#Multiomics2024 was amazing and I was very proud to be invited to speak for @standardbiology.bsky.social. Here’s the cartoon version.
Huge thanks to @aruthak.bsky.social for bringing it all together. #spatialbio
Huge thanks to @aruthak.bsky.social for bringing it all together. #spatialbio
December 6, 2024 at 1:33 AM
#Multiomics2024 was amazing and I was very proud to be invited to speak for @standardbiology.bsky.social. Here’s the cartoon version.
Huge thanks to @aruthak.bsky.social for bringing it all together. #spatialbio
Huge thanks to @aruthak.bsky.social for bringing it all together. #spatialbio
Wow! What a big day for #multipleximaging and #spatialbio! I am proud to have played a role in the genesis of this field in I-O. And more to come! @standardbiology.bsky.social
I could not be more thrilled to announce the Nature Methods @naturemethods.bsky.social Method of the Year is Spatial Proteomics! Please see our editorial as a roadmap to the fantastic content in this special issue! 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 2:29 AM
Wow! What a big day for #multipleximaging and #spatialbio! I am proud to have played a role in the genesis of this field in I-O. And more to come! @standardbiology.bsky.social
Glad to be part of such an open and collaborative community pushing #SpatialBio forward! Thanks for inviting and hosting us @kevinyamauchi.bsky.social @lucamarconato.bsky.social & Giovanni Palla 🙏
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
January 20, 2025 at 8:11 PM
Glad to be part of such an open and collaborative community pushing #SpatialBio forward! Thanks for inviting and hosting us @kevinyamauchi.bsky.social @lucamarconato.bsky.social & Giovanni Palla 🙏
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->
Closing the 2nd #DukeSCIRIP Colloquium, @dukemedschool.bsky.social #SpatialBio talks cont'd... #AnoopPatel of @dukeneurosurgery.bsky.social on #GBM & #Xenium; #ErikaCrosby of @dukesurgery.bsky.social on Xenium & #PDAC; and #JohnHickey of @dukeubme.bsky.social on #SpatialOmics in #BrainNeckCancer 🧬🧠🥼
May 12, 2025 at 10:57 PM
Closing the 2nd #DukeSCIRIP Colloquium, @dukemedschool.bsky.social #SpatialBio talks cont'd... #AnoopPatel of @dukeneurosurgery.bsky.social on #GBM & #Xenium; #ErikaCrosby of @dukesurgery.bsky.social on Xenium & #PDAC; and #JohnHickey of @dukeubme.bsky.social on #SpatialOmics in #BrainNeckCancer 🧬🧠🥼
It's been a minute but I found my way back to a conference; I'll be at AGBT this week representing @stellaromics.bsky.social to lend my experience communicating all things #spatialbio #bioinformatics #techbio #ai ! Looking forward to meeting new folks, please reach out if interested! 🧬🔬
February 22, 2026 at 1:57 PM
It's been a minute but I found my way back to a conference; I'll be at AGBT this week representing @stellaromics.bsky.social to lend my experience communicating all things #spatialbio #bioinformatics #techbio #ai ! Looking forward to meeting new folks, please reach out if interested! 🧬🔬
Amazing experience to share the stage with spatial biology experts @European Society of Spatial Biology (ESSB) and present our work of 3D spatial-Omics to an audience of 550 plus from 26 countries 🤩 Kudos to the founding members of @SpatialBio for putting together such a fantastic event 🎉👏 #3D #Omic
December 14, 2024 at 1:14 PM
Amazing experience to share the stage with spatial biology experts @European Society of Spatial Biology (ESSB) and present our work of 3D spatial-Omics to an audience of 550 plus from 26 countries 🤩 Kudos to the founding members of @SpatialBio for putting together such a fantastic event 🎉👏 #3D #Omic
On my way to Chicago for #AACR25! Hope to see a few of you there. If you can, stop by and check out the joint @standardbiology.bsky.social @visiopharm.bsky.social poster on AI analysis for highplex proteomic images.
www.abstractsonline.com/pp8/#!/20273...
#SpatialBio #IMC #Phenoplex
www.abstractsonline.com/pp8/#!/20273...
#SpatialBio #IMC #Phenoplex
Program Planner
www.abstractsonline.com
April 26, 2025 at 1:49 PM
On my way to Chicago for #AACR25! Hope to see a few of you there. If you can, stop by and check out the joint @standardbiology.bsky.social @visiopharm.bsky.social poster on AI analysis for highplex proteomic images.
www.abstractsonline.com/pp8/#!/20273...
#SpatialBio #IMC #Phenoplex
www.abstractsonline.com/pp8/#!/20273...
#SpatialBio #IMC #Phenoplex
Two standout papers from @johnshopkinssph.bsky.social teams using IMC via the imaging program led by @wonjinho.bsky.social:
🧬 Neutrophils & tumor necrosis (Nature): www.nature.com/articles/s41...
🧬 UNG inhibition in CRC: pubmed.ncbi.nlm.nih.gov/40663394/
#SpatialBio @standardbiology.bsky.social
🧬 Neutrophils & tumor necrosis (Nature): www.nature.com/articles/s41...
🧬 UNG inhibition in CRC: pubmed.ncbi.nlm.nih.gov/40663394/
#SpatialBio @standardbiology.bsky.social
Neutrophils drive vascular occlusion, tumour necrosis and metastasis - Nature
Neutrophils actively induce tumour necrosis, driving vascular occlusion, pleomorphic necrosis and metastasis.
www.nature.com
July 20, 2025 at 2:56 PM
Two standout papers from @johnshopkinssph.bsky.social teams using IMC via the imaging program led by @wonjinho.bsky.social:
🧬 Neutrophils & tumor necrosis (Nature): www.nature.com/articles/s41...
🧬 UNG inhibition in CRC: pubmed.ncbi.nlm.nih.gov/40663394/
#SpatialBio @standardbiology.bsky.social
🧬 Neutrophils & tumor necrosis (Nature): www.nature.com/articles/s41...
🧬 UNG inhibition in CRC: pubmed.ncbi.nlm.nih.gov/40663394/
#SpatialBio @standardbiology.bsky.social
Software available here: github.com/camlab-bioml...
Great collaboration with @hartjackson.bsky.social with support from @sinaihealth.bsky.social @oicr.on.ca @uoft.bsky.social
#spatialbio #singlecell #multiplexedimaging #machinelearning
Great collaboration with @hartjackson.bsky.social with support from @sinaihealth.bsky.social @oicr.on.ca @uoft.bsky.social
#spatialbio #singlecell #multiplexedimaging #machinelearning
GitHub - camlab-bioml/starling: Segmentation error aware clustering for multiplexed imaging
Segmentation error aware clustering for multiplexed imaging - camlab-bioml/starling
github.com
January 6, 2025 at 3:06 PM
Software available here: github.com/camlab-bioml...
Great collaboration with @hartjackson.bsky.social with support from @sinaihealth.bsky.social @oicr.on.ca @uoft.bsky.social
#spatialbio #singlecell #multiplexedimaging #machinelearning
Great collaboration with @hartjackson.bsky.social with support from @sinaihealth.bsky.social @oicr.on.ca @uoft.bsky.social
#spatialbio #singlecell #multiplexedimaging #machinelearning
Hey #genomics / #bioinformatics / #SpatialBio world! Any examples of successfully integrating custom count norm methods into a Seurat pipeline for #singlecell data? I’m trying to introduce cell area-based normalization for spatial data but I keep getting strange errors from RunUMAP/uwot 🧬🖥️
December 10, 2024 at 8:12 PM
Hey #genomics / #bioinformatics / #SpatialBio world! Any examples of successfully integrating custom count norm methods into a Seurat pipeline for #singlecell data? I’m trying to introduce cell area-based normalization for spatial data but I keep getting strange errors from RunUMAP/uwot 🧬🖥️
New from @hartjackson.bsky.social: 104‑plex #IMC on 3 serial PDAC sections, 200+ patients, whole-slide & cellular modes. Spatial proteomics guides LCM + genomics to define tumor–immune–stromal spectra. A tour de force.
biorxiv.org/content/10.1...
@standardbiology.bsky.social #SpatialBio #IMC
biorxiv.org/content/10.1...
@standardbiology.bsky.social #SpatialBio #IMC
Integrated spatial proteomics of human PDAC uncovers an expanded tumour–immune– stroma spectrum with genomic associations
Distinctively, pancreatic ductal adenocarcinoma (PDAC) consists of sparse tumour lesions intertwined with extensive desmoplastic stroma. The complexity of tumour–microenvironment interactions within t...
biorxiv.org
August 23, 2025 at 12:00 PM
New from @hartjackson.bsky.social: 104‑plex #IMC on 3 serial PDAC sections, 200+ patients, whole-slide & cellular modes. Spatial proteomics guides LCM + genomics to define tumor–immune–stromal spectra. A tour de force.
biorxiv.org/content/10.1...
@standardbiology.bsky.social #SpatialBio #IMC
biorxiv.org/content/10.1...
@standardbiology.bsky.social #SpatialBio #IMC
An excellent paper by Joel Eliason, Jared K. Burks, Suhendan Ekmekcioglu et al on characterizing the spatial immune architecture in melanoma using imaging mass cytometry #IMC.
www.frontiersin.org/journals/imm...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialBio #ImagingMassCytometry
www.frontiersin.org/journals/imm...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialBio #ImagingMassCytometry
www.frontiersin.org
May 3, 2025 at 2:48 PM
An excellent paper by Joel Eliason, Jared K. Burks, Suhendan Ekmekcioglu et al on characterizing the spatial immune architecture in melanoma using imaging mass cytometry #IMC.
www.frontiersin.org/journals/imm...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialBio #ImagingMassCytometry
www.frontiersin.org/journals/imm...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialBio #ImagingMassCytometry
I had not heard of DVP until two weeks ago, and now I see it everywhere :-)
Joe Yeong (NUS, don't think he's on Bluesky) is very excited about it. @aruthak.bsky.social #SpatialBio
Joe Yeong (NUS, don't think he's on Bluesky) is very excited about it. @aruthak.bsky.social #SpatialBio
December 8, 2024 at 10:30 PM
I had not heard of DVP until two weeks ago, and now I see it everywhere :-)
Joe Yeong (NUS, don't think he's on Bluesky) is very excited about it. @aruthak.bsky.social #SpatialBio
Joe Yeong (NUS, don't think he's on Bluesky) is very excited about it. @aruthak.bsky.social #SpatialBio
And thank you to #ErikSodeblom of @dukecellbiology.bsky.social for hosting the 2nd installment of #SpatialBio talks!!
Closing the 2nd #DukeSCIRIP Colloquium, @dukemedschool.bsky.social #SpatialBio talks cont'd... #AnoopPatel of @dukeneurosurgery.bsky.social on #GBM & #Xenium; #ErikaCrosby of @dukesurgery.bsky.social on Xenium & #PDAC; and #JohnHickey of @dukeubme.bsky.social on #SpatialOmics in #BrainNeckCancer 🧬🧠🥼
May 12, 2025 at 11:03 PM
And thank you to #ErikSodeblom of @dukecellbiology.bsky.social for hosting the 2nd installment of #SpatialBio talks!!
And an additional thanks to @tatalab-duke.bsky.social for hosting the first #SpatialBio session!! 🧬
For the 1st part of the afternoon
@dukemedschool.bsky.social #SpatialBiology talks #CarolynCoyne of #DukeMolecularGenetics & #Microbiology spoke on #enterovirus in #T1D, #JingXu of #DukeAnesthesiology on #SpatialTranscriptomics in #hDRG, and #ZachReitman of #DukeRadiology on #MidlineGlioma 🧬🥼💻🧠🐀🧪🧫
@dukemedschool.bsky.social #SpatialBiology talks #CarolynCoyne of #DukeMolecularGenetics & #Microbiology spoke on #enterovirus in #T1D, #JingXu of #DukeAnesthesiology on #SpatialTranscriptomics in #hDRG, and #ZachReitman of #DukeRadiology on #MidlineGlioma 🧬🥼💻🧠🐀🧪🧫
May 12, 2025 at 10:28 PM
And an additional thanks to @tatalab-duke.bsky.social for hosting the first #SpatialBio session!! 🧬
Duke #SCIRIP Colloquium on May 12th 👏 Join us for a day of #singlecell, #bioinformatics, #spatialbio, #proteomics and more, with #Duke researchers & external guest speakers! Registration is free (and easy!) - just email DukeSCI@duke.edu 🧬🧠💻🧑🔬 Visit dmpi.duke.edu/duke-single-...
April 30, 2025 at 12:48 PM
Duke #SCIRIP Colloquium on May 12th 👏 Join us for a day of #singlecell, #bioinformatics, #spatialbio, #proteomics and more, with #Duke researchers & external guest speakers! Registration is free (and easy!) - just email DukeSCI@duke.edu 🧬🧠💻🧑🔬 Visit dmpi.duke.edu/duke-single-...
Duke #SCIRIP Colloquium on May 12th 👏 Join us for a day of #singlecell, #bioinformatics, #spatialbio, #proteomics and more, with #Duke researchers & external guest speakers! Registration is free (and easy!) - just email DukeSCI@duke.edu 🧬🧠💻🧑🔬
Visit dmpi.duke.edu/duke-single-... for more information
Visit dmpi.duke.edu/duke-single-... for more information
April 2, 2025 at 12:35 PM
Duke #SCIRIP Colloquium on May 12th 👏 Join us for a day of #singlecell, #bioinformatics, #spatialbio, #proteomics and more, with #Duke researchers & external guest speakers! Registration is free (and easy!) - just email DukeSCI@duke.edu 🧬🧠💻🧑🔬
Visit dmpi.duke.edu/duke-single-... for more information
Visit dmpi.duke.edu/duke-single-... for more information
Nice to see #IMC and #Phenoplex coming together to investigate immune landscapes. Two great tastes that taste great together.
ascopubs.org/doi/abs/10.1...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialProteomics #SpatialBio
ascopubs.org/doi/abs/10.1...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialProteomics #SpatialBio
Immune landscape of sarcoma patients treated with an autologous dendritic cell vaccine.
e23530Background: The role of the sarcoma immune tumor microenvironment (TME) is a critical area of
ongoing research, particularly to understand responses to immunotherapy. We previously
conducted a p...
ascopubs.org
June 5, 2025 at 11:12 AM
Nice to see #IMC and #Phenoplex coming together to investigate immune landscapes. Two great tastes that taste great together.
ascopubs.org/doi/abs/10.1...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialProteomics #SpatialBio
ascopubs.org/doi/abs/10.1...
@standardbiology.bsky.social @visiopharm.bsky.social #SpatialProteomics #SpatialBio
An excellent paper by Daniel W Rosenberg et al using #IMC makes the cover of the issue of AACR Journals Cancer Prevention Research being handed out at #AACR25. Congratulations!
aacrjournals.org/cancerpreven...
#ImagingMassCytometry @standardbiology.bsky.social #SpatialBio
aacrjournals.org/cancerpreven...
#ImagingMassCytometry @standardbiology.bsky.social #SpatialBio
April 29, 2025 at 11:33 AM
An excellent paper by Daniel W Rosenberg et al using #IMC makes the cover of the issue of AACR Journals Cancer Prevention Research being handed out at #AACR25. Congratulations!
aacrjournals.org/cancerpreven...
#ImagingMassCytometry @standardbiology.bsky.social #SpatialBio
aacrjournals.org/cancerpreven...
#ImagingMassCytometry @standardbiology.bsky.social #SpatialBio
I love that the #SpatialBio feed is being used both by the microscopic biology spatial proteomics and spatial transcriptomics people and by the macroscopic biology spatial biodistribution people like crop dynamics or fish distributions across a landscape!
January 15, 2025 at 1:05 PM
I love that the #SpatialBio feed is being used both by the microscopic biology spatial proteomics and spatial transcriptomics people and by the macroscopic biology spatial biodistribution people like crop dynamics or fish distributions across a landscape!
@johnshopkinssph.bsky.social: Another excellent paper from @wonjinho.bsky.social uses #IMC to profile liver immune microenvironments during inflammation, revealing complex immune cell compositions.
www.tandfonline.com/doi/full/10....
@standardbiology.bsky.social #SpatialBio #Spatialproteomics
www.tandfonline.com/doi/full/10....
@standardbiology.bsky.social #SpatialBio #Spatialproteomics
A phase 2 trial of CXCR4 antagonism and PD1 inhibition in metastatic pancreatic adenocarcinoma reveals recruitment of T cells but also immunosuppressive macrophages
Pancreatic ductal adenocarcinoma (PDAC) is characterized by dense stroma and myeloid-rich microenvironment that confer resistance to immunotherapies. Previous studies demonstrated that disrupting t...
www.tandfonline.com
August 19, 2025 at 4:34 PM
@johnshopkinssph.bsky.social: Another excellent paper from @wonjinho.bsky.social uses #IMC to profile liver immune microenvironments during inflammation, revealing complex immune cell compositions.
www.tandfonline.com/doi/full/10....
@standardbiology.bsky.social #SpatialBio #Spatialproteomics
www.tandfonline.com/doi/full/10....
@standardbiology.bsky.social #SpatialBio #Spatialproteomics
New from @usc.edu : Peter Kuhn & James Hicks use CyTOF + IMC to profile rare immune-like CTCs (CD45⁺/CK⁺) in metastatic breast cancer. A novel hybrid cell type with clinical potential.
www.nature.com/articles/s43...
#SpatialBio @standardbiology.bsky.social #ImagingMassCytometry
www.nature.com/articles/s43...
#SpatialBio @standardbiology.bsky.social #ImagingMassCytometry
Simultaneous expression of epithelial and immune cell markers in circulating tumor cells identified in patients with stage 4 breast cancer - Communications Medicine
Higa et al. analyzed circulating cells expressing cancer and immune cell markers in breast cancer patients. Based on genomic and protein expression profiling, they show that the cells were unlike prev...
www.nature.com
July 27, 2025 at 3:54 PM
New from @usc.edu : Peter Kuhn & James Hicks use CyTOF + IMC to profile rare immune-like CTCs (CD45⁺/CK⁺) in metastatic breast cancer. A novel hybrid cell type with clinical potential.
www.nature.com/articles/s43...
#SpatialBio @standardbiology.bsky.social #ImagingMassCytometry
www.nature.com/articles/s43...
#SpatialBio @standardbiology.bsky.social #ImagingMassCytometry
Bodenmiller et al. showing that the consistency and quality of @standardbiology.bsky.social CyTOF and IMC technologies can provide immune profiling insights to clinicians —highlighting their real-world impact on patient management.
onlinelibrary.wiley.com/doi/10.1002/...
#SpatialBio
onlinelibrary.wiley.com/doi/10.1002/...
#SpatialBio
May 25, 2025 at 1:19 PM
Bodenmiller et al. showing that the consistency and quality of @standardbiology.bsky.social CyTOF and IMC technologies can provide immune profiling insights to clinicians —highlighting their real-world impact on patient management.
onlinelibrary.wiley.com/doi/10.1002/...
#SpatialBio
onlinelibrary.wiley.com/doi/10.1002/...
#SpatialBio
2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices.
www.biorxiv.org/content/10.1...
A much-needed paper for #SpatialBio (plus a fabulous title). Cells in tissue sections are highly overlapping (even in a 5 um section). Just being aware of it in regular 2D analysis is good.
www.biorxiv.org/content/10.1...
A much-needed paper for #SpatialBio (plus a fabulous title). Cells in tissue sections are highly overlapping (even in a 5 um section). Just being aware of it in regular 2D analysis is good.
2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices
Imaging-based spatially resolved transcriptomics can localise transcripts within cells in 3D. Cell egmentation precedes assignment of transcripts to cells and nnotation of cell function. However, cell...
www.biorxiv.org
January 16, 2025 at 10:38 AM
2D, or not 2D? Investigating Vertical Signal Integrity of Tissue Slices.
www.biorxiv.org/content/10.1...
A much-needed paper for #SpatialBio (plus a fabulous title). Cells in tissue sections are highly overlapping (even in a 5 um section). Just being aware of it in regular 2D analysis is good.
www.biorxiv.org/content/10.1...
A much-needed paper for #SpatialBio (plus a fabulous title). Cells in tissue sections are highly overlapping (even in a 5 um section). Just being aware of it in regular 2D analysis is good.