Stefania Marcotti
@lankylaste.bsky.social
Data and image analysis for all things bio | Computational tinkerer | Researcher | Bioimage analyst
Pinned
Stefania Marcotti
@lankylaste.bsky.social
· Dec 18
Enhancing Research Through Image Analysis Workshops: Experiences and Best Practices
This graphical abstract illustrates the structure of interactive image analysis workshops, where participants engage in hands-on learning with open-source tools under expert guidance to improve resea...
doi.org
New paper out! We share our experiences from conducting #bioimageanalysis workshops, using open-source software and building a community around training: doi.org/10.1002/jemt...
Thanks to the dream team of rockstars, @david-j-barry.bsky.social, @martinjones.bsky.social and Tom Slater
Thanks to the dream team of rockstars, @david-j-barry.bsky.social, @martinjones.bsky.social and Tom Slater
Reposted by Stefania Marcotti
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 12, 2025 at 2:04 PM
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...
Reposted by Stefania Marcotti
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
November 13, 2025 at 2:32 PM
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
Reposted by Stefania Marcotti
Another week, another training course!
We focused on #Python today, with our internal introductory workshop to image analysis.
Well-done to all attendees! 💻🔬and thanks to the “Bioinformatics and Biostatistics” and “Software Engineering and AI” teams for helping us deliver the course 🙏
We focused on #Python today, with our internal introductory workshop to image analysis.
Well-done to all attendees! 💻🔬and thanks to the “Bioinformatics and Biostatistics” and “Software Engineering and AI” teams for helping us deliver the course 🙏
November 7, 2025 at 6:06 PM
Another week, another training course!
We focused on #Python today, with our internal introductory workshop to image analysis.
Well-done to all attendees! 💻🔬and thanks to the “Bioinformatics and Biostatistics” and “Software Engineering and AI” teams for helping us deliver the course 🙏
We focused on #Python today, with our internal introductory workshop to image analysis.
Well-done to all attendees! 💻🔬and thanks to the “Bioinformatics and Biostatistics” and “Software Engineering and AI” teams for helping us deliver the course 🙏
Very proud of the students for progressing very quickly over the course of the workshop! 🔬💻
And grateful to be working with an amazing team 🙏✨ @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, Sara and Cameron
And grateful to be working with an amazing team 🙏✨ @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, Sara and Cameron
And it’s a wrap! Thanks to all attendees for your hard work in analysing bioimages with open source software to make science more reproducible. Best of luck for your image analysis adventures!
October 29, 2025 at 5:19 PM
Very proud of the students for progressing very quickly over the course of the workshop! 🔬💻
And grateful to be working with an amazing team 🙏✨ @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, Sara and Cameron
And grateful to be working with an amazing team 🙏✨ @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, Sara and Cameron
Reposted by Stefania Marcotti
All set up and ready to go for our 2-day Introduction to Image Analysis workshop for external attendees at @crick.ac.uk!
With Sara Salgueiro Torres, @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, @lankylaste.bsky.social and Cameron Shand
With Sara Salgueiro Torres, @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, @lankylaste.bsky.social and Cameron Shand
October 27, 2025 at 4:33 PM
All set up and ready to go for our 2-day Introduction to Image Analysis workshop for external attendees at @crick.ac.uk!
With Sara Salgueiro Torres, @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, @lankylaste.bsky.social and Cameron Shand
With Sara Salgueiro Torres, @david-j-barry.bsky.social, @martinjones.bsky.social, @k-meech.bsky.social, @lankylaste.bsky.social and Cameron Shand
Reposted by Stefania Marcotti
🇬🇧 Are you based in the UK?
💻 Do you spend a significant amount of time working on #BioImageAnalysis?
🧑🤝🧑 Want to spend time supporting external users?
The UK BioImage Analysis Network (UK-BIAS) might be for you.
Apply below before November 5th.
forms.gle/XhP15nxg2ZgW...
💻 Do you spend a significant amount of time working on #BioImageAnalysis?
🧑🤝🧑 Want to spend time supporting external users?
The UK BioImage Analysis Network (UK-BIAS) might be for you.
Apply below before November 5th.
forms.gle/XhP15nxg2ZgW...
Expression of Interest: UK Bioimage Analysis Network (UK-BIAS)
The UK node of Euro-BioImaging, a major European initiative providing open access to biological and biomedical imaging technologies, currently offers assistance with Biological Image Data Analysis. Ho...
forms.gle
October 21, 2025 at 8:35 AM
🇬🇧 Are you based in the UK?
💻 Do you spend a significant amount of time working on #BioImageAnalysis?
🧑🤝🧑 Want to spend time supporting external users?
The UK BioImage Analysis Network (UK-BIAS) might be for you.
Apply below before November 5th.
forms.gle/XhP15nxg2ZgW...
💻 Do you spend a significant amount of time working on #BioImageAnalysis?
🧑🤝🧑 Want to spend time supporting external users?
The UK BioImage Analysis Network (UK-BIAS) might be for you.
Apply below before November 5th.
forms.gle/XhP15nxg2ZgW...
Reposted by Stefania Marcotti
A month to go! Will you be at #CBIAS2025?
The program is almost ready, and we look forward to welcoming you in London to discuss all things #BioImageAnalysis, from tool development, to biomedical applications and community building.
Register now! 🔗⬇️
www.crick.ac.uk/whats-on/cri...
The program is almost ready, and we look forward to welcoming you in London to discuss all things #BioImageAnalysis, from tool development, to biomedical applications and community building.
Register now! 🔗⬇️
www.crick.ac.uk/whats-on/cri...
Crick BioImage Analysis Symposium 2025
www.crick.ac.uk
October 24, 2025 at 8:48 AM
A month to go! Will you be at #CBIAS2025?
The program is almost ready, and we look forward to welcoming you in London to discuss all things #BioImageAnalysis, from tool development, to biomedical applications and community building.
Register now! 🔗⬇️
www.crick.ac.uk/whats-on/cri...
The program is almost ready, and we look forward to welcoming you in London to discuss all things #BioImageAnalysis, from tool development, to biomedical applications and community building.
Register now! 🔗⬇️
www.crick.ac.uk/whats-on/cri...
...and it’s on the official Fiji/ImageJ documentation! 🥹
Want to automate workflows in #FIJI?
Don't know where to start?
We (@lankylaste.bsky.social, Alicja Skórkowska and Sara Salgueiro Torres) have added a step-by-step tutorial to the wiki to get you started.
Thanks @ctrue.bsky.social for adding!
imagej.github.io/tutorials/ba...
Don't know where to start?
We (@lankylaste.bsky.social, Alicja Skórkowska and Sara Salgueiro Torres) have added a step-by-step tutorial to the wiki to get you started.
Thanks @ctrue.bsky.social for adding!
imagej.github.io/tutorials/ba...
Batch Processing with the ImageJ Macro Language
The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants...
imagej.github.io
October 23, 2025 at 5:33 PM
...and it’s on the official Fiji/ImageJ documentation! 🥹
Reposted by Stefania Marcotti
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
#HappyFluorescenceFriday!
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!
Learn more & sign up: buff.ly/esGIotD
September 23, 2025 at 3:48 PM
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
Reposted by Stefania Marcotti
The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
September 23, 2025 at 12:06 PM
The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.
Space is limited - register now!
www.crick.ac.uk/whats-on/cri...
Reposted by Stefania Marcotti
The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there!
🔗⬇️
www.crick.ac.uk/whats-on/cri...
🔗⬇️
www.crick.ac.uk/whats-on/cri...
September 23, 2025 at 1:13 PM
The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there!
🔗⬇️
www.crick.ac.uk/whats-on/cri...
🔗⬇️
www.crick.ac.uk/whats-on/cri...
Reposted by Stefania Marcotti
The Danish BioImaging Infrastructure is hiring!
We are looking for a highly motivated and independent Image Analysis Application Specialist with a strong bioimage analysis background and drive to collaborate in multidisciplinary environments
More information
candidate.hr-manager.net/ApplicationI...
We are looking for a highly motivated and independent Image Analysis Application Specialist with a strong bioimage analysis background and drive to collaborate in multidisciplinary environments
More information
candidate.hr-manager.net/ApplicationI...
August 22, 2025 at 1:04 PM
The Danish BioImaging Infrastructure is hiring!
We are looking for a highly motivated and independent Image Analysis Application Specialist with a strong bioimage analysis background and drive to collaborate in multidisciplinary environments
More information
candidate.hr-manager.net/ApplicationI...
We are looking for a highly motivated and independent Image Analysis Application Specialist with a strong bioimage analysis background and drive to collaborate in multidisciplinary environments
More information
candidate.hr-manager.net/ApplicationI...
Reposted by Stefania Marcotti
Today we say farewell to Alicja Skórkowska, who returns to @jagiellonskiuni.bsky.social after a very productive 6 month stay with us. Alicja will be missed!
However, we also welcome @lankylaste.bsky.social, who is now officially a @crick.ac.uk person!
However, we also welcome @lankylaste.bsky.social, who is now officially a @crick.ac.uk person!
August 29, 2025 at 7:36 AM
Today we say farewell to Alicja Skórkowska, who returns to @jagiellonskiuni.bsky.social after a very productive 6 month stay with us. Alicja will be missed!
However, we also welcome @lankylaste.bsky.social, who is now officially a @crick.ac.uk person!
However, we also welcome @lankylaste.bsky.social, who is now officially a @crick.ac.uk person!
Reposted by Stefania Marcotti
Last few days to submit an abstract for #CBIAS2025 (deadline 31/08)!
We invite submissions on all topics related to #bioimageanalysis, from new software tools to discoveries made using existing methods. Early career researchers are especially encouraged to submit!
www.crick.ac.uk/whats-on/cri...
We invite submissions on all topics related to #bioimageanalysis, from new software tools to discoveries made using existing methods. Early career researchers are especially encouraged to submit!
www.crick.ac.uk/whats-on/cri...
August 28, 2025 at 9:01 AM
Last few days to submit an abstract for #CBIAS2025 (deadline 31/08)!
We invite submissions on all topics related to #bioimageanalysis, from new software tools to discoveries made using existing methods. Early career researchers are especially encouraged to submit!
www.crick.ac.uk/whats-on/cri...
We invite submissions on all topics related to #bioimageanalysis, from new software tools to discoveries made using existing methods. Early career researchers are especially encouraged to submit!
www.crick.ac.uk/whats-on/cri...
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!
Reposted by Stefania Marcotti
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 Stefania Marcotti
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 Stefania Marcotti
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 Stefania Marcotti
At #CBIAS2025 we will also hear from Ewa Paluch from @cam.ac.uk. Ewa and their team take an interdisciplinary approach combining biology, imaging, mechanical testing and physical modelling to investigate the basic principles underlying animal cell morphogenesis
🔗👇
www.pdn.cam.ac.uk/directory/ew...
🔗👇
www.pdn.cam.ac.uk/directory/ew...
Professor Ewa K Paluch | Department of Physiology, Development and Neuroscience
www.pdn.cam.ac.uk
August 24, 2025 at 9:19 AM
At #CBIAS2025 we will also hear from Ewa Paluch from @cam.ac.uk. Ewa and their team take an interdisciplinary approach combining biology, imaging, mechanical testing and physical modelling to investigate the basic principles underlying animal cell morphogenesis
🔗👇
www.pdn.cam.ac.uk/directory/ew...
🔗👇
www.pdn.cam.ac.uk/directory/ew...
Reposted by Stefania Marcotti
Once is an exception, twice is a trend, thrice is a tradition!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
We're happy to announce the 2025 International OME-NGFF workshop 🎉
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025
📍 Location: Zurich, Switzerland
Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...
#bioimaging #openscience #OMENGFF #OMEZarr
(1/x 🧵)
August 25, 2025 at 1:50 PM
Once is an exception, twice is a trend, thrice is a tradition!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!
Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
Reposted by Stefania Marcotti
We continue the #CBIAS2025 speaker line-up with Dominik Kutra, senior research software engineer in the @ilastik-team.bsky.social. Dominik is one of the core developers of Ilastik, a user-friendly software that leverages machine learning algorithms to easily analyse bioimages
🔗👇
www.ilastik.org
🔗👇
www.ilastik.org
ilastik - ilastik
www.ilastik.org
August 23, 2025 at 9:38 AM
We continue the #CBIAS2025 speaker line-up with Dominik Kutra, senior research software engineer in the @ilastik-team.bsky.social. Dominik is one of the core developers of Ilastik, a user-friendly software that leverages machine learning algorithms to easily analyse bioimages
🔗👇
www.ilastik.org
🔗👇
www.ilastik.org
Reposted by Stefania Marcotti
Next up at #CBIAS2025 is @helenajambor.bsky.social from the University of Applied Sciences of the Grisons. Helena researches data visualisation in the life sciences, combining their expertise with large datasets and their interest in data communication
🔗👇
helenajamborwrites.netlify.app/about
🔗👇
helenajamborwrites.netlify.app/about
HelenaJamborWrites - About
helenajamborwrites.netlify.app
August 22, 2025 at 6:57 PM
Next up at #CBIAS2025 is @helenajambor.bsky.social from the University of Applied Sciences of the Grisons. Helena researches data visualisation in the life sciences, combining their expertise with large datasets and their interest in data communication
🔗👇
helenajamborwrites.netlify.app/about
🔗👇
helenajamborwrites.netlify.app/about
Reposted by Stefania Marcotti
Our first #CBIAS2025 invited speaker is Andrew French from @uniofnottingham.bsky.social, who specialises in using AI to understand images. Their research interests include image analysis of plants and complex structures and image capture automation
🔗👇
www.nottingham.ac.uk/biosciences/...
🔗👇
www.nottingham.ac.uk/biosciences/...
People - The University of Nottingham
www.nottingham.ac.uk
August 21, 2025 at 10:17 AM
Our first #CBIAS2025 invited speaker is Andrew French from @uniofnottingham.bsky.social, who specialises in using AI to understand images. Their research interests include image analysis of plants and complex structures and image capture automation
🔗👇
www.nottingham.ac.uk/biosciences/...
🔗👇
www.nottingham.ac.uk/biosciences/...
Reposted by Stefania Marcotti
ONLY 11 MORE DAYS TO SUBMIT AN ABSTRACT FOR #CBIAS2025!!!
August 20, 2025 at 1:16 PM
ONLY 11 MORE DAYS TO SUBMIT AN ABSTRACT FOR #CBIAS2025!!!
Reposted by Stefania Marcotti
📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
CBIAS napari workshop 2025
crick.ac.uk
August 11, 2025 at 2:26 PM
📢 After #CBIAS2025, join our hands-on 2-day napari training by @crick.ac.uk @ucl.ac.uk @liverpooluni.bsky.social
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025
From conda to plugins to Jupyter, practicals on real data with expert guidance.
For Python/ImageJ coders. Apply by 1 Sept – limited to 30! crick.ac.uk/whats-on/cbias-napari-workshop-2025