Marie Held
@makaefer.bsky.social
Image analyst at the Centre for Cell Imaging, the University of Liverpool.
didyouknowimageanalysis.wordpress.com
CCI.liv.ac.uk
didyouknowimageanalysis.wordpress.com
CCI.liv.ac.uk
Reposted by Marie Held
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
opencollective.com/napari/donate
December 18, 2025 at 12:03 PM
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
opencollective.com/napari/donate
Come on, do it. You know you want to. ⬇️
🔬 Hands-on bioimage data stewardship workshop
27/2/2026
Uni of Liverpool
Learn the complete data lifecycle from acquisition to repository submission.
Train-the-trainer format - take materials back to your facility!
✓ 25 places
✓ Up to £100 travel
✓ Apply by 7 Jan
Apply👇
3 more in Scotland, SW, SE
27/2/2026
Uni of Liverpool
Learn the complete data lifecycle from acquisition to repository submission.
Train-the-trainer format - take materials back to your facility!
✓ 25 places
✓ Up to £100 travel
✓ Apply by 7 Jan
Apply👇
3 more in Scotland, SW, SE
December 5, 2025 at 6:35 PM
Come on, do it. You know you want to. ⬇️
Reposted by Marie Held
If you or your trainees are just getting started with image analysis of cells & are #CellProfiler -curious, here is a fairly thorough walk-through demo I did recently. Loading files, extracting metadata (fun with Regex!), identifying objects, measuring, filtering, QC, exporting:
youtu.be/fO5nJdhj_7I
youtu.be/fO5nJdhj_7I
Introduction to CellProfiler - by a biologist, for biologists!
YouTube video by CellMorphoJSero
youtu.be
December 4, 2025 at 12:37 PM
If you or your trainees are just getting started with image analysis of cells & are #CellProfiler -curious, here is a fairly thorough walk-through demo I did recently. Loading files, extracting metadata (fun with Regex!), identifying objects, measuring, filtering, QC, exporting:
youtu.be/fO5nJdhj_7I
youtu.be/fO5nJdhj_7I
Reposted by Marie Held
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Toward better 2D - 3D registration in BigWarp
BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...
forum.image.sc
November 29, 2025 at 6:03 PM
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
forum.image.sc/t/toward-bet...
Reposted by Marie Held
No CBIAS would be complete without an image analysis workshop! Thanks Rocco, @giuliapaci.bsky.social and @makaefer.bsky.social for organising, we had fun helping out with teaching 🔬💻
And that’s a wrap for the @cbias.bsky.social napari workshop as well. Two days of learning, working collaboratively and finished off with a presentation from each of five project groups detailing the progress they made. Organised by Rocco D’Antuono, @giuliapaci.bsky.social and yours truly
November 28, 2025 at 7:45 AM
No CBIAS would be complete without an image analysis workshop! Thanks Rocco, @giuliapaci.bsky.social and @makaefer.bsky.social for organising, we had fun helping out with teaching 🔬💻
And that’s a wrap for the @cbias.bsky.social napari workshop as well. Two days of learning, working collaboratively and finished off with a presentation from each of five project groups detailing the progress they made. Organised by Rocco D’Antuono, @giuliapaci.bsky.social and yours truly
November 27, 2025 at 7:24 PM
And that’s a wrap for the @cbias.bsky.social napari workshop as well. Two days of learning, working collaboratively and finished off with a presentation from each of five project groups detailing the progress they made. Organised by Rocco D’Antuono, @giuliapaci.bsky.social and yours truly
Reposted by Marie Held
November 25, 2025 at 1:06 PM
Reposted by Marie Held
An immense thank you again to @cbias.bsky.social committee, sponsors and fellow imaging friends for this fantastic symposium!
It's is not the end but the beginning of tons of papers to read, colleagues to contact, new collaborations to form. And most importantly, it's a 'see you soon' #CBIAS2026 🔬🥰
It's is not the end but the beginning of tons of papers to read, colleagues to contact, new collaborations to form. And most importantly, it's a 'see you soon' #CBIAS2026 🔬🥰
November 25, 2025 at 6:26 PM
An immense thank you again to @cbias.bsky.social committee, sponsors and fellow imaging friends for this fantastic symposium!
It's is not the end but the beginning of tons of papers to read, colleagues to contact, new collaborations to form. And most importantly, it's a 'see you soon' #CBIAS2026 🔬🥰
It's is not the end but the beginning of tons of papers to read, colleagues to contact, new collaborations to form. And most importantly, it's a 'see you soon' #CBIAS2026 🔬🥰
Reposted by Marie Held
Topical conclusion from @helenajambor.bsky.social
Scientists have tools to fight and make life better
#CBiAS2025
Scientists have tools to fight and make life better
#CBiAS2025
November 25, 2025 at 11:45 AM
Topical conclusion from @helenajambor.bsky.social
Scientists have tools to fight and make life better
#CBiAS2025
Scientists have tools to fight and make life better
#CBiAS2025
And we’re off. #CBIAS2025 6th Edition, first outside of the Crick but impressed by the localities at @wellcomecollection.bsky.social
@david-j-barry.bsky.social welcoming the community
@david-j-barry.bsky.social welcoming the community
November 24, 2025 at 10:23 AM
And we’re off. #CBIAS2025 6th Edition, first outside of the Crick but impressed by the localities at @wellcomecollection.bsky.social
@david-j-barry.bsky.social welcoming the community
@david-j-barry.bsky.social welcoming the community
It’s that time of year that I make my pilgrimage to London for the #CBIAS2025 and its trilogy of Ps: presentations, posters and panel discussions. But first I did some exploring…
🎶 London calling to the faraway towns 🎶
🎶 London calling to the faraway towns 🎶
November 24, 2025 at 6:55 AM
It’s that time of year that I make my pilgrimage to London for the #CBIAS2025 and its trilogy of Ps: presentations, posters and panel discussions. But first I did some exploring…
🎶 London calling to the faraway towns 🎶
🎶 London calling to the faraway towns 🎶
Reposted by Marie Held
Less than a week to go for #CBIAS2025! A few hours left to register, in person in London or online over Zoom (registration deadline on Nov 20th)
Find out all the information at the link below:
www.crick.ac.uk/whats-on/cri...
Find out all the information at the link below:
www.crick.ac.uk/whats-on/cri...
Crick BioImage Analysis Symposium 2025
www.crick.ac.uk
November 18, 2025 at 4:40 PM
Less than a week to go for #CBIAS2025! A few hours left to register, in person in London or online over Zoom (registration deadline on Nov 20th)
Find out all the information at the link below:
www.crick.ac.uk/whats-on/cri...
Find out all the information at the link below:
www.crick.ac.uk/whats-on/cri...
Reposted by Marie Held
Time is running out to register for #CBIAS2025
November 13, 2025 at 9:12 PM
Time is running out to register for #CBIAS2025
Don’t miss out on this inclusive, friendly, stimulating, fun event!
Last chance to register for #CBIAS2025, registrations are closing on November 20th - join us to discuss all things #bioimageanalysis and don’t miss a great networking opportunity!
Will you be there?
www.crick.ac.uk/whats-on/cri...
Will you be there?
www.crick.ac.uk/whats-on/cri...
Crick BioImage Analysis Symposium 2025
www.crick.ac.uk
November 13, 2025 at 4:06 PM
Don’t miss out on this inclusive, friendly, stimulating, fun event!
What a pertinent read today: www.science.org/content/arti...
Let us not forget, champion the “invisible women“, fight for what’s right.
What a coincidence that I had the privilege to name new @cci-liv.bsky.social workstations today: Henrietta Lacks, Bibha Chowdhuri and Katherine Johnson 👩🔬🔬⚛️🔭👩🔬
Let us not forget, champion the “invisible women“, fight for what’s right.
What a coincidence that I had the privilege to name new @cci-liv.bsky.social workstations today: Henrietta Lacks, Bibha Chowdhuri and Katherine Johnson 👩🔬🔬⚛️🔭👩🔬
Rosalind Franklin and the damage of gender harassment
Spurred by a recent report on sexual harassment in academia, our columnist revisits a historical case and reflects on what has changed—and what hasn’t
www.science.org
November 7, 2025 at 10:27 PM
What a pertinent read today: www.science.org/content/arti...
Let us not forget, champion the “invisible women“, fight for what’s right.
What a coincidence that I had the privilege to name new @cci-liv.bsky.social workstations today: Henrietta Lacks, Bibha Chowdhuri and Katherine Johnson 👩🔬🔬⚛️🔭👩🔬
Let us not forget, champion the “invisible women“, fight for what’s right.
What a coincidence that I had the privilege to name new @cci-liv.bsky.social workstations today: Henrietta Lacks, Bibha Chowdhuri and Katherine Johnson 👩🔬🔬⚛️🔭👩🔬
📢 Enhance your bioimage analysis skills - 2-day hands-on napari workshop.
Learn to:
- Set up conda envis install napari
- Navigate napari GUI install plugins
- Jupyter notebooks for basic IA
- Apply new skills to real datasets w expert guidance
📅 Apply by NOW!
www.crick.ac.uk/whats-on/cbi...
Learn to:
- Set up conda envis install napari
- Navigate napari GUI install plugins
- Jupyter notebooks for basic IA
- Apply new skills to real datasets w expert guidance
📅 Apply by NOW!
www.crick.ac.uk/whats-on/cbi...
CBIAS napari workshop 2025
www.crick.ac.uk
November 7, 2025 at 10:49 AM
📢 Enhance your bioimage analysis skills - 2-day hands-on napari workshop.
Learn to:
- Set up conda envis install napari
- Navigate napari GUI install plugins
- Jupyter notebooks for basic IA
- Apply new skills to real datasets w expert guidance
📅 Apply by NOW!
www.crick.ac.uk/whats-on/cbi...
Learn to:
- Set up conda envis install napari
- Navigate napari GUI install plugins
- Jupyter notebooks for basic IA
- Apply new skills to real datasets w expert guidance
📅 Apply by NOW!
www.crick.ac.uk/whats-on/cbi...
Reposted by Marie Held
Want to enhance your image analysis skills with napari?
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
CBIAS napari workshop 2025
www.crick.ac.uk
September 12, 2025 at 10:08 AM
Want to enhance your image analysis skills with napari?
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data.
🕒 Applications close on 15 September.
Learn more and apply 👇
www.crick.ac.uk/whats-on/cbi...
Last chance saloon 🤠 to register for the hands-on 2-day napari training. Application deadline has been extended.
www.crick.ac.uk/whats-on/cbi...
www.crick.ac.uk/whats-on/cbi...
September 12, 2025 at 9:53 AM
Last chance saloon 🤠 to register for the hands-on 2-day napari training. Application deadline has been extended.
www.crick.ac.uk/whats-on/cbi...
www.crick.ac.uk/whats-on/cbi...
Reposted by Marie Held
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
www.nature.com
September 10, 2025 at 9:37 AM
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Marie Held
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 11, 2025 at 2:25 PM
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Great news. Inclusive CBIAS all the way.
The abstract submission deadline for #CBIAS2025 has just closed and, for the first time, we have a near perfect gender-balance in our abstract submissions.
In fact, we have slightly more submissions from women than men.
In fact, we have slightly more submissions from women than men.
a man with his arms crossed is smiling and saying noice !
ALT: a man with his arms crossed is smiling and saying noice !
media.tenor.com
September 1, 2025 at 10:56 AM
Great news. Inclusive CBIAS all the way.
Reposted by Marie Held
Next guest speaker at #CBIAS2025 is Christa Walther, community manager for @globias.bsky.social. GloBIAS is a worldwide association that brings together all those interested in #bioimageanalysis, offering opportunities for knowledge exchange, events, training, and resources.
🔗👇
www.globias.org
🔗👇
www.globias.org
Home
News
Next BIA seminar series: "Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit" by Anna Klemm on 27th of August, 2pm CEST
GloBIAS held its inaugu...
www.globias.org
August 25, 2025 at 3:21 PM
Next guest speaker at #CBIAS2025 is Christa Walther, community manager for @globias.bsky.social. GloBIAS is a worldwide association that brings together all those interested in #bioimageanalysis, offering opportunities for knowledge exchange, events, training, and resources.
🔗👇
www.globias.org
🔗👇
www.globias.org
Reposted by Marie Held
We continue the #CBIAS2025 speaker intros with @jytinevez.bsky.social, research engineer and core facility manager at the Institut Pasteur. Jean-Yves is one of the minds behind TrackMate and is part of F-BIAS, a federation of bioimage analysts across France
🔗👇
research.pasteur.fr/fr/member/je...
🔗👇
research.pasteur.fr/fr/member/je...
August 26, 2025 at 10:26 AM
We continue the #CBIAS2025 speaker intros with @jytinevez.bsky.social, research engineer and core facility manager at the Institut Pasteur. Jean-Yves is one of the minds behind TrackMate and is part of F-BIAS, a federation of bioimage analysts across France
🔗👇
research.pasteur.fr/fr/member/je...
🔗👇
research.pasteur.fr/fr/member/je...
Reposted by Marie Held
Last but not least for our #CBIAS2025 guest speaker line-up is Ilaria Testa, fellow at @scilifelab.se. Ilaria and team develop and apply novel super resolution microscopy approaches to understand fundamental biological processes relevant for health and disease
🔗👇
www.scilifelab.se/researchers/...
🔗👇
www.scilifelab.se/researchers/...
August 27, 2025 at 8:39 AM
Last but not least for our #CBIAS2025 guest speaker line-up is Ilaria Testa, fellow at @scilifelab.se. Ilaria and team develop and apply novel super resolution microscopy approaches to understand fundamental biological processes relevant for health and disease
🔗👇
www.scilifelab.se/researchers/...
🔗👇
www.scilifelab.se/researchers/...
Reposted by Marie Held
Applications close at the end of the week!
Ready to automate your #microscopy #imageanalysis tasks? Applications are now open for our next "Introduction to Image Analysis" training course, in London at the @crick.ac.uk on October 27th-28th, 2025! 🔬💻
More info ⬇️
www.crick.ac.uk/whats-on/int...
More info ⬇️
www.crick.ac.uk/whats-on/int...
Introduction to image analysis
www.crick.ac.uk
August 27, 2025 at 2:49 PM
Applications close at the end of the week!