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Chiara Schiller @chiaraschiller.bsky.social · 17/04/2026

3/ Big thanks to @denisschapiro.bsky.social , @miguelib.bsky.social , @kbestak.bsky.social , and @tanevski.bsky.social - and to everyone else who helped along the way 🤝. This project took its time, and I couldn’t have brought it this far without you.

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Chiara Schiller @chiaraschiller.bsky.social · 17/04/2026

2/ 🫵 If you want to try out COZI, it is available as a package in Python (pypi.org/project/cozi...), R (github.com/SchapiroLabo...) and now also as a part of IMCRtools (github.com/BodenmillerG...)!

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Chiara Schiller @chiaraschiller.bsky.social · 17/04/2026

1/ A PhD milestone 👏 My work on comparing neighbor preference methods for spatial data analysis is out in Nature Communications. We compared 9+ neighbor preference methods and propose a new approach that combines the most relevant analysis features: COZI. Read more: www.nature.com/articles/s41...

nature.com

Comparison and optimization of cellular neighbor preference methods for quantitative tissue analysis - Nature Communications

Schiller and colleagues present a systematic comparison of methods that quantify whether pairs of cell types preferentially co-occur in tissues, highlighting their strengths and limitations. This stud...

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Reposted by Chiara Schiller

Jonas Schiller @jonas-bio.bsky.social · 10/02/2026

Never thought I'd co-first author a paper that appears on the screens on campus, that makes me very happy😃 www.cell.com/cell/fulltex... Check out the paper and get amazing summaries from the EMBL communications team and a thread by @chanyeong-kim.bsky.social

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Reposted by Chiara Schiller

Lukas Hatscher @loggas.bsky.social · 13/09/2025

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...

biorxiv.org

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...

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Reposted by Chiara Schiller

Schapiro Lab @schapirolab.bsky.social · 16/10/2025

If you missed @chiaraschiller.bsky.social’s talk at #EMBLSpatialBiology you can catch her at Poster 188 this evening

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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025

5/ Real data validation In myocardial infarction tissues, COZI uniquely detects: - Early neutrophil infiltration - Monocyte targeting of stressed cardiomyocytes - Spatial infiltration gradients

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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025

4/ One step in the right direction: COZI COZI (Conditional Z-score) combines advantageous method features by normalizing neighbor counts based on context and providing a z-score. It captures directional preferences and performs robustly across conditions, cell types, and neighborhood structures.

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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025

3/ The Comparison Using simulated tissues with known patterns, we show that existing methods often: - Miss directionality of NEP - Struggle with low-abundance cell types - Lack sensitivity to detect subtle NEP changes

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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025

2/ The problem Cell-cell spatial relationships are key to tissue function, but comparing NEP across datasets or conditions is tricky. Existing methods differ in how they define neighborhoods, count neighbors, and score NEP—leading to inconsistent results. We identified the common building blocks.

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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025

1/ 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 · 30/01/2025

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...

karriere.klinikum.uni-heidelberg.de

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

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Reposted by Chiara Schiller

scverse @scverse.bsky.social · 20/01/2025

Quentin Blampey, Lotte Pollaris, @clarencemah.me Laurens Lehner @chiaraschiller.bsky.social @miguelib.bsky.social We worked on easing the learning curve of the SpatialData framework by improving the documentation and APIs. We prepared new beginner-friendly notebooks and introduced a new more...

A presenter showing a slide on the importance of learning resources for beginners on spatial omics analysis.

screenshot of the new spatialdata-io command line interface for converting common spatial omics technologies to the SpatialData Zarr format.

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