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Schapiro Lab @schapirolab.bsky.social · 1h

Day 2 at Spatial biology: the melting pot #EMBLSpatialBiology

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Schapiro Lab @schapirolab.bsky.social · 21h

And we’re off

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Schapiro Lab @schapirolab.bsky.social · 23h

We’re excited to be at @embl.org this week for Spatial Biology: the melting pot. We’re looking forward to hearing about some awesome science 🔬 #EMBLSpatialBiology

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Schapiro Lab @schapirolab.bsky.social · Sep 13

We’re excited to share our latest preprint with the Bone Microenvironment Group led by Therese Standal at NTNU. Congratulations @loggas.bsky.social and everyone involved!

Lukas Hatscher @loggas.bsky.social · Sep 13

I am excited to share my first work in @schapirolab.bsky.social on Multiple Myeloma (MM) in collaboration with the Standal Lab from NTNU Norway. We use Imaging Mass Cytometry (IMC) on bone marrow biopsies from MM and precursor patients (details below): www.biorxiv.org/content/10.1...

Highly multiplexed imaging recovers immune and metabolic niches in multiple myeloma associated with disease progression and bone involvement

Multiple myeloma (MM) is a cancer arising from genetically aberrant plasma cells (PCs) that remain dependent on the bone marrow (BM) microenvironment for disease establishment and progression. Here, w...

www.biorxiv.org

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Reposted by Schapiro Lab

EMBL Events @events.embl.org · Aug 25

Register by 2 Sep and join us in Heidelberg for #EMBLSpatialBiology 👉 https://s.embl.org/spb25-01-bs

Co-organised with #ESSB, this conference will bring together top scientists and young investigators for 4 days of cutting-edge science and networking ✨

📅 14–17 Oct | 📍EMBL Heidelberg and Virtual

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Schapiro Lab @schapirolab.bsky.social · Aug 19

We were thrilled to host visiting scholar @berombau.bsky.social earlier this year. He shares his experience in our lab and at @uniheidelberg.bsky.social here: www.uni-heidelberg.de/de/alumni/ne.... Check it out!

Internationaler Austausch als hervorragendes Beispiel für gemeinschaftliches Lernen - Universität Heidelberg

Benjamin Rombaut, Bioinformatik – Doktorand in der Forschungsgruppe „Data Mining and Modelling for Biomedicine“ am VIB-UGent Zentrum für Entzündungsforschung an

www.uni-heidelberg.de

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Schapiro Lab @schapirolab.bsky.social · Jul 17

New lab pic dropped 📸 #schapirolab

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Schapiro Lab @schapirolab.bsky.social · Jul 4

Spotted: @loggas.bsky.social and @arojhada.bsky.social teaching phenotyping to our Advanced Systems Biology students

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Schapiro Lab @schapirolab.bsky.social · Jul 1

We're excited to be at the Kick Off Heidelberg Spatial-Omics Lunch Seminar Series with our very own @chiaraschiller.bsky.social presenting some of her PhD work!

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Schapiro Lab @schapirolab.bsky.social · Jul 1

Big congratulations to @sabrinalewis.bsky.social on being awarded 2nd place for her talk at the Heidelberg Postdoc Symposium 🥳🎉

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Schapiro Lab @schapirolab.bsky.social · Jun 30

Great to see @miguelib.bsky.social attending the Medizin Informatik Initiative (MII) summer school 2025 at Kassel 👨‍💻💅

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Reposted by Schapiro Lab

Chiara Schiller @chiaraschiller.bsky.social · Apr 15

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Ever wondered how to best quantify cell-cell neighbor preferences in tissues?
We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨

Read more: doi.org/10.1101/2025...

Schematic overview of NEP analysis steps (Neighborhood definition, Quantification and NEP score) and the systematic method performance comparison using simulated data for cohort distinction.

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Schapiro Lab @schapirolab.bsky.social · Mar 13

We're hiring! 🎉
We are recruiting a project / grant manager at the Institute for Computational Biomedicine in Heidelberg. Apply now and come join our team!

Project- / Grants Manager (m/f/d)

karriere.klinikum.uni-heidelberg.de

Schapiro Lab @schapirolab.bsky.social · Mar 7

www.nature.com/articles/s42...

micronuclAI enables automated quantification of micronuclei for assessment of chromosomal instability - Communications Biology

micronuclAI, a deep-learning based pipeline, enables automated and reliable quantification of micronuclei from nuclei-stained human and murine cancer cell lines for quantification of chromosomal insta...

www.nature.com

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Schapiro Lab @schapirolab.bsky.social · Mar 7

Many thanks to all the collaborators from Benjamin Izar's lab at @columbiauniversity.bsky.social, @denisschapiro.bsky.social, and the Schapiro lab from @uniheidelberg.bsky.social.

@arojhada.bsky.social
@kbestak.bsky.social
@flowuenne.bsky.social

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Schapiro Lab @schapirolab.bsky.social · Mar 7

micronuclAI is easily accessible; you can try it out for small datasets at micronuclai.streamlit.app or use the Python implementation here: github.com/SchapiroLabo...

streamlit.CIN prediction

logo.png

micronuclai.streamlit.app

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Schapiro Lab @schapirolab.bsky.social · Mar 7

micronuclAI accurately quantifies MN in multiple cell lines, microscopy conditions, model organisms, and nuclear staining, such as DAPI and Hoechst.

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Schapiro Lab @schapirolab.bsky.social · Mar 7

micronuclAI image processing relies on a nuclear segmentation mask to extract bounding boxes around each cell. These bounding boxes are then pre-processed to ensure an accurate MN inference.

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Schapiro Lab @schapirolab.bsky.social · Mar 7

Here, we present micronuclAI, a pipeline for the automated and reliable quantification of MN of varying size and morphology in cells stained only for DNA. micronuclAI can achieve close to human-level performance on various human and murine cancer cell line datasets.

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Schapiro Lab @schapirolab.bsky.social · Mar 7

Chromosomal instability (CIN) is a hallmark of #cancer that drives metastasis, immune evasion, and treatment resistance. CIN may result from chromosome mis-segregation errors, and excessive chromatin is frequently packaged in micronuclei (MN), which can be enumerated to quantify CIN.

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Schapiro Lab @schapirolab.bsky.social · Mar 7

🧵 We are excited to share our new paper, showcasing micronuclAI, which leverages #AI and #ComputerVision to detect #chromosomal_instability #CIN #micronuclei

Congratulations to @miguelib.bsky.social and Lindsay Caprio for leading this project.

Communications Biology @commsbio.nature.com · Mar 6

@arojhada.bsky.social, @miguelib.bsky.social, @denisschapiro.bsky.social, @schapirolab.bsky.social

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Reposted by Schapiro Lab

Communications Biology @commsbio.nature.com · Mar 6

@arojhada.bsky.social, @miguelib.bsky.social, @denisschapiro.bsky.social, @schapirolab.bsky.social

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Reposted by Schapiro Lab

Schapiro Lab @schapirolab.bsky.social · Jan 30

We are searching for a highly motivated and talented computational postdoc with an interest in translational spatial omics to join our team in Heidelberg. Apply now!

karriere.klinikum.uni-heidelberg.de/index.php?ac...

Postdoc – Computational Tissue Analysis (m/f/d)

karriere.klinikum.uni-heidelberg.de

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Schapiro Lab @schapirolab.bsky.social · Jan 30

We are searching for a highly motivated and talented computational postdoc with an interest in translational spatial omics to join our team in Heidelberg. Apply now!

karriere.klinikum.uni-heidelberg.de/index.php?ac...

Postdoc – Computational Tissue Analysis (m/f/d)

karriere.klinikum.uni-heidelberg.de

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Schapiro Lab @schapirolab.bsky.social · Dec 19

Laser tag lab edition #happyholidays 🎄🎁🎅🏼

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