Peter Sobolewski
@psobolewskiphd.bsky.social
#Duke #UCSD Alum; Recovering Academic; Research IT
@jacksonlab.bsky.social; core dev @napari.fosstodon.org.ap.brid.gy
@jacksonlab.bsky.social; core dev @napari.fosstodon.org.ap.brid.gy
Reposted by Peter Sobolewski
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Scientific Workflows Developer
The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...
embl.wd103.myworkdayjobs.com
January 14, 2026 at 9:37 AM
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Peter Sobolewski
Won best thesis award with this video! 4 years of research and play in 3 minutes :')
youtu.be/so0fPlK1-LM
youtu.be/so0fPlK1-LM
Smart microscopy, computer vision, and controlling cells with light -- my PhD thesis in 3 minutes
YouTube video by Pertz Lab
youtu.be
January 7, 2026 at 11:27 AM
Won best thesis award with this video! 4 years of research and play in 3 minutes :')
youtu.be/so0fPlK1-LM
youtu.be/so0fPlK1-LM
Reposted by Peter Sobolewski
Kind of flew under the radar, BUT we released napari-omero 0.6 recently 🥳 @openmicroscopy.org
You can now down-/upload ROIs from and to OMERO inside @napari.org 🤩Bringing the power of napari for annotation to the management of OMERO :)
Thanks @psobolewskiphd.bsky.social and other maintainers!
You can now down-/upload ROIs from and to OMERO inside @napari.org 🤩Bringing the power of napari for annotation to the management of OMERO :)
Thanks @psobolewskiphd.bsky.social and other maintainers!
January 7, 2026 at 1:27 PM
Kind of flew under the radar, BUT we released napari-omero 0.6 recently 🥳 @openmicroscopy.org
You can now down-/upload ROIs from and to OMERO inside @napari.org 🤩Bringing the power of napari for annotation to the management of OMERO :)
Thanks @psobolewskiphd.bsky.social and other maintainers!
You can now down-/upload ROIs from and to OMERO inside @napari.org 🤩Bringing the power of napari for annotation to the management of OMERO :)
Thanks @psobolewskiphd.bsky.social and other maintainers!
Reposted by Peter Sobolewski
Very pleased to announce the release of #OMERO.figure 7.3.0 including ROI Labels, Colorbars and lots of bug fixes. Thanks to contributors: Rémy Dornier, @tom-bssnnt.bsky.social, Jens Wendt, Niraj Kandpal. www.youtube.com/watch?v=cUy5...
OMERO.figure: ROI Labels and Colorbars: New in 7.3.0
YouTube video by Open Microscopy Environment
www.youtube.com
January 5, 2026 at 4:42 PM
Very pleased to announce the release of #OMERO.figure 7.3.0 including ROI Labels, Colorbars and lots of bug fixes. Thanks to contributors: Rémy Dornier, @tom-bssnnt.bsky.social, Jens Wendt, Niraj Kandpal. www.youtube.com/watch?v=cUy5...
Reposted by Peter Sobolewski
It's new annual conference budget time! I've updated the public, filterable Chemistry Conference Database with hundreds of new conferences.
There are currently 564 conferences in the list.
supersciencegrl.co.uk/conferences #chemsky #chemchat
There are currently 564 conferences in the list.
supersciencegrl.co.uk/conferences #chemsky #chemchat
Nessa Carson: Conference Database
A researcher-endorsed database of global conferences relevant to all chemists, with particular focus on the UK and Europe.
supersciencegrl.co.uk
January 3, 2026 at 2:01 PM
It's new annual conference budget time! I've updated the public, filterable Chemistry Conference Database with hundreds of new conferences.
There are currently 564 conferences in the list.
supersciencegrl.co.uk/conferences #chemsky #chemchat
There are currently 564 conferences in the list.
supersciencegrl.co.uk/conferences #chemsky #chemchat
Reposted by Peter Sobolewski
🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
www.janelia.org
December 28, 2025 at 7:06 PM
🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026
✍️ Jan 15 2026 ✍️
🔁 pls!!
www.janelia.org/you-janelia/...
Someone making some copycat #chemistry accounts:
mastodon.social/@matthartingss
And
mastodon.social/@fraserstoddar
#ChemSky
mastodon.social/@matthartingss
And
mastodon.social/@fraserstoddar
#ChemSky
Matt Hartings (@matthartingss@mastodon.social) - Mastodon
40 Posts, 259 Following, 8 Followers · Chemist - 3D Printing, Food and Cooking
Faculty - American University
Author - Chemistry in Your Kitchen
Twitter - Sciencegeist
Pronouns - he/him/his
mastodon.social
December 21, 2025 at 9:16 PM
Someone making some copycat #chemistry accounts:
mastodon.social/@matthartingss
And
mastodon.social/@fraserstoddar
#ChemSky
mastodon.social/@matthartingss
And
mastodon.social/@fraserstoddar
#ChemSky
Reposted by Peter Sobolewski
New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...
Using Appose with Pixi and Napari for reproducible deep learning segmentation workflows.
YouTube video by Brian Northan
www.youtube.com
December 19, 2025 at 1:43 PM
New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...
Reposted by Peter Sobolewski
🚀⭐️ Trackastra update 🚀⭐️
We just released a new model that uses pre-trained image features from Meta’s SAM2 model.
This improves performance on many datasets, most notably for bacteria tracking.
To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...
We just released a new model that uses pre-trained image features from Meta’s SAM2 model.
This improves performance on many datasets, most notably for bacteria tracking.
To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...
December 11, 2025 at 5:43 PM
🚀⭐️ Trackastra update 🚀⭐️
We just released a new model that uses pre-trained image features from Meta’s SAM2 model.
This improves performance on many datasets, most notably for bacteria tracking.
To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...
We just released a new model that uses pre-trained image features from Meta’s SAM2 model.
This improves performance on many datasets, most notably for bacteria tracking.
To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...
Reposted by Peter Sobolewski
💻 🧬 How does #CompSci power biomedical research?
Celebrate Computer Science Education Week with @jacksonlab.bsky.social's Beginner's Guide to Genomic Databases, a 🆓 self-paced course on genomic data structures, annotation & sequence alignment: education.learning.jax.org/genomic-data...
#CSEdWeek
Celebrate Computer Science Education Week with @jacksonlab.bsky.social's Beginner's Guide to Genomic Databases, a 🆓 self-paced course on genomic data structures, annotation & sequence alignment: education.learning.jax.org/genomic-data...
#CSEdWeek
December 10, 2025 at 1:37 PM
💻 🧬 How does #CompSci power biomedical research?
Celebrate Computer Science Education Week with @jacksonlab.bsky.social's Beginner's Guide to Genomic Databases, a 🆓 self-paced course on genomic data structures, annotation & sequence alignment: education.learning.jax.org/genomic-data...
#CSEdWeek
Celebrate Computer Science Education Week with @jacksonlab.bsky.social's Beginner's Guide to Genomic Databases, a 🆓 self-paced course on genomic data structures, annotation & sequence alignment: education.learning.jax.org/genomic-data...
#CSEdWeek
Reposted by Peter Sobolewski
Thanks to an up to $30M contract award from ARPA-H, JAX aims to revolutionize drug safety testing with the #CARDIOVERSE—a new project that combines #AI, #stemcells, and #genetic variation to predict #drugsafety before human trials. 💊 🧪 🔬 🤖
go.jax.org/cardioverse
go.jax.org/cardioverse
December 8, 2025 at 9:44 PM
Thanks to an up to $30M contract award from ARPA-H, JAX aims to revolutionize drug safety testing with the #CARDIOVERSE—a new project that combines #AI, #stemcells, and #genetic variation to predict #drugsafety before human trials. 💊 🧪 🔬 🤖
go.jax.org/cardioverse
go.jax.org/cardioverse
Reposted by Peter Sobolewski
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking.
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
December 8, 2025 at 9:48 AM
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking.
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
December 6, 2025 at 7:17 PM
Reposted by Peter Sobolewski
📅 We're excited to share @jacksonlab.bsky.social's 2026 Courses & Workshops lineup and invite you to join us!
Our programs in Maine and Conn., along with virtual options for many events, will accelerate your development and support your success in #BiomedicalResearch: www.jax.org/education-an...
Our programs in Maine and Conn., along with virtual options for many events, will accelerate your development and support your success in #BiomedicalResearch: www.jax.org/education-an...
Courses and Workshops offered by The Jackson Laboratory
List of courses, conferences, webinars and workshops at The Jackson Laboratory.
www.jax.org
December 4, 2025 at 1:15 PM
📅 We're excited to share @jacksonlab.bsky.social's 2026 Courses & Workshops lineup and invite you to join us!
Our programs in Maine and Conn., along with virtual options for many events, will accelerate your development and support your success in #BiomedicalResearch: www.jax.org/education-an...
Our programs in Maine and Conn., along with virtual options for many events, will accelerate your development and support your success in #BiomedicalResearch: www.jax.org/education-an...
OMG Black Thought doing a Biggie impression on the new #TheRoots DYWM anniversary live album is amazing. The whole album is really great.
December 4, 2025 at 1:27 AM
OMG Black Thought doing a Biggie impression on the new #TheRoots DYWM anniversary live album is amazing. The whole album is really great.
Reposted by Peter Sobolewski
The EMBO Practical Course "Hack your microscope" in Oeiras, PT, 20–25 Apr 2026 aims to innovate, democratize advanced #imaging technologies and shape the future of open-source #microscopy – Apply now!
Deadline: 12 Dec
https://meetings.embo.org/event/26-microscope
#EMBOmicroscope #EMBOevents 🧪
Deadline: 12 Dec
https://meetings.embo.org/event/26-microscope
#EMBOmicroscope #EMBOevents 🧪
December 3, 2025 at 4:15 PM
The EMBO Practical Course "Hack your microscope" in Oeiras, PT, 20–25 Apr 2026 aims to innovate, democratize advanced #imaging technologies and shape the future of open-source #microscopy – Apply now!
Deadline: 12 Dec
https://meetings.embo.org/event/26-microscope
#EMBOmicroscope #EMBOevents 🧪
Deadline: 12 Dec
https://meetings.embo.org/event/26-microscope
#EMBOmicroscope #EMBOevents 🧪
December 3, 2025 at 2:52 AM
Reposted by Peter Sobolewski
Applications for the next @royalmicrosoc.bsky.social “Introduction to image analysis” workshop are now open!
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Introduction to Image Analysis 2026
www.rms.org.uk
December 1, 2025 at 10:09 AM
Applications for the next @royalmicrosoc.bsky.social “Introduction to image analysis” workshop are now open!
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Reposted by Peter Sobolewski
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
youtu.be
September 19, 2025 at 7:35 AM
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
Reposted by Peter Sobolewski
Trackastra is part of the brand-new TrackMate v8.
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖
November 20, 2025 at 8:18 PM
Trackastra is part of the brand-new TrackMate v8.
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖