February 14, 2025 at 4:26 PM
Spatialproteomics: a Python-based toolbox for end-to-end analysis of highly multiplexed imaging data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data - Nature Methods
Spatialproteomics is a Python-based toolbox that supports end-to-end analysis of highly multiplexed imaging data.
www.nature.com
August 5, 2026 at 1:31 PM
Spatialproteomics: a Python-based toolbox for end-to-end analysis of highly multiplexed imaging data.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Nice talk on #SpatialProteomics from @coscialab.bsky.social at #FoG2025 @fogenomics.bsky.social
Essential to unlock phenotype & prelude to biomarker discovery
Essential to unlock phenotype & prelude to biomarker discovery
January 30, 2025 at 2:33 PM
Nice talk on #SpatialProteomics from @coscialab.bsky.social at #FoG2025 @fogenomics.bsky.social
Essential to unlock phenotype & prelude to biomarker discovery
Essential to unlock phenotype & prelude to biomarker discovery
Pumped to finally show off our spatial proteomics work presented a few weeks ago at the EAS Congress @eassociety.bsky.social and now live on @biorxivpreprint.bsky.social 🥳
Time for a science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵
www.biorxiv.org/content/10.1...
Time for a science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵
www.biorxiv.org/content/10.1...
www.biorxiv.org
June 23, 2025 at 6:56 PM
Pumped to finally show off our spatial proteomics work presented a few weeks ago at the EAS Congress @eassociety.bsky.social and now live on @biorxivpreprint.bsky.social 🥳
Time for a science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵
www.biorxiv.org/content/10.1...
Time for a science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵
www.biorxiv.org/content/10.1...
MouseMapper
An imaging-omics workflow of whole-mouse analysis
Up to single-cell resolution!👹
vDISCO WildDISCO whole-mouse optical clearing
#SpatialProteomics Trigeminal ganglia
VR annotation of major organs, peripheral nerve & Mφ
@erturklab.bsky.social Nature 2026
www.nature.com/articles/s41...
An imaging-omics workflow of whole-mouse analysis
Up to single-cell resolution!👹
vDISCO WildDISCO whole-mouse optical clearing
#SpatialProteomics Trigeminal ganglia
VR annotation of major organs, peripheral nerve & Mφ
@erturklab.bsky.social Nature 2026
www.nature.com/articles/s41...
June 5, 2026 at 11:51 AM
MouseMapper
An imaging-omics workflow of whole-mouse analysis
Up to single-cell resolution!👹
vDISCO WildDISCO whole-mouse optical clearing
#SpatialProteomics Trigeminal ganglia
VR annotation of major organs, peripheral nerve & Mφ
@erturklab.bsky.social Nature 2026
www.nature.com/articles/s41...
An imaging-omics workflow of whole-mouse analysis
Up to single-cell resolution!👹
vDISCO WildDISCO whole-mouse optical clearing
#SpatialProteomics Trigeminal ganglia
VR annotation of major organs, peripheral nerve & Mφ
@erturklab.bsky.social Nature 2026
www.nature.com/articles/s41...
Waking up our sleeping beauty!
Super excited to have Xenium and PhenoCycler now running in the same room 🤩
#SpatialOmics #SpatialBiology #SpatialProteomics #SpatialTranscriptomics #Immunology
Super excited to have Xenium and PhenoCycler now running in the same room 🤩
#SpatialOmics #SpatialBiology #SpatialProteomics #SpatialTranscriptomics #Immunology
April 3, 2025 at 9:05 AM
Waking up our sleeping beauty!
Super excited to have Xenium and PhenoCycler now running in the same room 🤩
#SpatialOmics #SpatialBiology #SpatialProteomics #SpatialTranscriptomics #Immunology
Super excited to have Xenium and PhenoCycler now running in the same room 🤩
#SpatialOmics #SpatialBiology #SpatialProteomics #SpatialTranscriptomics #Immunology
New preprint out!
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
May 5, 2025 at 11:30 AM
New preprint out!
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data
By @matthiasmeybe.bsky.social et al. Great collaboration with the group of Sascha Dietrich and Peter-Martin Bruch.
doi.org/10.1038/s415...
By @matthiasmeybe.bsky.social et al. Great collaboration with the group of Sascha Dietrich and Peter-Martin Bruch.
doi.org/10.1038/s415...
July 28, 2026 at 8:53 AM
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data
By @matthiasmeybe.bsky.social et al. Great collaboration with the group of Sascha Dietrich and Peter-Martin Bruch.
doi.org/10.1038/s415...
By @matthiasmeybe.bsky.social et al. Great collaboration with the group of Sascha Dietrich and Peter-Martin Bruch.
doi.org/10.1038/s415...
EMBL and collaborators have developed spatialproteomics, an open-source package that helps researchers analyse how cells are organised within tumours.
In lymphoma samples, it revealed spatial patterns that distinguish indolent from aggressive entities.
www.embl.org/news/science...
In lymphoma samples, it revealed spatial patterns that distinguish indolent from aggressive entities.
www.embl.org/news/science...
New software helps researchers decode the cellular architecture of lymphoma | EMBL
EMBL scientists and collaborators developed spatialproteomics, an open-source tool that helps researchers analyse how cells are organised within tumours.
www.embl.org
July 28, 2026 at 12:28 PM
EMBL and collaborators have developed spatialproteomics, an open-source package that helps researchers analyse how cells are organised within tumours.
In lymphoma samples, it revealed spatial patterns that distinguish indolent from aggressive entities.
www.embl.org/news/science...
In lymphoma samples, it revealed spatial patterns that distinguish indolent from aggressive entities.
www.embl.org/news/science...
Spatialproteomics using microscopy slides of tissue taken from patients. From Heidelberg, Germany. www.nature.com/articles/s41...
Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data - Nature Methods
Spatialproteomics is a Python-based toolbox that supports end-to-end analysis of highly multiplexed imaging data.
www.nature.com
July 25, 2026 at 3:31 PM
Spatialproteomics using microscopy slides of tissue taken from patients. From Heidelberg, Germany. www.nature.com/articles/s41...
I highly recommend adding tonsil core(s) when creating tissue microarrays (TMAs) with human tissues. They have almost all the immune cells, structural cells, etc. for a robust positive control for #SpatialBiology.🧪🔬 #science #histology #SpatialOmics #SpatialProteomics (1/3)
March 4, 2025 at 6:31 AM
I highly recommend adding tonsil core(s) when creating tissue microarrays (TMAs) with human tissues. They have almost all the immune cells, structural cells, etc. for a robust positive control for #SpatialBiology.🧪🔬 #science #histology #SpatialOmics #SpatialProteomics (1/3)
Another tour de force from @mannlab.bsky.social, this time on a topic dear to my heart - Atherosclerosis! An impressive amount of both laser capture & plasma proteomics in here. #proteomics #spatialproteomics
Spatially resolved proteomic signatures of atherosclerotic carotid artery disease https://www.medrxiv.org/content/10.1101/2025.02.09.25321955v1
February 17, 2025 at 4:46 PM
Another tour de force from @mannlab.bsky.social, this time on a topic dear to my heart - Atherosclerosis! An impressive amount of both laser capture & plasma proteomics in here. #proteomics #spatialproteomics
Free space for what’s to come. Stay tuned! Good news for @irbbarcelona.org coming soon! 😉 #MassSpectrometry #Proteomics #SpatialProteomics #SingleCell
April 15, 2025 at 11:03 AM
Free space for what’s to come. Stay tuned! Good news for @irbbarcelona.org coming soon! 😉 #MassSpectrometry #Proteomics #SpatialProteomics #SingleCell
Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data https://www.biorxiv.org/content/10.1101/2025.04.29.651202v1
May 3, 2025 at 11:47 PM
Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data https://www.biorxiv.org/content/10.1101/2025.04.29.651202v1
Other stuff:
#SpatialProteomics - #STEM
#Fantasy - #SciFi - #comics - #TV
#Gothic - #Magick - #corvids
#Health - #MentalHealth - #AuDHD
#Snark - #RainbowsAndUnicorns (sometimes true, sometimes snark)
Love #America 🇺🇲 but NOT all Americans (especially now)
Blocked: 🚫DM🚫crypto🚫porn🚫sales🚫
#SpatialProteomics - #STEM
#Fantasy - #SciFi - #comics - #TV
#Gothic - #Magick - #corvids
#Health - #MentalHealth - #AuDHD
#Snark - #RainbowsAndUnicorns (sometimes true, sometimes snark)
Love #America 🇺🇲 but NOT all Americans (especially now)
Blocked: 🚫DM🚫crypto🚫porn🚫sales🚫
February 21, 2025 at 2:01 AM
Other stuff:
#SpatialProteomics - #STEM
#Fantasy - #SciFi - #comics - #TV
#Gothic - #Magick - #corvids
#Health - #MentalHealth - #AuDHD
#Snark - #RainbowsAndUnicorns (sometimes true, sometimes snark)
Love #America 🇺🇲 but NOT all Americans (especially now)
Blocked: 🚫DM🚫crypto🚫porn🚫sales🚫
#SpatialProteomics - #STEM
#Fantasy - #SciFi - #comics - #TV
#Gothic - #Magick - #corvids
#Health - #MentalHealth - #AuDHD
#Snark - #RainbowsAndUnicorns (sometimes true, sometimes snark)
Love #America 🇺🇲 but NOT all Americans (especially now)
Blocked: 🚫DM🚫crypto🚫porn🚫sales🚫
Next we’ll hear from a panel about the future needs of spatial multi-omics
I’m guessing that it’ll mostly be about #SpatialTranscriptomics + #SpatialProteomics
Though I know that there’s also spatial ATAC and spatial methylation
I’m guessing that it’ll mostly be about #SpatialTranscriptomics + #SpatialProteomics
Though I know that there’s also spatial ATAC and spatial methylation
December 4, 2024 at 10:41 PM
Next we’ll hear from a panel about the future needs of spatial multi-omics
I’m guessing that it’ll mostly be about #SpatialTranscriptomics + #SpatialProteomics
Though I know that there’s also spatial ATAC and spatial methylation
I’m guessing that it’ll mostly be about #SpatialTranscriptomics + #SpatialProteomics
Though I know that there’s also spatial ATAC and spatial methylation
So great to see #SpatialProteomics, including #MassSpectrometry based methods, recognized as method of the year!
Kudos to all those who made it possible!
Very exciting science and discoveries to come!
www.nature.com/articles/s41...
Kudos to all those who made it possible!
Very exciting science and discoveries to come!
www.nature.com/articles/s41...
Method of the Year 2024: spatial proteomics - Nature Methods
Approaches for profiling the spatial proteome in tissues are the basis of atlas-scale projects that are delivering on their promise for understanding biological complexity in health and disease.
www.nature.com
December 7, 2024 at 12:51 PM
So great to see #SpatialProteomics, including #MassSpectrometry based methods, recognized as method of the year!
Kudos to all those who made it possible!
Very exciting science and discoveries to come!
www.nature.com/articles/s41...
Kudos to all those who made it possible!
Very exciting science and discoveries to come!
www.nature.com/articles/s41...
Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data https://www.biorxiv.org/content/10.1101/2025.04.29.651202v1
May 3, 2025 at 11:47 PM
Spatialproteomics - an interoperable toolbox for analyzing highly multiplexed fluorescence image data https://www.biorxiv.org/content/10.1101/2025.04.29.651202v1
Recruiting TWO #postdocs in immunology to work with me on the tissue biology of human macrophages @stanford.edu. NIH R01 funded. #scRNAseq #SpatialTranscriptomics #SpatialProteomics. Please RT!
March 13, 2025 at 8:23 PM
Recruiting TWO #postdocs in immunology to work with me on the tissue biology of human macrophages @stanford.edu. NIH R01 funded. #scRNAseq #SpatialTranscriptomics #SpatialProteomics. Please RT!
Surprise, surprise! 😳
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
December 27, 2024 at 1:19 AM
Surprise, surprise! 😳
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
This raises an important question…
How will our @naturemethods 2024 Method of the Year, #SpatialProteomics, will tackle this before it becomes a potential pitfall?
Why Bax detection in >1400 publications might be flawed | Cell Death & Disease
www.nature.com/articles/s41...
#spatialproteomics #spatialbiology #multiplexedimaging #bioinformatics #python #scverse #opensource #singlecell #akoya #codex
May 5, 2025 at 11:30 AM
I work on both the exploratory and targeted sides of #SpatialProteomics (SP). I'm incorporating Xenium #SpatialTranscriptomics these days for a more #SpatialOmics approach, but I'm still definitely an SP girl. 😀
(Not my paper)
(Not my paper)
Spatial proteomics in translational and clinical research | Molecular Systems Biology www.embopress.org/do...
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#proteomics #prot-paper
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#proteomics #prot-paper
April 16, 2025 at 3:31 AM
I work on both the exploratory and targeted sides of #SpatialProteomics (SP). I'm incorporating Xenium #SpatialTranscriptomics these days for a more #SpatialOmics approach, but I'm still definitely an SP girl. 😀
(Not my paper)
(Not my paper)
In this longer YouTube interview, Emma Lundberg gives her views on #VirtualCells; #SpatialProteomics – its past, present and future; atlas building, explaining why cilia are so hard to map and more 🧪
www.youtube.com/watch?v=Ifc1...
#WomenInSTEM #AI #ArtificialIntelligence
www.youtube.com/watch?v=Ifc1...
#WomenInSTEM #AI #ArtificialIntelligence
Emma Lundberg: AI Virtual Cells could revolutionize biological science
YouTube video by SciLifeLab
www.youtube.com
January 21, 2025 at 11:48 AM
In this longer YouTube interview, Emma Lundberg gives her views on #VirtualCells; #SpatialProteomics – its past, present and future; atlas building, explaining why cilia are so hard to map and more 🧪
www.youtube.com/watch?v=Ifc1...
#WomenInSTEM #AI #ArtificialIntelligence
www.youtube.com/watch?v=Ifc1...
#WomenInSTEM #AI #ArtificialIntelligence
This is pretty damn cool. Turning 2D proteomics data into 3D. Wish there was a viz portal to play with the data. #SpatialProteomics
In-depth and high-throughput spatial proteomics for whole-tissue slice profiling by deep learning-facilitated sparse sampling strategy www.nature.com/artic...
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#proteomics #prot-paper
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#proteomics #prot-paper
March 17, 2025 at 3:33 PM
This is pretty damn cool. Turning 2D proteomics data into 3D. Wish there was a viz portal to play with the data. #SpatialProteomics