#spatialomics — Public Fediverse posts

Pipeline release! nf-core/sopa v1.0.0 - v1.0.0 - [2026-07-15]!
Nextflow version of Sopa - spatial omics pipeline and analysis
Please see the changelog: https://github.com/nf-core/sopa/releases/tag/1.0.0

#segmentation #spatialomics #spatialproteomics #spatialtranscriptomics #spatialdata #nfcore #openscience #nextflow #bioinformatics

Pipeline release! nf-core/sopa v1.0.0 - v1.0.0 - [2026-07-15]!
Nextflow version of Sopa - spatial omics pipeline and analysis
Please see the changelog: https://github.com/nf-core/sopa/releases/tag/1.0.0

#segmentation #spatialomics #spatialproteomics #spatialtranscriptomics #spatialdata #nfcore #openscience #nextflow #bioinformatics

🧬 Earlier this year, members of the Bioconductor community met on San Servolo Island, Italy, for a three-day hackathon on spatial omics and bioimaging. They tackled challenges in spatial data infrastructure, interoperability, image analysis, visualisation, differential expression, and foundation models, producing new code, documentation, and a collaborative preprint to bolster spatial omics support across Bioconductor.

📖 Read more: https://blog.bioconductor.org/posts/2026-06-17-venice/

#Bioconductor #SpatialOmics

🧬 Earlier this year, members of the Bioconductor community met on San Servolo Island, Italy, for a three-day hackathon on spatial omics and bioimaging. They tackled challenges in spatial data infrastructure, interoperability, image analysis, visualisation, differential expression, and foundation models, producing new code, documentation, and a collaborative preprint to bolster spatial omics support across Bioconductor.

📖 Read more: https://blog.bioconductor.org/posts/2026-06-17-venice/

#Bioconductor #SpatialOmics

Postdoctoral Fellow in Computational Biology
Temple University

See the full job description on jobRxiv: https://jobrxiv.org/job/temple-university-27778-postdoctoral-fellow-in-computational-biology/

#BioinformaticsandComputationalBiology #cancergenomics #epigenomics #singlecellomics #spatialomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/temple-university-27778-postdoctoral-fellow-in-computational-biology/?fsp_sid=12613

Postdoctoral Fellow in Computational Biology
Temple University

See the full job description on jobRxiv: https://jobrxiv.org/job/temple-university-27778-postdoctoral-fellow-in-computational-biology/

#BioinformaticsandComputationalBiology #cancergenomics #epigenomics #singlecellomics #spatialomics #ScienceJobs #hiring #research
https://jobrxiv.org/job/temple-university-27778-postdoctoral-fellow-in-computational-biology/?fsp_sid=12613

📢 Call for Papers: Computational Spatial Omics - Multimodal Strategies for Systems Biology and Biomedical Discovery

⏳ Submission Deadline: 31 December 2026

🔗 Submit your work: https://spj.science.org/journal/csbj/si/computational-spatial-omics

#CallForPapers #SpatialOmics #SpatialTranscriptomics #SpatialProteomics #Metabolomics #Lipidomics #Multiomics #ComputationalBiology #SystemsBiology #Bioinformatics #AIinHealthcare #DigitalPathology #GraphNeuralNetworks #PrecisionMedicine

📢 Call for Papers: Computational Spatial Omics - Multimodal Strategies for Systems Biology and Biomedical Discovery

⏳ Submission Deadline: 31 December 2026

🔗 Submit your work: https://spj.science.org/journal/csbj/si/computational-spatial-omics

#CallForPapers #SpatialOmics #SpatialTranscriptomics #SpatialProteomics #Metabolomics #Lipidomics #Multiomics #ComputationalBiology #SystemsBiology #Bioinformatics #AIinHealthcare #DigitalPathology #GraphNeuralNetworks #PrecisionMedicine

New tool for #SpatialOmics: With C-COMPASS, researchers can analyze the distribution of proteins and lipids in cells – no programming skills required. Developed by #HelmholtzMunich, #DZD & #UniBonn.
https://nachrichten.idw-online.de/2025/12/04/c-compass-ai-based-software-maps-proteins-and-lipids-within-cells

Neues Tool für #SpatialOmics: Mit C-COMPASS können Forschende die Verteilung von Proteinen und Lipiden in Zellen analysieren – ganz ohne Programmierkenntnisse. Entwickelt von #HelmholtzMunich, #DZD & #UniBonn.
https://nachrichten.idw-online.de/2025/12/04/c-compass-ki-basierte-software-kartiert-proteine-und-lipide-in-zellen

The Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025.
https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/

@galaxyfreiburg
#UseGalaxy #GalaxyProject #EOSC #SingleCell #SpatialOmics #Omics #Transcriptomics #Bioinformatics #Genomics #ComputationalBiology #EuroScienceGateway #OpenScience #ReproducibleResearch #GalaxyCommunity #SPOC (1/2)

The Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025.
https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/

@galaxyfreiburg
#UseGalaxy #GalaxyProject #EOSC #SingleCell #SpatialOmics #Omics #Transcriptomics #Bioinformatics #Genomics #ComputationalBiology #EuroScienceGateway #OpenScience #ReproducibleResearch #GalaxyCommunity #SPOC (1/2)

The Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025.
https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/

@galaxyproject
#UseGalaxy #GalaxyProject #EOSC #UniFreiburg #SingleCell #SpatialOmics #Omics #Transcriptomics #Bioinformatics #Genomics #ComputationalBiology #EuroScienceGateway #OpenScience #ReproducibleResearch (1/2)

The Galaxy single-cell and spatial omics community (SPOC) is thrilled to share the latest updates on tools, datasets, and collaborative initiatives driving open and reproducible single-cell and spatial omics research in 2025.
https://galaxyproject.org/news/2025-10-14-spoc-cellgenomics/

@galaxyproject
#UseGalaxy #GalaxyProject #EOSC #UniFreiburg #SingleCell #SpatialOmics #Omics #Transcriptomics #Bioinformatics #Genomics #ComputationalBiology #EuroScienceGateway #OpenScience #ReproducibleResearch (1/2)

How merging several advanced techniques will enable Generative Digital Twins. #digitalTwins #generativeAI #spatialOmics #imaging https://www.csbj.org/article/S2001-0370%2824%2900319-2/fulltext

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=84784

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=84784

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=83054

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=83054

Latest addition to our #SpatialOmics Methods series tackles the challenge of integrating multiple spatially resolved transcriptomics datasets. That employs the expression of all measured genes and the spatial location of cells, to integrate multiple tissue sections.

spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics https://doi.org/10.1093/gigascience/giae042

See the series here: https://academic.oup.com/gigascience/pages/spatial-omics-methods-and-applications

Latest addition to our #SpatialOmics Methods series tackles the challenge of integrating multiple spatially resolved transcriptomics datasets. That employs the expression of all measured genes and the spatial location of cells, to integrate multiple tissue sections.

spatiAlign: an unsupervised contrastive learning model for data integration of spatially resolved transcriptomics https://doi.org/10.1093/gigascience/giae042

See the series here: https://academic.oup.com/gigascience/pages/spatial-omics-methods-and-applications

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=78140

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=78140

Our second parallel session is about to start at #SIBdays24: “#SingleCell Biology: #Biology Through the Lens of Single-Cell and #SpatialOmics Technologies” chaired by Aurélie Gabriel @fondationisrec et @markrobinsonca https://sibdays.sib.swiss/session-descriptions#Single-cell …

Our second parallel session is about to start at #SIBdays24: “#SingleCell Biology: #Biology Through the Lens of Single-Cell and #SpatialOmics Technologies” chaired by Aurélie Gabriel @fondationisrec et @markrobinsonca https://sibdays.sib.swiss/session-descriptions#Single-cell …

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=76684

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=76684

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=76376

Postdoc in dynamic causal gene network from single-cell & spatial multiomic

University of Massachusetts Chan Medical School

We seek #postdoc to decode dynamic #GeneRegulatoryNetwork from #SingleCell & #SpatialOmics with #CausalInference. Quantitative bg needed. Apply now!????

See the full job description on jobRxiv: https://...
https://jobrxiv.org/job/university-of-massachusetts-chan-medical-school-27778-postdoc-in-dynamic-causal-gene-network-from-single-cell-spatial-multiomic/?feed_id=76376

“CellCharter is a remarkable tool to identify, characterize and compare cell communities in spatial -omics datasets.”

🥁 One of the #SIBRemarkableOutputs 2023 👏

👉 Find out more about this and the other outputs: https://tinyurl.com/4v66b235
#CellPlasticity #SpatialOmics

“CellCharter is a remarkable tool to identify, characterize and compare cell communities in spatial -omics datasets.”

🥁 One of the #SIBRemarkableOutputs 2023 👏

👉 Find out more about this and the other outputs: https://tinyurl.com/4v66b235
#CellPlasticity #SpatialOmics

Taking Spatial Omics into the Next Dimension.

A multitude of papers on novel methods for #SpatialOmics are published in a cross-journal series launching today in GigaScience and GigaByteJournal.

http://gigasciencejournal.com/blog/spatial-omics-series/

Taking Spatial Omics into the Next Dimension.

A multitude of papers on novel methods for #SpatialOmics are published in a cross-journal series launching today in GigaScience and GigaByteJournal.

http://gigasciencejournal.com/blog/spatial-omics-series/

Interested in #SpatialOmics? Have a look at our course

During this course we will discuss basics and introduce state-of-the-art software-tools tailored for spatial omics and multiplexed image analysis.

https://www.physalia-courses.org/courses-workshops/multiplexed-image-analysis/

Interested in #SpatialOmics? Have a look at our course

During this course we will discuss basics and introduce state-of-the-art software-tools tailored for spatial omics and multiplexed image analysis.

https://www.physalia-courses.org/courses-workshops/multiplexed-image-analysis/

🎓 #biocsmorgasbord! starts today! New workshop added ✨ Learn "Introduction to SpatialOmicsOverlay" with the #NanoString #GeoMx Team 🧬💻

📅 May 22-26
➡️ https://gallantries.github.io/video-library/modules/bioconductor
#Bioinformatics #RStats #SpatialOmics

🎓 #biocsmorgasbord! starts today! New workshop added ✨ Learn "Introduction to SpatialOmicsOverlay" with the #NanoString #GeoMx Team 🧬💻

📅 May 22-26
➡️ https://gallantries.github.io/video-library/modules/bioconductor
#Bioinformatics #RStats #SpatialOmics

Making an #introduction post. Am an R using, Brisbane based bioinformatician with an interest in single cell analysis. Very easy to distract with a cool technology or visualisation!

(Might follow some unrelated accounts while I'm here, gotta get outside this corner of the internet!)

#bioinformatics #rstats #omics #singlecell #spatialomics #sustainability #brisbane