology Robert Prevedel, European Molecular Biology Laboratory (EMBL) Hari Shroff,
https://www.janelia.org/you-janelia/conferences/imaging-mouse-development-0?utm_source=Janelia+Science+%26+Training+Opportunities&utm_campaign=b285c91fb8-EMAIL_CAMPAIGN_2017_04_21_COPY_01&utm_medium=email&utm_term=0_0a4490f01f-b285c91fb8-70106953&mc_cid=b285c91fb8&mc_eid=5703478fa2
22 days ago
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Oh yeah, we do pay these tariffs...
23 days ago
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reposted by
Kevin Dean
Zach Marin
29 days ago
Now out in
@natcomms.nature.com
:
www.nature.com/articles/s41...
! The latest GitHub commits/Colab notebooks enable simulation with 3D sequences.
add a skeleton here at some point
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High-res 3D imaging in patient samples + xenografts shows bleb-associated survival signaling is enriched in poorly adherent melanoma cells in vivo. Pharmacologic disruption reduces metastatic burden.
@muthrnaturzson.bsky.social
www.biorxiv.org/content/10.6...
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In vivo evidence for bleb-induced survival signaling in metastatic melanoma
Bleb signaling is a cellular process in which pressure-driven plasma membrane protrusions generate localized micron-scale membrane curvature that recruits cytosolic septin complexes, assembling signal...
https://www.biorxiv.org/content/10.64898/2026.01.05.697601v1
30 days ago
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A new book, just out! Includes chapters from Dodt, Ueda, Kubitscheck, Gao,
@adamkglaser.bsky.social
, Silvestri, and yours truly!
link.springer.com/book/10.1007...
about 1 month ago
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reposted by
Kevin Dean
Reto Fiolka
about 1 month ago
The cryo cyclical multiplexing expansion microscopy (Cy-ExM) preprint from
@seweryn-galecki.bsky.social
,
@kevin-dean.bsky.social
et al is online. 20 targets across an entire cell. Mr. Snouty also joined the fun.
www.biorxiv.org/content/10.6...
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Introducing Cyclically Multiplexed Expansion Microscopy (Cy-ExM): a workflow for 3D nanoscale, high-plex imaging in whole cells. Cryo-preserved ultrastructure + iterative labeling + expansion microscopy → 20 targets in one dataset with ~70 nm lateral resolution.
www.biorxiv.org/content/10.6...
add a skeleton here at some point
about 1 month ago
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20-plex volumetric super-resolution imaging of cellular ultrastructure. Preprint, led by
@seweryn-galecki.bsky.social
, dropping soon.
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about 1 month ago
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In
@elife.bsky.social
: Altair-LSFM: A High-Resolution, Easy-to-Build Light-Sheet Microscope for Sub-Cellular Imaging
doi.org/10.7554/eLif...
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https://doi.org/10.7554/eLife.106910
about 1 month ago
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Check out this instagram feed…
about 2 months ago
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Interested? Apply on Facebook.
about 2 months ago
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RESOLFT time lapse imaging empowered by deep learning.
www.researchsquare.com/article/rs-8...
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RESOLFT time lapse imaging empowered by deep learning
Capturing the dynamic interplay of proteins and organelles within cells requires microscopy methods with high spatial and temporal resolution. RESOLFT nanoscopy demonstrated great potential for live c...
https://www.researchsquare.com/article/rs-8059028/v1
2 months ago
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Cell Modeling in Space and Time, at Cold Spring Harbor.
meetings.cshl.edu/meetings.asp...
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Cell Modeling in Space and Time
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
https://meetings.cshl.edu/meetings.aspx?meet=COMP
2 months ago
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Fun to see photos from the
@mesospim.bsky.social
Symposium this last October.
2 months ago
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Flew over Greenland yesterday, and it is astonishingly beautiful.
3 months ago
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I simply love Dask.
3 months 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
3 months ago
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reposted by
Kevin Dean
Wildtype One
3 months 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
3 months ago
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I am excited to see this resubmitted.
3 months ago
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reposted by
Kevin Dean
James Manton
3 months 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/
3 months 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
3 months ago
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reposted by
Kevin Dean
Real Python
4 months 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!
4 months ago
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reposted by
Kevin Dean
Bede Portz
4 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.
4 months ago
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reposted by
Kevin Dean
Assaf Zaritsky
4 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.
4 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
4 months ago
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An exciting opportunity for recent PhD graduates.
bit.ly/ShanahanFellow
5 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
5 months ago
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Look who’s on the cover of Cell Reports Methods!
5 months ago
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Great to hear a seminar from the world famous
@haesleinhuepf.bsky.social
!
5 months ago
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reposted by
Kevin Dean
E11 Bio
6 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
5 months ago
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When your continuous integration pipeline betrays you...
5 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
5 months ago
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reposted by
Kevin Dean
Virginie Uhlmann
6 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
6 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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Kevin Dean
mesoSPIM: Clear Images. Big samples. Open source.
6 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
6 months ago
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reposted by
Kevin Dean
Rita Strack
6 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
6 months ago
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reposted by
Kevin Dean
mesoSPIM: Clear Images. Big samples. Open source.
6 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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