Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social
May 13, 2025 at 7:57 AM
Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social
Also true for #bioimageanalysis!
1/"I have a presentation tomorrow."
If you've ever collaborated with wet lab scientists as a bioinformatician…
you’ve heard this. And died inside a little.
If you've ever collaborated with wet lab scientists as a bioinformatician…
you’ve heard this. And died inside a little.
May 28, 2025 at 7:45 PM
Also true for #bioimageanalysis!
Check out this masterpiece of systematic #BioImageAnalysis 🤩
August 30, 2025 at 9:34 AM
Check out this masterpiece of systematic #BioImageAnalysis 🤩
Exciting new #BioImageAnalysis #TrainTheTrainer event!
The Royal Microscopical Society @royalmicrosoc.bsky.social Data Analysis in IMaging (RMS DAIM), with the support of the @crick.ac.uk Crick and Partners Networking Fund, is organising a “Train the Trainers in Bioimage Analysis” workshop.
1/n
1/n
April 14, 2025 at 4:22 PM
Exciting new #BioImageAnalysis #TrainTheTrainer event!
1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant!
Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team!
#napari #bioimageanalysis #MCP @biohub
Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team!
#napari #bioimageanalysis #MCP @biohub
March 24, 2026 at 11:04 PM
1/ 🚀 Excited to release: napari-mcp - agentic control of napari from any MCP-capable AI assistant!
Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team!
#napari #bioimageanalysis #MCP @biohub
Use it for interactive image processing, analysis, and visualisation! Really cool project from @ilan-theodoro.bsky.social from my team!
#napari #bioimageanalysis #MCP @biohub
This award is such a beautiful surprise! 🤩 Tons of thanks to the @royalmicrosoc.bsky.social, the amazing #BioimageAnalysis, #Fiji, #ImageJ & #OpenSource communities, my mentors and mentees, my employers, and whoever nominated me (I still don't know how that person was 😅)!
We are very pleased to announce Dr Ignacio Arganda-Carreras @iarganda.eurosky.social as winner of the RMS Award for Data Analysis in Imaging (DAIM) 🙂 🔬
Read more about Ignacio's achievements: www.rms.org.uk/resource/dr-...
Read more about Ignacio's achievements: www.rms.org.uk/resource/dr-...
May 19, 2026 at 12:29 PM
This award is such a beautiful surprise! 🤩 Tons of thanks to the @royalmicrosoc.bsky.social, the amazing #BioimageAnalysis, #Fiji, #ImageJ & #OpenSource communities, my mentors and mentees, my employers, and whoever nominated me (I still don't know how that person was 😅)!
Are you a #BioImageAnalysis pro? Challenge your skills by playing #BIAbubbles! 🎉
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
April 25, 2025 at 7:28 PM
Are you a #BioImageAnalysis pro? Challenge your skills by playing #BIAbubbles! 🎉
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
Find the right workflows and reproduce the result! 🔬🖥️🕹️
And if you have challenging BIA tasks, new level contributions are welcome! 😀
github.com/haesleinhuep...
First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
July 14, 2025 at 1:30 PM
First day of #bobiac2025. Six days of intensive Python based #BioImageAnalysis. Intro by @fedegasparoli.bsky.social
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
- "This will be a long week, but it will change your life".
iac.hms.harvard.edu/bobiac/2025/
We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
December 1, 2025 at 8:27 AM
We’ll be at @neuripsconf.bsky.social on Wednesday, 3 December, from 11 a.m. to 2 p.m. (San Diego time). Come and chat with us about why distance matrices and invariances are cool! 🎉 #InterdisciplinaryML #neurips2025 #bioimageanalysis #shapequantification
My slides about "Learning and Training #BioImageAnalysis in the Age of AI" presented at the @globias.bsky.social @carpentries.carpentries.org workshop are available #openaccess. Big thanks for hosting us @istaustria-iof.bsky.social ! 🔬🖥️🤖
zenodo.org/records/1516...
zenodo.org/records/1516...
April 7, 2025 at 7:16 PM
My slides about "Learning and Training #BioImageAnalysis in the Age of AI" presented at the @globias.bsky.social @carpentries.carpentries.org workshop are available #openaccess. Big thanks for hosting us @istaustria-iof.bsky.social ! 🔬🖥️🤖
zenodo.org/records/1516...
zenodo.org/records/1516...
GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.
April 16, 2025 at 7:40 PM
GloBIAS #BioimageAnalysis #Conference 2025 – we have opened the registration for our 2025 in-person event. Please check the webpage www.globias.org/activities/b... for more information and the link to the registration form.
My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess.
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
August 12, 2025 at 5:57 PM
My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess.
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...
November 25, 2024 at 8:32 AM
🧵 It's a lazy Sunday afternoon -- let's do some #bioimageanalysis.
December 15, 2024 at 4:13 PM
🧵 It's a lazy Sunday afternoon -- let's do some #bioimageanalysis.
Hello #BioImageAnalysis world! Is the sky bluer here? 🦋
November 19, 2024 at 5:36 PM
Hello #BioImageAnalysis world! Is the sky bluer here? 🦋
Amazing talk by my dear colleague and friend @albertdm.bsky.social and his supervisor @maweigert.bsky.social showing the cool things you can do with Spotiflow at #CBIAS2025. Look at this beautiful learned spot detection in 3D! 👩🏻💻👩🏻💻🔬 #bioimageanalysis #spotdetection
November 24, 2025 at 11:31 AM
Amazing talk by my dear colleague and friend @albertdm.bsky.social and his supervisor @maweigert.bsky.social showing the cool things you can do with Spotiflow at #CBIAS2025. Look at this beautiful learned spot detection in 3D! 👩🏻💻👩🏻💻🔬 #bioimageanalysis #spotdetection
Great thread full of #bioimageanalysis goodies
November 27, 2024 at 3:25 PM
Great thread full of #bioimageanalysis goodies
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/
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Annotating Images in Cellpose - FocalPlane
Annotating Images in Cellpose - How to
focalplane.biologists.com
June 9, 2025 at 9:43 AM
New ‘How to’ post on FocalPlane 🔬💻
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
Lea Kabjesz shares a step-by-step guide to get you started annotating 2D and 3D images in Cellpose, including video tutorials.
focalplane.biologists.com/2025/06/05/a...
#bioimageanalysis #cellpose #imaging #HowTo
I gave two seminars at @embl.org Heidelberg these days: One about using LLMs via #biabob for #BioImageAnalysis and one about how LLMs impact BioImage #DataScience
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
September 16, 2025 at 7:02 PM
I gave two seminars at @embl.org Heidelberg these days: One about using LLMs via #biabob for #BioImageAnalysis and one about how LLMs impact BioImage #DataScience
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
Thanks EMBL for having me!
Materials #openaccess 🧑🏫🖥️🔓
zenodo.org/records/1705...
zenodo.org/records/1710...
scads.github.io/llm-bia-2025
Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis
April 8, 2025 at 2:32 PM
Bioimaging and bioimage analysis friends, some help if you have 2-3 mins; for a paper, we're trying to estimate the number of biologists trained in open source software or tools in the last ~5 years. (1/2) #bioimaging #microscopy #bioimageanalysis
If, hypothetically, a person were trying to set up a career panel series for bioimage analysis, what kinds of roles (or specific people) would you want to hear more about? Hypothetical nominations of all stripes welcome :) #bioimageanalysis
March 12, 2025 at 2:31 PM
If, hypothetically, a person were trying to set up a career panel series for bioimage analysis, what kinds of roles (or specific people) would you want to hear more about? Hypothetical nominations of all stripes welcome :) #bioimageanalysis
Raster image processing in progress at the #Nextflow for #BioImageAnalysis #Hackathon at #VIB #Leuven
December 6, 2024 at 5:14 PM
Raster image processing in progress at the #Nextflow for #BioImageAnalysis #Hackathon at #VIB #Leuven
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
F-BIAS: Towards a distributed national core facility for bioimage analysis †
Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...
journals.plos.org
June 11, 2025 at 8:29 AM
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
As part of our monthly meeting, we do a run-down of all* the new #bioimageanalysis tools that have been published in the last couple of weeks on BioRxiv**, so I thought I'd start sharing here as well.
*I will miss some, apologies if I miss your paper
*I will miss some, apologies if I miss your paper
October 17, 2025 at 7:17 AM
As part of our monthly meeting, we do a run-down of all* the new #bioimageanalysis tools that have been published in the last couple of weeks on BioRxiv**, so I thought I'd start sharing here as well.
*I will miss some, apologies if I miss your paper
*I will miss some, apologies if I miss your paper