Alex Kalinin
@alxndrkalinin.bsky.social
AI x Bioimaging @biohub.org | prev Broad Institute, CUHK-SZ & UMich
Pinned
Alex Kalinin
@alxndrkalinin.bsky.social
· Jul 10
🔬🤖 Introducing Spotlight: virtual staining (VS) improved by focusing on cells
VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground.
1/5
VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground.
1/5
Reposted by Alex Kalinin
1/ 🧬🔬
How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇
www.kaggle.com/competitions...
@biohub.org
How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇
www.kaggle.com/competitions...
@biohub.org
June 29, 2026 at 8:00 PM
1/ 🧬🔬
How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇
www.kaggle.com/competitions...
@biohub.org
How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇
www.kaggle.com/competitions...
@biohub.org
Reposted by Alex Kalinin
BIC @eccv.bsky.social 2026 is OPEN! Show us your new CV, AI & Bio work🦠🔬
🚪: openreview.net/group?id=the...
Thanks organisers for making it possible @alex-krull.bsky.social Peter Bajcsy @janfunkey.bsky.social @florianjug.bsky.social Qingjie Meng @virginieuhlmann.bsky.social @maweigert.bsky.social ✨
🚪: openreview.net/group?id=the...
Thanks organisers for making it possible @alex-krull.bsky.social Peter Bajcsy @janfunkey.bsky.social @florianjug.bsky.social Qingjie Meng @virginieuhlmann.bsky.social @maweigert.bsky.social ✨
June 15, 2026 at 5:48 PM
BIC @eccv.bsky.social 2026 is OPEN! Show us your new CV, AI & Bio work🦠🔬
🚪: openreview.net/group?id=the...
Thanks organisers for making it possible @alex-krull.bsky.social Peter Bajcsy @janfunkey.bsky.social @florianjug.bsky.social Qingjie Meng @virginieuhlmann.bsky.social @maweigert.bsky.social ✨
🚪: openreview.net/group?id=the...
Thanks organisers for making it possible @alex-krull.bsky.social Peter Bajcsy @janfunkey.bsky.social @florianjug.bsky.social Qingjie Meng @virginieuhlmann.bsky.social @maweigert.bsky.social ✨
Reposted by Alex Kalinin
The Cimini lab is hiring for both postdocs and interns! The postdoc role will cover bioimage analysis projects and educational material creation; the intern will be working on our Bilayers project for helping distribute and access deep learning tools for bioimage analysis. Click below to learn more!
Postdoctoral Associate and Data Science Intern roles - Broad Institute, Cambridge MA USA
The Broad Institute Imaging Platform (the team behind CellProfiler, Piximi, and Bilayers) is currently hiring for postdoctoral and intern roles! Postdoc role: we are looking for 1-2 candidates who ha...
forum.image.sc
May 7, 2026 at 9:50 PM
The Cimini lab is hiring for both postdocs and interns! The postdoc role will cover bioimage analysis projects and educational material creation; the intern will be working on our Bilayers project for helping distribute and access deep learning tools for bioimage analysis. Click below to learn more!
Reposted by Alex Kalinin
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
Reposted by Alex Kalinin
🚨 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/...
Reposted by Alex Kalinin
The new ShapeEmbed deep learning method helps quantify shapes in bioimages 🔬
It learns to encode 2D object outlines into descriptors that are invariant to several geometric transformations.
Great for robust cell shape analysis, classification & exploring phenotypes.
neurips.cc/virtual/2025...
It learns to encode 2D object outlines into descriptors that are invariant to several geometric transformations.
Great for robust cell shape analysis, classification & exploring phenotypes.
neurips.cc/virtual/2025...
December 18, 2025 at 8:56 AM
The new ShapeEmbed deep learning method helps quantify shapes in bioimages 🔬
It learns to encode 2D object outlines into descriptors that are invariant to several geometric transformations.
Great for robust cell shape analysis, classification & exploring phenotypes.
neurips.cc/virtual/2025...
It learns to encode 2D object outlines into descriptors that are invariant to several geometric transformations.
Great for robust cell shape analysis, classification & exploring phenotypes.
neurips.cc/virtual/2025...
Excited to be in sunny San Diego for #NeurIPS2025 🌴
Biohub @czbiohub.bsky.social has a booth! Stop by to see cool demos from our computational imaging group and chat about AI for bioimaging.
Biohub @czbiohub.bsky.social has a booth! Stop by to see cool demos from our computational imaging group and chat about AI for bioimaging.
December 4, 2025 at 7:56 PM
Excited to be in sunny San Diego for #NeurIPS2025 🌴
Biohub @czbiohub.bsky.social has a booth! Stop by to see cool demos from our computational imaging group and chat about AI for bioimaging.
Biohub @czbiohub.bsky.social has a booth! Stop by to see cool demos from our computational imaging group and chat about AI for bioimaging.
Reposted by Alex Kalinin
A game changer in our hands... www.nature.com/articles/s41...
Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
www.nature.com
November 11, 2025 at 6:48 PM
A game changer in our hands... www.nature.com/articles/s41...
Reposted by Alex Kalinin
Janelia is hosting a course on DL for bioimage analysis 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
November 6, 2025 at 5:02 PM
Janelia is hosting a course on DL for bioimage analysis www.janelia.org/you-janelia/...
Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling!
cytodata25.eu-openscreen.eu
cytodata25.eu-openscreen.eu
October 31, 2025 at 5:25 PM
Today is the last chance to register for #CytoData2025. Don’t miss a fantastic program covering the full spectrum of image-based profiling!
cytodata25.eu-openscreen.eu
cytodata25.eu-openscreen.eu
💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵
1/6 #iccv2025
1/6 #iccv2025
October 23, 2025 at 6:01 PM
💡Just presented our new paper at the @iccv.bsky.social BioImage Computing workshop: cubic: CUDA-accelerated 3D Bioimage Computing. We introduce a simple way to add GPU acceleration to scikit-image–based bioimage processing pipelines by swapping import statements. 🧵
1/6 #iccv2025
1/6 #iccv2025
Reposted by Alex Kalinin
Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues.
The paper: arxiv.org/abs/2503.19545 1/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
October 9, 2025 at 12:56 PM
Segment large images without tiling artifacts: sharing our work that should have been presented at ICCV in 2 weeks - the brilliant first author Elena can’t go because of visa issues.
The paper: arxiv.org/abs/2503.19545 1/🧵
The paper: arxiv.org/abs/2503.19545 1/🧵
Reposted by Alex Kalinin
Morph Map is now published in Nature Methods. Excited to see what the community discovers with this resource mapping ~15,000 human genes!
rdcu.be/ezGre
rdcu.be/ezGre
August 7, 2025 at 1:36 PM
Morph Map is now published in Nature Methods. Excited to see what the community discovers with this resource mapping ~15,000 human genes!
rdcu.be/ezGre
rdcu.be/ezGre
Reposted by Alex Kalinin
September 10, 2025 at 3:26 PM
🔬🤖 Introducing Spotlight: virtual staining (VS) improved by focusing on cells
VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground.
1/5
VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground.
1/5
July 10, 2025 at 6:52 PM
🔬🤖 Introducing Spotlight: virtual staining (VS) improved by focusing on cells
VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground.
1/5
VS models often learn to predict both cells and noisy background, because training treats all pixels equally. We address this by explicitly training models to prioritize foreground.
1/5
🔬API-first feature extraction for image-based profiling workflows
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
July 8, 2025 at 7:22 PM
🔬API-first feature extraction for image-based profiling workflows
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
Reposted by Alex Kalinin
If you’re interested in single cell data analysis, come give Image based profiles a try! Huge dataset being made available for exploration at this hackathon (+ symposium):
Berlin, November cytodata25.eu-openscreen.eu
Berlin, November cytodata25.eu-openscreen.eu
July 2, 2025 at 12:56 PM
If you’re interested in single cell data analysis, come give Image based profiles a try! Huge dataset being made available for exploration at this hackathon (+ symposium):
Berlin, November cytodata25.eu-openscreen.eu
Berlin, November cytodata25.eu-openscreen.eu
Reposted by Alex Kalinin
The 2nd AI4Life Challenge is live!
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
June 27, 2025 at 1:33 PM
The 2nd AI4Life Challenge is live!
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
Calling the AI & bioimaging community to tackle a key microscopy challenge: removing noise while preserving detail.
📦 Paired noisy/clean datasets
📈 Ground-truth evaluation
🧠 DL focus
Build, test, compete 👉 ai4life.eurobioimaging.eu/challenge-2/
There is still time to submit an abstract to CytoData 2025!
🌟 𝗥𝗲𝗺𝗶𝗻𝗱𝗲𝗿 🌟
The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching!
👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25!
cytodata25.eu-openscreen.eu/registration/
#BerlinConference #Imageanalysis #Microscopy
The deadline for abstract submissions for oral presentations at Cytodata 2025 in Berlin is approaching!
👉 𝗦𝘂𝗯𝗺𝗶𝘁 𝘆𝗼𝘂𝗿 𝗮𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝗯𝘆 𝗝𝘂𝗻𝗲 25!
cytodata25.eu-openscreen.eu/registration/
#BerlinConference #Imageanalysis #Microscopy
June 23, 2025 at 4:36 PM
There is still time to submit an abstract to CytoData 2025!
Reposted by Alex Kalinin
The submission for 2025's BioImage Computing @iccv.bsky.social is now open. If things go like the last years, I am looking forward to all you brilliant submissions.
www.bioimagecomputing.com
www.bioimagecomputing.com
BioImage Computing
a truly interdisciplinary workshop
www.bioimagecomputing.com
June 10, 2025 at 9:40 PM
The submission for 2025's BioImage Computing @iccv.bsky.social is now open. If things go like the last years, I am looking forward to all you brilliant submissions.
www.bioimagecomputing.com
www.bioimagecomputing.com
🚨 New paper alert! We developed a versatile information retrieval framework that uses mean average precision (mAP) to robustly quantify sample activity and similarity in large-scale profiling data. Now out @natcomms.nature.com: doi.org/10.1038/s414...
More in the 🧵 below:
1/7
More in the 🧵 below:
1/7
A versatile information retrieval framework for evaluating profile strength and similarity - Nature Communications
Profiling assays measure thousands of features to uncover biological insights but lack reliable methods for quality evaluation. Here, the authors develop a versatile information retrieval framework to...
doi.org
June 10, 2025 at 7:54 PM
🚨 New paper alert! We developed a versatile information retrieval framework that uses mean average precision (mAP) to robustly quantify sample activity and similarity in large-scale profiling data. Now out @natcomms.nature.com: doi.org/10.1038/s414...
More in the 🧵 below:
1/7
More in the 🧵 below:
1/7
Reposted by Alex Kalinin
The #CVPR2025 main conference open access proceedings is up:
openaccess.thecvf.com/CVPR2025
Workshop papers will be posted shortly. Stay tuned...
openaccess.thecvf.com/CVPR2025
Workshop papers will be posted shortly. Stay tuned...
June 3, 2025 at 2:46 PM
The #CVPR2025 main conference open access proceedings is up:
openaccess.thecvf.com/CVPR2025
Workshop papers will be posted shortly. Stay tuned...
openaccess.thecvf.com/CVPR2025
Workshop papers will be posted shortly. Stay tuned...
Reposted by Alex Kalinin
Our work “AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI” is finally out in
@biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️
@biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️
May 14, 2025 at 10:26 AM
Our work “AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI” is finally out in
@biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️
@biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️
Reposted by Alex Kalinin
Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...
Opinion | The Science I Would Be Doing if I Weren’t in ICE Detention
www.nytimes.com
May 13, 2025 at 12:33 PM
Lovely article from our colleague Kseniia Petrova, who has been wrongfully imprisoned for months: www.nytimes.com/2025/05/13/o...
CytoData is going to Berlin this November! Submit an abstract for oral presentation by June 25, 2025.
Join us in Berlin for CytoData 2025!
👉 Info & registration: cytodata25.eu-openscreen.eu
🔬 Hackathon: Nov 17–19
📢 Symposium: Nov 20–21
Explore advancements in image-based profiling & high-content screening and Tackle real-world challenges using EU-OPENSCREEN data.
👉 Info & registration: cytodata25.eu-openscreen.eu
🔬 Hackathon: Nov 17–19
📢 Symposium: Nov 20–21
Explore advancements in image-based profiling & high-content screening and Tackle real-world challenges using EU-OPENSCREEN data.
May 6, 2025 at 3:11 PM
CytoData is going to Berlin this November! Submit an abstract for oral presentation by June 25, 2025.