Stephan Preibisch
@preibischs.bsky.social
Open Science Software Enthusiast - Director of Scientific Computing Software at HHMI Janelia
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...
That only took 3.5 months 😅
May 27, 2025 at 6:24 PM
That only took 3.5 months 😅
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!
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
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:
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...
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 😎
When I start up the VPN, it changes completely ...
February 14, 2025 at 3:16 PM
When I start up the VPN, it changes completely ...
Now it happened ... spineless, note that I am not in the US right now.
February 14, 2025 at 3:13 PM
Now it happened ... spineless, note that I am not in the US right now.
Winter is coming in Leesburg near @hhmijanelia.bsky.social
December 16, 2024 at 1:01 PM
Winter is coming in Leesburg near @hhmijanelia.bsky.social
I wrote a little script that estimates the approximately equivalent sigma of a Gaussian convolution to the number of linear interpolations applied to images.
December 11, 2024 at 8:21 PM
I wrote a little script that estimates the approximately equivalent sigma of a Gaussian convolution to the number of linear interpolations applied to images.
That's why it is really important to avoid consecutive interpolations of your image when reconstructing your data. Try to use software that combines all transformations you need to apply to your images into a single interpolation operation.
December 11, 2024 at 8:18 PM
That's why it is really important to avoid consecutive interpolations of your image when reconstructing your data. Try to use software that combines all transformations you need to apply to your images into a single interpolation operation.
We are looking for a Scientific Computing Associate to develop AI/ML methods to identify the ancestors of genes of unknown origin, an exciting project with the Stern lab @ HHMI Janelia.
We are looking someone with AI/ML experience.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
@hhmi.bsky.social
We are looking someone with AI/ML experience.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
@hhmi.bsky.social
November 24, 2024 at 11:37 PM
We are looking for a Scientific Computing Associate to develop AI/ML methods to identify the ancestors of genes of unknown origin, an exciting project with the Stern lab @ HHMI Janelia.
We are looking someone with AI/ML experience.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
@hhmi.bsky.social
We are looking someone with AI/ML experience.
hhmi.wd1.myworkdayjobs.com/en-US/Extern...
@hhmi.bsky.social
My BSky handle now appears as "invalid handle" ... does anyone know how to fix that? Thanks so much
November 14, 2024 at 7:58 PM
My BSky handle now appears as "invalid handle" ... does anyone know how to fix that? Thanks so much
For us it’s almost over …
November 11, 2024 at 12:25 AM
For us it’s almost over …
#BigStitcherSpark can also be executed on AWS and Google Cloud, ping me for advice.
November 8, 2024 at 9:36 PM
#BigStitcherSpark can also be executed on AWS and Google Cloud, ping me for advice.
Major update of #BigStitcher & #BigStitcherSpark:
- 10x faster fusion
- cloud support (S3 & GS)
- improved interest-point alignment
- worst error visualization
- improved virtual image splitting
- Zarr/N5/HDF5 export
- consolidated menu structure
#OSSI @HHMIJanelia @FijiSc
- 10x faster fusion
- cloud support (S3 & GS)
- improved interest-point alignment
- worst error visualization
- improved virtual image splitting
- Zarr/N5/HDF5 export
- consolidated menu structure
#OSSI @HHMIJanelia @FijiSc
November 8, 2024 at 9:35 PM
Major update of #BigStitcher & #BigStitcherSpark:
- 10x faster fusion
- cloud support (S3 & GS)
- improved interest-point alignment
- worst error visualization
- improved virtual image splitting
- Zarr/N5/HDF5 export
- consolidated menu structure
#OSSI @HHMIJanelia @FijiSc
- 10x faster fusion
- cloud support (S3 & GS)
- improved interest-point alignment
- worst error visualization
- improved virtual image splitting
- Zarr/N5/HDF5 export
- consolidated menu structure
#OSSI @HHMIJanelia @FijiSc