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Nav @naveed-ishaque.bsky.social · Jul 4

Sainsc is a new tool for efficient whole organism spatial transcriptomics data analysis at the nanometre scale. It works with Stereo-seq, VisiumHD, Xenium and Nova-ST. Looking forward to see how it works with upcoming platforms (e.g. Illumina).
github.com/HiDiHlabs/sa...

GitHub - HiDiHlabs/sainsc: Segmentation-free Analysis of In Situ Capture data

Segmentation-free Analysis of In Situ Capture data - HiDiHlabs/sainsc

github.com

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Nav @naveed-ishaque.bsky.social · Jul 4

Spatial transcriptomics - helping authors wow reviewers with pretty pictures (... and interesting spatial biology).. and making it possible for bioinformaticians to submit journal cover art! Our Sainsc tool is featured as the back cover for Small Methods: onlinelibrary.wiley.com/doi/10.1002/...

Sainsc: A Computational Tool for Segmentation‐Free Analysis of In Situ Capture Data (Small Methods 5/2025)

Segmentation-Free Analyses Sainsc: a new tool for efficient whole organism spatial transcriptomics data analysis at the nanometre scale. Shown is a blended composite spatial map of total gene express...

onlinelibrary.wiley.com

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Nav @naveed-ishaque.bsky.social · Jul 3

And our tireless worker bees who dedicated every Wednesday evening for 18 months for this project: Jieran Sun, Kirti Biharie, Peiying Cai, Niklas Müller-Bötticher, Paul Kiessling, Meghan A. Turner, Søren H. Dam, Florian Heyl. 🙏

Nav @naveed-ishaque.bsky.social · Jul 3

I forgot the most important bit! This would not have been possible without the wonderful and amazing SpaceHack community. Special shout outs to Brain Long, Ahmed Mahfouz and @markrobinsonca.bsky.social for their work, ideas and resources...

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Nav @naveed-ishaque.bsky.social · Jul 2

We wrap up our analysis framework into SACCELERATOR, github.com/SpatialHacka..., and present two case studies on brain and colon cancer datasets to remind people that having domain expertise and performing interactive analysis is more important than picking the "best" tool.

GitHub - SpatialHackathon/SACCELERATOR

Contribute to SpatialHackathon/SACCELERATOR development by creating an account on GitHub.

github.com

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Nav @naveed-ishaque.bsky.social · Jul 2

General findings:
- benchmarking studies can be inconsistent
- methods do not scale to new datasets
- "ground truths" do not consider granularity of biological features
- looking at the differences between methods (entropy) is informative
- method performance doesn't match subjective importance

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Nav @naveed-ishaque.bsky.social · Jul 2

Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths".
More in our preprint: www.biorxiv.org/content/10.1...

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...

www.biorxiv.org

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Nav @naveed-ishaque.bsky.social · Mar 17

Accurate cell segmentation remains a major issue for spatial transcriptomics.
Elyas Heidari and colleagues from the Gerstung, Pe'er and Stegle Labs released Segger, a new algorithm that uses GNN to model both transcripts and cells. More details in their preprint: www.biorxiv.org/content/10.1...

Segger: Fast and accurate cell segmentation of imaging-based spatial transcriptomics data

The accurate assignment of transcripts to their cells of origin remains the Achilles heel of imaging-based spatial transcriptomics, despite being critical for nearly all downstream analyses. Current c...

www.biorxiv.org

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Reposted by Nav

Sergio Marco Salas @sergiomarcosalas.bsky.social · Mar 14

🧬If you work with @10xgenomics.bsky.social Xenium, this might be of your interest.

Our new study on Xenium exploration best practice and comparing it with other commercial platforms is now out in @naturemethods.bsky.social

www.nature.com/articles/s41...

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows - Nature Methods

This study presents a comprehensive evaluation of Xenium In Situ datasets and provides recommendations on analysis workflows.

www.nature.com

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Nav @naveed-ishaque.bsky.social · Feb 8

We also released the ovrl.py tool to identify areas of cell overlaps in imaging-based spatial transcriptomic data (e.g. #Xenium, #MERSCOPE, #cosMX).
GitHub: github.com/HiDiHlabs/ov...

GitHub - HiDiHlabs/ovrl.py: A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data.

A python tool to investigate cell overlaps in imaging-based spatial transcriptomics data. - HiDiHlabs/ovrl.py

github.com

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Nav @naveed-ishaque.bsky.social · Feb 8

Have you been bothered that practically every #SpatialTranscriptomic analysis tool assumes data to be 2D? Well, you were right - overlapping cells are a really big problem. Check out our report on bioRxiv: 2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices. t.ly/CQX8K

2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices

Imaging-based spatially resolved transcriptomics can localise transcripts within cells in 3D. Cell segmentation precedes assignment of transcripts to cells and annotation of cell function. However, ce...

t.ly

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Nav @naveed-ishaque.bsky.social · Feb 8

We also sneak in a python implementation for the spatially aware MULTISPATI-PCA. We think this should pretty much replace "non-spatial" PCA for all spatial modalities in most cases.
GitHub: github.com/HiDiHlabs/mu...
RtD: multispaeti.readthedocs.io/1.0.0/genera...

GitHub - HiDiHlabs/multiSPAETI: Implementation of MULTISPATI-PCA in Python

Implementation of MULTISPATI-PCA in Python. Contribute to HiDiHlabs/multiSPAETI development by creating an account on GitHub.

github.com

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Nav @naveed-ishaque.bsky.social · Feb 8

SpatialLeiden integrates with the #scverse by leveraging #scanpy and #anndata but can also be used independently.
GitHub: github.com/HiDiHlabs/sp...
RtD: spatialleiden.readthedocs.io/stable/

GitHub - HiDiHlabs/SpatialLeiden: Implementation of multiplex Leiden for analysis of spatial omics data

Implementation of multiplex Leiden for analysis of spatial omics data - HiDiHlabs/SpatialLeiden

github.com

Nav @naveed-ishaque.bsky.social · Feb 8

SpatialLeiden is out in #GenomeBiology: t.ly/WQppF. It models both gene expression and spatial information for clustering. This allows you to perform e.g. spatially aware cell typing or domain identification. It's fast, scalable and intuitive for single-cell researchers. Try it out!

SpatialLeiden: spatially aware Leiden clustering - Genome Biology

Clustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Le...

t.ly

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Nav @naveed-ishaque.bsky.social · Jan 8

The HISTOMAP projects aims to use AI and spatial transcriptomics data to accelerate biomarker detection for bladder cancer. We will work closely with the clinic, pathology, and regulatory experts to investigate how best to get these models into clinical routine.

Nav @naveed-ishaque.bsky.social · Jan 8

Do you also think that #SpatialTranstriptomics and #AI will give rise to #DigitalPathology 2.0? We have an open PhD position for the HISTOMAP (Histology-based Molecular Analysis Platform) project to accelerate biomarker detection. Please apply here: www.bihealth.org/en/notices/b....
Spread the word!

BIH PhD Program - Call for PhD candidates 2025 - News - BIH at Charité

The BIH PhD program aims to promote interdisciplinarity and support young translational talents. The program co-funds PhD positions for excellent translational projects that fit one of the four BIH re...

www.bihealth.org

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Reposted by Nav

Ehsan Razaghi @ehsanrazaghi.bsky.social · Dec 5

I tried Sainsc for our MERSCOPE data and Naveed, it works wonderfully! Importantly, the documentation is excellent. Thank you so much for the clear tutorial and explanations. This is truly a life saver for my analysis at the moment. Props to the team, this is awesome work!

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Nav @naveed-ishaque.bsky.social · Dec 19

Everyone knows by now that 42 is the answer to the ultimate question of life, the universe, and everything. But as I turn 42 today, I’ve realised something profound: it’s not the answer that matters - it’s the prompt!

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Nav @naveed-ishaque.bsky.social · Dec 17

Am I really the first to repost Mats Nilsson? What an honour!

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Reposted by Nav

Mats Nilsson's Lab @nilssonlab.org · Dec 12

Hello world. Our lab has a new home here on Bluesky! We will post about spatial omics, science, nice papers and lab activities. The account will be collectively managed by lab members. Happy spatial-omics everyone!

a cartoon of a man looking out a window at the stars

ALT: a cartoon of a man looking out a window at the stars

media.tenor.com

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Nav @naveed-ishaque.bsky.social · Dec 8

The calm before the storm... #SpaceHack starts tomorrow! Looking forward to 3 intense days of addressing unsolved data analysis problems for #SpatialTranscriptomics.
More here: spatialhackathon.github.io

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Nav @naveed-ishaque.bsky.social · Dec 3

SpatialLeiden adds spatial support to the Leiden clustering algrithm. It has 3 parameters. Two we know from scRNAseq analysis (resolution and num of neighbors), and the other is the weight of the spatial info. We thin it is the natural choice for spatial clustering for the single-cell community!

Nav @naveed-ishaque.bsky.social · Dec 3

... we will also implement multi-omics and multi-sample support at #SpaceHack spatialhackathon.github.io

Home

Github Pages for SpatialHackathon

spatialhackathon.github.io

Nav @naveed-ishaque.bsky.social · Dec 3

Try out SpatialLeiden for identifying spatial domains/clusters in your #SpatialTranscriptomics data: www.biorxiv.org/content/10.1...
github.com/HiDiHlabs/sp...
It's as easy as Leiden, but as performant as the best in class. Give it a try and let us know if it works for you!

SpatialLeiden - Spatially-aware Leiden clustering

Clustering can identify the natural structure that is inherent to measured data. For single-cell omics, clustering finds cells with similar molecular phenotype after which cell types are annotated. Le...

www.biorxiv.org

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Reposted by Nav

Luciano Martelotto @lgmartelotto.bsky.social · Nov 29

@gestaltsp.bsky.social welcome to BlueSky!

@jasmineplummer.bsky.social @ioavlachos.bsky.social

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