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🧬 How can AI bridge the gap between histology and spatial transcriptomics?

🔗 SegDecon bridges histology and transcriptomics through AI-based nuclei segmentation and image-informed spatial deconvolution. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.041

📚 CSBJ: https://www.csbj.org/

#SpatialTranscriptomics #Histology #Genomics #SystemsBiology #NucleiSegmentation #AI #CellBiology #TissueBiology #Bioimaging

SegDecon bridges histology and transcriptomics through AI-based nuclei segmentation and image-informed spatial deconvolution. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.10.041

Is spatial transcriptomics data preprocessing giving you a headache? You're not alone! 🤯
Join our webinar designed for new researchers to simplify the complex world of image-based spatial omics. We'll walk through the practical workflow step-by-step, from initial cell segmentation to cleaning up your data.
Get the foundational skills you need. 📅 Sign up here: https://t1p.de/lqbg1

#Transcriptomics #SpatialTranscriptomics #Omics #DataScience #ResearchWebinar #GHGA #ELIXIR #deNBI

Digital announcement for the webinar series “The Knowledge Series – Empowering Research: Practical Bioinformatics and Data Management.” Date: November 20, 2025, 13:00 CET. Title of the webinar: “Beginners guide of data processing for image-based spatial transcriptomics technologies” with Florian Heyl. More information on GHGA and de.NBI websites.

Celltrion has entered a joint R&D agreement with Portrai to leverage spatial transcriptomics and AI for new drug discovery, securing exclusive rights to up to 10 targets in a deal worth up to $87.75 million, with additional royalties upon commercialization.
#YonhapInfomax #Celltrion #Portrai #SpatialTranscriptomics #DrugDiscovery #AITechnology #Economics #FinancialMarkets #Banking #Securities #Bonds #StockMarket
https://en.infomaxai.com/news/articleView.html?idxno=87894

KODAMA goes spatial
https://doi.org/10.1101/2025.05.28.656544
#spatialtranscriptomics #visium #visiumhd

Want a sneak peek or to try it on your own data? Try EnrichMap https://enrichmap.readthedocs.io/en/latest/
#SpatialTranscriptomics #ComputationalBiology #EnrichMap #spatialomics

🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us! #MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍 job-boards.greenhouse.io/chanzuckerbe...

Scientist, Spatial Molecular C...

Decoding cell–cell communication using spatial transcriptomics

#spatialtranscriptomics #omics #ccc
https://www.nature.com/articles/s41576-025-00824-3

📣 Listen up: you only have a few more days to apply for #EMBOSpatialOmics!

Would you like to get a comprehensive introduction to the various methods of spatial-omics and in particular those of multiplex immunofluorescence and spatial transcriptomics?

Then apply for this hands-on EMBO Practical Course by 10 March ✍️

🌍 EMBL Heidelberg
📅 15 – 20 June 2025
💻 https://s.embl.org/iso25-01-ma

#spatialtranscriptomics #microscopy #imageanalysis #spatialbiology #spatialomics

Spatiotemporal single-cell roadmap of human skin wound healing
#scRNA-seq

#spatialtranscriptomics

#visium

#RNAScope
https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(24)00412-0?dgcid=raven_jbs_aip_email

#job alert: junior/mid-career PI opportunities in cancer research @ Oxford university: https://www.ludwig.ox.ac.uk/news/vacancies-assistant-or-associate-professor-level-cancer-researchers

Areas we're looking for:
#epigenetics #chromatin #epitranscriptomics #RNA #myeloidCells #spatialTranscriptomics

Please boost for visibility! @academicchatter #hiring

Tools (#preprint from 10x Genomics).
'Here, we introduce Visium HD Spatial Gene Expression (“Visium HD”) and demonstrate its use as a discovery platform for profiling CRC in multiple patients using FFPE tissue blocks. Visium HD slides provide a dramatically increased oligonucleotide barcode density over the Visium v2 slides (11,000,000 continuous features in a 6.5 mm Visium HD capture area, compared to 5,000 features with gaps between them in a 6.5 mm Visium v2 capture area). The single cell scale resolution of Visium HD allowed us to map distinct populations of immune cells, specifically macrophages and T cells, and evaluate differential gene expression at the tumor boundary to explore the potential contribution of these immune cell populations in the TME.'
#Immunology #Immunotherapy #SpatialTranscriptomics
https://www.biorxiv.org/content/10.1101/2024.06.04.597233v1

Some really great talks and discussions today on advances in virus-livestock omics at the #Turing institute, who kindly supported the event. Talks include those by Ge Wu and Marie Di Placido (pictures) from the #Pirbright Institute.

Great to have input from the #BBSRC and #SFTC #Harttree Centre too.

Looking forward to new adventures in this area...

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

Last chance to register for our meeting "Advancing virus-livestock omics" on Thurs 28th Sept at the Alan Turing Institute.

Registration closes end of Mon 25th.

See https://www.turing.ac.uk/events/advancing-virus-livestock-omics

Register here: https://t.ly/wYA7d

Schedule below

Zoom stream possible for those from further afield

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

Marius Lange #BC2basel: increasing complexity of #SingleCell data leads to problems of temporal, spatial and spatio-temporal mapping. The solution proposed is optimal transport applications, implemented in Moscot:
https://moscot.readthedocs.io/en/latest/
https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2 #SpatialTranscriptomics #scRNAseq

Excellent conclusions of Jean Fan #BC2basel on #machinelearning applied to #scRNAseq #SpatialTranscriptomics

. Additional food for thought (for users)
Machine learning tools will always give you a solution Whether the solution is reasonable must be evaluated with your expertise and human intelligence
Understanding where the data comes from, its LS and qualities, will allow you to evaluate whether a machine learning tool should be applied
(automatically detected text)

Additional food for thought (for developers)
As machine learning is integrated into more sensitive domains like healthcare, we must emphasize:
Transparent algorithms e open source: open code, open training data, reproducible
Enables user judicial review
Augmentation, not replacement
(automatically detected text)

Impressive work by Jean Fan's lab #BC2basel: aligning different spatial transcriptomics results, not only from different experiments but different protocols, e.g. MERFISH - Visium. Combining with #scRNAseq clustering and her lab's spot deconvolution allows to compare directly gene expression between these different experiments, https://www.biorxiv.org/content/10.1101/2023.04.11.534630v2.abstract #SpatialTranscriptomics

Excited for participating in this #spatialtranscriptomics #Visium platform study with an expert team from @NICHD_NIH, in the first step of studying the spatial biology of #pituitary corticotroph tumors, revealing their heterogeneity.

https://www.medrxiv.org/content/10.1101/2023.08.04.23293576v1