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@naveed-ishaque.bsky.social
Bioinformatics research group leader at the Berlin Institute of Health, ELIXIR and de.NBI. Main focus: cancer, immunology, placenta, and all things omics... especially spatial omics.
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
July 4, 2025 at 5:43 AM
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/...
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...
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
July 2, 2025 at 12:05 PM
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...
More in our preprint: www.biorxiv.org/content/10.1...
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...
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
March 17, 2025 at 12:06 PM
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...
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...
Reposted by Nav
🧬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...
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
March 14, 2025 at 2:38 PM
🧬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...
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...
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
February 8, 2025 at 9:43 AM
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
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
February 8, 2025 at 9:33 AM
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!
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!
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
January 8, 2025 at 8:29 AM
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!
Spread the word!
Reposted by Nav
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!
December 5, 2024 at 9:42 AM
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!
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!
December 19, 2024 at 7:26 PM
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!
Reposted by Nav
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
December 12, 2024 at 4:24 PM
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!
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
More here: spatialhackathon.github.io
December 8, 2024 at 5:27 PM
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
More here: spatialhackathon.github.io
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!
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
December 3, 2024 at 7:55 PM
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!
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!
Reposted by Nav
November 29, 2024 at 9:59 AM
Check out our new tools for #SpatialTranscriptomics. It's called Sainsc: onlinelibrary.wiley.com/doi/10.1002/....
#Sainsc can map cell types in high resolution spatial transcriptomics data, without segmenting cells! It's light weight, fast, and easy to use: sainsc.readthedocs.io/tutorials/in...
#Sainsc can map cell types in high resolution spatial transcriptomics data, without segmenting cells! It's light weight, fast, and easy to use: sainsc.readthedocs.io/tutorials/in...
Sainsc: A Computational Tool for Segmentation‐Free Analysis of In Situ Capture Data
Spatially resolved transcriptomics methods can now profile the entire transcriptome, at full organism scale with nanometre resolution. Analysis frameworks that can efficiently and intuitively process....
onlinelibrary.wiley.com
November 29, 2024 at 10:10 AM
Check out our new tools for #SpatialTranscriptomics. It's called Sainsc: onlinelibrary.wiley.com/doi/10.1002/....
#Sainsc can map cell types in high resolution spatial transcriptomics data, without segmenting cells! It's light weight, fast, and easy to use: sainsc.readthedocs.io/tutorials/in...
#Sainsc can map cell types in high resolution spatial transcriptomics data, without segmenting cells! It's light weight, fast, and easy to use: sainsc.readthedocs.io/tutorials/in...
Reposted by Nav
Whole-brain spatial transcriptional analysis at cellular resolution
Incredible study - 3D single cell imaging of the entire mouse brain - also on the cover of this week's #Science
🧪🔬🤯
www.science.org/doi/10.1126/...
Incredible study - 3D single cell imaging of the entire mouse brain - also on the cover of this week's #Science
🧪🔬🤯
www.science.org/doi/10.1126/...
November 22, 2024 at 4:16 PM
Whole-brain spatial transcriptional analysis at cellular resolution
Incredible study - 3D single cell imaging of the entire mouse brain - also on the cover of this week's #Science
🧪🔬🤯
www.science.org/doi/10.1126/...
Incredible study - 3D single cell imaging of the entire mouse brain - also on the cover of this week's #Science
🧪🔬🤯
www.science.org/doi/10.1126/...