Stephan Preibisch
@preibischs.bsky.social
Open Science Software Enthusiast - Director of Scientific Computing Software at HHMI Janelia
Reposted by Stephan Preibisch
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
September 4, 2025 at 8:22 AM
We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)
Reposted by Stephan Preibisch
Excited to share more widely: I am starting the Dorkenwald Lab at MIT (McGovern Institute + BCS) in January 2026. We study the organizational principles of neuronal circuits using connectomics.
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
MIT’s McGovern Institute and Department of Brain and Cognitive Sciences welcome new faculty member Sven Dorkenwald - MIT McGovern Institute
The McGovern Institute and the Department of Brain and Cognitive Sciences are pleased to announce the appointment of Sven Dorkenwald as an assistant professor starting in January 2026. A trailblazer i...
mcgovern.mit.edu
October 15, 2025 at 4:57 PM
Excited to share more widely: I am starting the Dorkenwald Lab at MIT (McGovern Institute + BCS) in January 2026. We study the organizational principles of neuronal circuits using connectomics.
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
And we are hiring postdocs & tech associates! dorkenwaldlab.com/join
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 11, 2025 at 1:30 PM
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Stephan Preibisch
Preprint -
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
September 8, 2025 at 4:25 PM
Preprint -
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
Excited to present WHOLISTIC, which extends the concept of whole-brain functional imaging to the entire body. Pioneering work by incredibly talented Virginia Ruetten @vmsruetten.bsky.social, this platform reveals whole-organism cellular dynamics in vivo.
www.biorxiv.org/content/10.1...
Reposted by Stephan Preibisch
What does a neural network look like? Maybe like this view of Larissa Heinrich's U-net for organelle segmentation, with edges between layer inputs and outputs.
Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
July 23, 2025 at 9:22 AM
What does a neural network look like? Maybe like this view of Larissa Heinrich's U-net for organelle segmentation, with edges between layer inputs and outputs.
Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Want to help build networks like this? Join #HHMIJanelia's new AI initiative as a data engineer:
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
Reposted by Stephan Preibisch
🎉 Call for Abstracts! 🎉
We’re celebrating 10 years of #mesoSPIM #opensource initiative – join us at the symposium for talks, demos & posters on open-source light-sheet microscopy, tissue clearing, and imaging!
Dates: October 13-15, 2025
Location: Zurich, Switzerland
Registration: ema.uzh.ch/R7YRN
We’re celebrating 10 years of #mesoSPIM #opensource initiative – join us at the symposium for talks, demos & posters on open-source light-sheet microscopy, tissue clearing, and imaging!
Dates: October 13-15, 2025
Location: Zurich, Switzerland
Registration: ema.uzh.ch/R7YRN
June 12, 2025 at 9:15 AM
🎉 Call for Abstracts! 🎉
We’re celebrating 10 years of #mesoSPIM #opensource initiative – join us at the symposium for talks, demos & posters on open-source light-sheet microscopy, tissue clearing, and imaging!
Dates: October 13-15, 2025
Location: Zurich, Switzerland
Registration: ema.uzh.ch/R7YRN
We’re celebrating 10 years of #mesoSPIM #opensource initiative – join us at the symposium for talks, demos & posters on open-source light-sheet microscopy, tissue clearing, and imaging!
Dates: October 13-15, 2025
Location: Zurich, Switzerland
Registration: ema.uzh.ch/R7YRN
Reposted by Stephan Preibisch
How bad will it be? Catastrophic.
Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come.
But, this is the WH's *proposed* budget.
Speak up now before it is too late.
(inflation adjusted $-s below)
Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come.
But, this is the WH's *proposed* budget.
Speak up now before it is too late.
(inflation adjusted $-s below)
May 31, 2025 at 2:50 AM
That only took 3.5 months 😅
May 27, 2025 at 6:24 PM
That only took 3.5 months 😅
Looking forward!
May 16, 2025 at 12:40 PM
Looking forward!
Found some pretty cool books at the Marine Biological Laboratory @mblscience.bsky.social library alongside pictures of renowned stylish scientists, with @markkitti.bsky.social, @joshmoore.bsky.social and Graham Johnson. It was overall a very inspiring OME community meeting in Woods Hole!
May 1, 2025 at 1:19 PM
Found some pretty cool books at the Marine Biological Laboratory @mblscience.bsky.social library alongside pictures of renowned stylish scientists, with @markkitti.bsky.social, @joshmoore.bsky.social and Graham Johnson. It was overall a very inspiring OME community meeting in Woods Hole!
Reposted by Stephan Preibisch
#GloBIAS has a blog series - new post out today!
Two GloBIAS volunteers reflect on the first version of GloBIAS Free Help (previously Call4Help), explain the idea behind this activity and what was learned during the pilot session.
Please check out the webpage: www.globias.org/resources/gl...
Two GloBIAS volunteers reflect on the first version of GloBIAS Free Help (previously Call4Help), explain the idea behind this activity and what was learned during the pilot session.
Please check out the webpage: www.globias.org/resources/gl...
May 1, 2025 at 1:12 PM
#GloBIAS has a blog series - new post out today!
Two GloBIAS volunteers reflect on the first version of GloBIAS Free Help (previously Call4Help), explain the idea behind this activity and what was learned during the pilot session.
Please check out the webpage: www.globias.org/resources/gl...
Two GloBIAS volunteers reflect on the first version of GloBIAS Free Help (previously Call4Help), explain the idea behind this activity and what was learned during the pilot session.
Please check out the webpage: www.globias.org/resources/gl...
The STIM paper is out! We build on established computer vision techniques to automatically create 3D volumes of spatial transcriptomics datasets with human-level accuracy, and useful, interactive visualizations.
www.sciencedirect.com/science/arti...
@hhmijanelia.bsky.social @mdc-bimsb.bsky.social
www.sciencedirect.com/science/arti...
@hhmijanelia.bsky.social @mdc-bimsb.bsky.social
April 22, 2025 at 3:44 PM
The STIM paper is out! We build on established computer vision techniques to automatically create 3D volumes of spatial transcriptomics datasets with human-level accuracy, and useful, interactive visualizations.
www.sciencedirect.com/science/arti...
@hhmijanelia.bsky.social @mdc-bimsb.bsky.social
www.sciencedirect.com/science/arti...
@hhmijanelia.bsky.social @mdc-bimsb.bsky.social
Reposted by Stephan Preibisch
Join us in Potsdam for the #HIConference25 by @helmholtzimaging.bsky.social – three days of talks, workshops, community challenges, and some stunning scientific visuals!
🗓 Abstract deadline: May 1, 2025
More info and registration:
🔗 events.hifis.net/event/2061/ #HelmholtzImaging #mdcBerlin
🗓 Abstract deadline: May 1, 2025
More info and registration:
🔗 events.hifis.net/event/2061/ #HelmholtzImaging #mdcBerlin
April 17, 2025 at 11:14 AM
Join us in Potsdam for the #HIConference25 by @helmholtzimaging.bsky.social – three days of talks, workshops, community challenges, and some stunning scientific visuals!
🗓 Abstract deadline: May 1, 2025
More info and registration:
🔗 events.hifis.net/event/2061/ #HelmholtzImaging #mdcBerlin
🗓 Abstract deadline: May 1, 2025
More info and registration:
🔗 events.hifis.net/event/2061/ #HelmholtzImaging #mdcBerlin
Reposted by Stephan Preibisch
Our 3D study of the tumor microenvironment is finally out!
Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 )
Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!
Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 )
Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!
April 16, 2025 at 10:40 AM
Our 3D study of the tumor microenvironment is finally out!
Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 )
Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!
Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 )
Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!
Reposted by Stephan Preibisch
www.cell.com/cell-systems...
CosMx data by @brukerspatial.bsky.social
Second harmonics by Andrew Woehler
Immunofluorescence by @sonjafritzsche.bsky.social and @josenimo.bsky.social in Fabian Coscia lab
STIM for 3D alignment by @preibischs.bsky.social @nukappa.bsky.social et al (coming very soon!)
CosMx data by @brukerspatial.bsky.social
Second harmonics by Andrew Woehler
Immunofluorescence by @sonjafritzsche.bsky.social and @josenimo.bsky.social in Fabian Coscia lab
STIM for 3D alignment by @preibischs.bsky.social @nukappa.bsky.social et al (coming very soon!)
Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment
Pentimalli et al. extend imaging-based spatial transcriptomics to 3D and combine it
with ECM profiling. The multimodal analysis of cellular neighborhoods in a clinical
lung adenocarcinoma sample revea...
www.cell.com
April 16, 2025 at 10:40 AM
www.cell.com/cell-systems...
CosMx data by @brukerspatial.bsky.social
Second harmonics by Andrew Woehler
Immunofluorescence by @sonjafritzsche.bsky.social and @josenimo.bsky.social in Fabian Coscia lab
STIM for 3D alignment by @preibischs.bsky.social @nukappa.bsky.social et al (coming very soon!)
CosMx data by @brukerspatial.bsky.social
Second harmonics by Andrew Woehler
Immunofluorescence by @sonjafritzsche.bsky.social and @josenimo.bsky.social in Fabian Coscia lab
STIM for 3D alignment by @preibischs.bsky.social @nukappa.bsky.social et al (coming very soon!)
Shout out to my dear #BigStitcher #Windows users :) I finally got access to a Windows VM and fixed many Windows bugs. I hope most functionality is restored. I still advise switching to Linux/Mac, but I will be able to provide more Windows support in the future if necessary.
April 5, 2025 at 2:57 PM
Shout out to my dear #BigStitcher #Windows users :) I finally got access to a Windows VM and fixed many Windows bugs. I hope most functionality is restored. I still advise switching to Linux/Mac, but I will be able to provide more Windows support in the future if necessary.
I recently visited #Amazon HQ2, to present at the AWS Imagine Nonprofit conference 2025. It was exciting to see use cases & opinions from other areas than biomedicine, to make new contacts, and to see how people at AWS work.
#AWS has an interesting line up of #conferences & #funding opportunities:
#AWS has an interesting line up of #conferences & #funding opportunities:
April 4, 2025 at 10:57 AM
I recently visited #Amazon HQ2, to present at the AWS Imagine Nonprofit conference 2025. It was exciting to see use cases & opinions from other areas than biomedicine, to make new contacts, and to see how people at AWS work.
#AWS has an interesting line up of #conferences & #funding opportunities:
#AWS has an interesting line up of #conferences & #funding opportunities:
Reposted by Stephan Preibisch
Check out this new & exciting #postdoc program from Max Planck Society 🤩 - My lab is thrilled to move to MPI MB in Muenster - positions available in #chromatin #mechanobiology #cancer #stemcells #transcription join us!
🚀 Apply now 🚀
The new Max Planck #Postdoc Program offers a guaranteed contract of at least 3 years, targeted mentoring, and career workshops.
postdocprogram.mpg.de
#ScienceCareer #PostdocProgram
The new Max Planck #Postdoc Program offers a guaranteed contract of at least 3 years, targeted mentoring, and career workshops.
postdocprogram.mpg.de
#ScienceCareer #PostdocProgram
April 1, 2025 at 5:05 PM
Check out this new & exciting #postdoc program from Max Planck Society 🤩 - My lab is thrilled to move to MPI MB in Muenster - positions available in #chromatin #mechanobiology #cancer #stemcells #transcription join us!
Reposted by Stephan Preibisch
The Trump administration's erasure of federal data has put the Internet Archive in the spotlight. The organization, with its small but mighty team, is working to help save the world's digital history.
Humming along in an old church, the Internet Archive is more relevant than ever
The Trump administration's erasure of federal data has put the Internet Archive in the spotlight. The organization, with its small but mighty team, is working to help save the world's digital history.
www.npr.org
March 23, 2025 at 2:02 PM
The Trump administration's erasure of federal data has put the Internet Archive in the spotlight. The organization, with its small but mighty team, is working to help save the world's digital history.
Reposted by Stephan Preibisch
🔜 Starting at 5 PM tonight, the @dfg.de will present the 2025 #LeibnizPreis to #mdcBerlin researcher @apombo1.bsky.social and nine other recipients. Congratulations to all of them! 🥳
📺 You can join the action via livestream – click the link below! 👇
#mdcBIMSB | @www.helmholtz.de
📺 You can join the action via livestream – click the link below! 👇
#mdcBIMSB | @www.helmholtz.de
👉 LIVESTREAM | Verleihung der Leibniz-Preise 2025 👈
Seien Sie ab 17 Uhr live dabei!
www.youtube.com
March 19, 2025 at 2:01 PM
🔜 Starting at 5 PM tonight, the @dfg.de will present the 2025 #LeibnizPreis to #mdcBerlin researcher @apombo1.bsky.social and nine other recipients. Congratulations to all of them! 🥳
📺 You can join the action via livestream – click the link below! 👇
#mdcBIMSB | @www.helmholtz.de
📺 You can join the action via livestream – click the link below! 👇
#mdcBIMSB | @www.helmholtz.de
Pretty awesome setting for today’s workshop on enabling access to emerging bioimaging techniques organized by Ian Dobbie at JHU’s downtown DC campus. We had great presentations and discussions; sites.krieger.jhu.edu/iic/workshop...
March 12, 2025 at 7:54 PM
Pretty awesome setting for today’s workshop on enabling access to emerging bioimaging techniques organized by Ian Dobbie at JHU’s downtown DC campus. We had great presentations and discussions; sites.krieger.jhu.edu/iic/workshop...
Reposted by Stephan Preibisch
Happy #InternationalWomensDay ‼️
Over the past weeks, we’ve shared insights from #mdcBerlin's inspiring #WomenInSTEM – highlighting their work, challenges, and career advice.
🔗 Explore all of their stories here:
➡️ www.mdc-berlin.de/about/values... ⬅️ #WomenInScience #mdcDiversity #IWD2025
Over the past weeks, we’ve shared insights from #mdcBerlin's inspiring #WomenInSTEM – highlighting their work, challenges, and career advice.
🔗 Explore all of their stories here:
➡️ www.mdc-berlin.de/about/values... ⬅️ #WomenInScience #mdcDiversity #IWD2025
March 8, 2025 at 9:00 AM
Happy #InternationalWomensDay ‼️
Over the past weeks, we’ve shared insights from #mdcBerlin's inspiring #WomenInSTEM – highlighting their work, challenges, and career advice.
🔗 Explore all of their stories here:
➡️ www.mdc-berlin.de/about/values... ⬅️ #WomenInScience #mdcDiversity #IWD2025
Over the past weeks, we’ve shared insights from #mdcBerlin's inspiring #WomenInSTEM – highlighting their work, challenges, and career advice.
🔗 Explore all of their stories here:
➡️ www.mdc-berlin.de/about/values... ⬅️ #WomenInScience #mdcDiversity #IWD2025
Reposted by Stephan Preibisch
Amazing news on thr #Fiji front. The new launcher holds beautiful promises for better bioimage analysis tools, and not only for Fiji!!
See this summary thread by Curtis
forum.image.sc/t/fiji-2024-...
See this summary thread by Curtis
forum.image.sc/t/fiji-2024-...
Fiji 2024 Year in Review: Milestones and Roadmap
Introduction The Fiji team at LOCI is pleased to share significant progress on several major initiatives as we work towards raising the technological standards of Fiji. These include Fiji 2.16.0, feat...
forum.image.sc
March 1, 2025 at 8:49 AM
Amazing news on thr #Fiji front. The new launcher holds beautiful promises for better bioimage analysis tools, and not only for Fiji!!
See this summary thread by Curtis
forum.image.sc/t/fiji-2024-...
See this summary thread by Curtis
forum.image.sc/t/fiji-2024-...
Reposted by Stephan Preibisch
Calling the #bioimageanalysis community! Remember the #GatherIsland used during the online #I2K? Remember #Hebedas?
#Woodstockbio2025 will be like this, in real life on a #YMCA #campsite in #Czech woods.
Bioimage Geeks of the World - Unite and Register!
woodstock.img.cas.cz/registration/
#Woodstockbio2025 will be like this, in real life on a #YMCA #campsite in #Czech woods.
Bioimage Geeks of the World - Unite and Register!
woodstock.img.cas.cz/registration/
March 7, 2025 at 3:54 PM
Calling the #bioimageanalysis community! Remember the #GatherIsland used during the online #I2K? Remember #Hebedas?
#Woodstockbio2025 will be like this, in real life on a #YMCA #campsite in #Czech woods.
Bioimage Geeks of the World - Unite and Register!
woodstock.img.cas.cz/registration/
#Woodstockbio2025 will be like this, in real life on a #YMCA #campsite in #Czech woods.
Bioimage Geeks of the World - Unite and Register!
woodstock.img.cas.cz/registration/
Stephan (@herrsaalfeld.bsky.social) of @hhmijanelia.bsky.social explains to the interested Ashburn community how AI can help us understanding biological systems at Old Ox Brewery 😎
March 6, 2025 at 11:48 PM
Stephan (@herrsaalfeld.bsky.social) of @hhmijanelia.bsky.social explains to the interested Ashburn community how AI can help us understanding biological systems at Old Ox Brewery 😎