Denis Schapiro
@denisschapiro.bsky.social
Group leader @schapirolab.bsky.social at the Heidelberg University Hospital focusing on #HighlyMultiplexedImaging and #spatialomics #spatialbiology technologies and analysis. President of the European Society for Spatial Biology e.V. (ESSB)
First new histCAT release in 5 years! Please help to shape the next updates by participating in our very short survey!
We're excited to share that we have released histoCAT_1.78.3 🐈
For the next major update, we would like to learn more about your individual use cases and current needs.
Please fill out this survey to let us know your opinions:
tinyurl.com/histoCAT
#spatialomics #spatialproteomics
For the next major update, we would like to learn more about your individual use cases and current needs.
Please fill out this survey to let us know your opinions:
tinyurl.com/histoCAT
#spatialomics #spatialproteomics
histoCAT user survey 2025
Dear histoCAT users,
We have now release histoCAT_1.78.3, which now works on updated Windows and MacOS systems and leverages MATLAB2022b.
For the next major update, we would like to learn more about...
tinyurl.com
October 29, 2025 at 5:40 PM
First new histCAT release in 5 years! Please help to shape the next updates by participating in our very short survey!
Reposted by Denis Schapiro
We're excited to be at GloBIAS 2025 in Kobe Japan! Come say hi to @arojhada.bsky.social (presenting cell phenotyping) and @miguelib.bsky.social (presenting micronuclAI)
October 29, 2025 at 2:57 PM
We're excited to be at GloBIAS 2025 in Kobe Japan! Come say hi to @arojhada.bsky.social (presenting cell phenotyping) and @miguelib.bsky.social (presenting micronuclAI)
Reposted by Denis Schapiro
Last week our lab came together for our annual lab retreat, kindly hosted by @hlsalliance.bsky.social! We exchanged ideas about our research, spatial omics, and took part in some fun (albeit slightly competitive) activities.
October 29, 2025 at 3:45 PM
Last week our lab came together for our annual lab retreat, kindly hosted by @hlsalliance.bsky.social! We exchanged ideas about our research, spatial omics, and took part in some fun (albeit slightly competitive) activities.
Reposted by Denis Schapiro
Happy to co-chair the #Pathology Working Group of the European Society for Spatial Biology (ESSB) e.V. #ESSB with Francesca Maria Bosisio, MD, PhD and Christian Matek, MD!
Please join the group and let us promote science together!
Link to join: docs.google.com/forms/d/e/1F...
Please join the group and let us promote science together!
Link to join: docs.google.com/forms/d/e/1F...
ESSB Working Group survey
Please enter your information to join an ESSB working group
docs.google.com
October 16, 2025 at 2:39 PM
Happy to co-chair the #Pathology Working Group of the European Society for Spatial Biology (ESSB) e.V. #ESSB with Francesca Maria Bosisio, MD, PhD and Christian Matek, MD!
Please join the group and let us promote science together!
Link to join: docs.google.com/forms/d/e/1F...
Please join the group and let us promote science together!
Link to join: docs.google.com/forms/d/e/1F...
Reposted by Denis Schapiro
Are you at #EMBLSpatialBiology #ESSB2025? Catch our posters this evening:
- Nils Englert, Poster 83
- @arojhada.bsky.social, Poster 97
- @loggas.bsky.social, Poster 185
- @jawadalaaedeen.bsky.social, Poster 187
- Nils Englert, Poster 83
- @arojhada.bsky.social, Poster 97
- @loggas.bsky.social, Poster 185
- @jawadalaaedeen.bsky.social, Poster 187
October 15, 2025 at 2:01 PM
Are you at #EMBLSpatialBiology #ESSB2025? Catch our posters this evening:
- Nils Englert, Poster 83
- @arojhada.bsky.social, Poster 97
- @loggas.bsky.social, Poster 185
- @jawadalaaedeen.bsky.social, Poster 187
- Nils Englert, Poster 83
- @arojhada.bsky.social, Poster 97
- @loggas.bsky.social, Poster 185
- @jawadalaaedeen.bsky.social, Poster 187
Reposted by Denis Schapiro
Excited to be at #EMBLSpatialBiology #ESSB2025 this week and present our new 3D imaging and analysis pipeline ‘LeGO-3D’
October 15, 2025 at 1:36 PM
Excited to be at #EMBLSpatialBiology #ESSB2025 this week and present our new 3D imaging and analysis pipeline ‘LeGO-3D’
Reposted by Denis Schapiro
Reposted by Denis Schapiro
Reposted by Denis Schapiro
We’re excited to be at @embl.org this week for Spatial Biology: the melting pot. We’re looking forward to hearing about some awesome science 🔬 #EMBLSpatialBiology
October 14, 2025 at 9:52 AM
We’re excited to be at @embl.org this week for Spatial Biology: the melting pot. We’re looking forward to hearing about some awesome science 🔬 #EMBLSpatialBiology
Reposted by Denis Schapiro
On location for a short video about the innovation campus Heidelberg/Mannheim @embl.org and @dkfz.bsky.social
Thanks to @denisschapiro.bsky.social and Nina Papavasiliou for sharing your research and the precious time of your students and postdocs for our video team.
#sciencecommunication
Thanks to @denisschapiro.bsky.social and Nina Papavasiliou for sharing your research and the precious time of your students and postdocs for our video team.
#sciencecommunication
#innovationcampus #computationalbiomedicine #spatialomics #immunology #genesquencing #genomics | Health + Life Science Alliance
📹On assignment for a short video about the innovation campus models in Baden-Württemberg. Here in Heidelberg we are the health + live science #InnovationCampus, aka Health + Life Science Alliance.
🎥R...
www.linkedin.com
October 10, 2025 at 8:37 AM
On location for a short video about the innovation campus Heidelberg/Mannheim @embl.org and @dkfz.bsky.social
Thanks to @denisschapiro.bsky.social and Nina Papavasiliou for sharing your research and the precious time of your students and postdocs for our video team.
#sciencecommunication
Thanks to @denisschapiro.bsky.social and Nina Papavasiliou for sharing your research and the precious time of your students and postdocs for our video team.
#sciencecommunication
Congratulations to @loggas.bsky.social, Ingrid Roseth, Therese Standal, and all co-authors!
In our latest work, we leveraged @standardbiology.bsky.social Imaging Mass Cytometry to analyze bone marrow biopsies from multiple myeloma and precursor disease patients.
www.biorxiv.org/content/10.1...
In our latest work, we leveraged @standardbiology.bsky.social Imaging Mass Cytometry to analyze bone marrow biopsies from multiple myeloma and precursor disease patients.
www.biorxiv.org/content/10.1...
September 14, 2025 at 9:50 AM
Congratulations to @loggas.bsky.social, Ingrid Roseth, Therese Standal, and all co-authors!
In our latest work, we leveraged @standardbiology.bsky.social Imaging Mass Cytometry to analyze bone marrow biopsies from multiple myeloma and precursor disease patients.
www.biorxiv.org/content/10.1...
In our latest work, we leveraged @standardbiology.bsky.social Imaging Mass Cytometry to analyze bone marrow biopsies from multiple myeloma and precursor disease patients.
www.biorxiv.org/content/10.1...
Reposted by Denis Schapiro
I am excited to share my first work in @schapirolab.bsky.social on Multiple Myeloma (MM) in collaboration with the Standal Lab from NTNU Norway. We use Imaging Mass Cytometry (IMC) on bone marrow biopsies from MM and precursor patients (details below): www.biorxiv.org/content/10.1...
Highly multiplexed imaging recovers immune and metabolic niches in multiple myeloma associated with disease progression and bone involvement
Multiple myeloma (MM) is a cancer arising from genetically aberrant plasma cells (PCs) that remain dependent on the bone marrow (BM) microenvironment for disease establishment and progression. Here, w...
www.biorxiv.org
September 13, 2025 at 8:25 AM
I am excited to share my first work in @schapirolab.bsky.social on Multiple Myeloma (MM) in collaboration with the Standal Lab from NTNU Norway. We use Imaging Mass Cytometry (IMC) on bone marrow biopsies from MM and precursor patients (details below): www.biorxiv.org/content/10.1...
Reposted by Denis Schapiro
Register by 2 Sep and join us in Heidelberg for #EMBLSpatialBiology 👉 https://s.embl.org/spb25-01-bs
Co-organised with #ESSB, this conference will bring together top scientists and young investigators for 4 days of cutting-edge science and networking ✨
📅 14–17 Oct | 📍EMBL Heidelberg and Virtual
Co-organised with #ESSB, this conference will bring together top scientists and young investigators for 4 days of cutting-edge science and networking ✨
📅 14–17 Oct | 📍EMBL Heidelberg and Virtual
August 25, 2025 at 11:00 AM
Register by 2 Sep and join us in Heidelberg for #EMBLSpatialBiology 👉 https://s.embl.org/spb25-01-bs
Co-organised with #ESSB, this conference will bring together top scientists and young investigators for 4 days of cutting-edge science and networking ✨
📅 14–17 Oct | 📍EMBL Heidelberg and Virtual
Co-organised with #ESSB, this conference will bring together top scientists and young investigators for 4 days of cutting-edge science and networking ✨
📅 14–17 Oct | 📍EMBL Heidelberg and Virtual
Reposted by Denis Schapiro
Big congratulations to @sabrinalewis.bsky.social on being awarded 2nd place for her talk at the Heidelberg Postdoc Symposium 🥳🎉
July 1, 2025 at 7:31 AM
Big congratulations to @sabrinalewis.bsky.social on being awarded 2nd place for her talk at the Heidelberg Postdoc Symposium 🥳🎉
Reposted by Denis Schapiro
We're excited to be at the Kick Off Heidelberg Spatial-Omics Lunch Seminar Series with our very own @chiaraschiller.bsky.social presenting some of her PhD work!
July 1, 2025 at 9:52 AM
We're excited to be at the Kick Off Heidelberg Spatial-Omics Lunch Seminar Series with our very own @chiaraschiller.bsky.social presenting some of her PhD work!
Reposted by Denis Schapiro
Don't forget to submit your abstract for #EMBLSpatialBiology by 8 July 👉 https://s.embl.org/spb25-01-bl
📅 14 – 17 Oct 2025 | 📍 EMBL Heidelberg and Virtual
✨ Top 100 abstracts will get a €350 reg fee subsidy from ESSB! To be eligible, enter your membership number when submitting ✨
#ESSB2025
📅 14 – 17 Oct 2025 | 📍 EMBL Heidelberg and Virtual
✨ Top 100 abstracts will get a €350 reg fee subsidy from ESSB! To be eligible, enter your membership number when submitting ✨
#ESSB2025
July 2, 2025 at 9:10 AM
Don't forget to submit your abstract for #EMBLSpatialBiology by 8 July 👉 https://s.embl.org/spb25-01-bl
📅 14 – 17 Oct 2025 | 📍 EMBL Heidelberg and Virtual
✨ Top 100 abstracts will get a €350 reg fee subsidy from ESSB! To be eligible, enter your membership number when submitting ✨
#ESSB2025
📅 14 – 17 Oct 2025 | 📍 EMBL Heidelberg and Virtual
✨ Top 100 abstracts will get a €350 reg fee subsidy from ESSB! To be eligible, enter your membership number when submitting ✨
#ESSB2025
Reposted by Denis Schapiro
Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.
We are looking for additional Group Leaders to join the growing computational biology community at VIB.
If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!
https://vib.ai/en/opportunities#/job-description/110906
If you are excited about combining AI and machine learning with fundamental biology, we would love to hear from you!
https://vib.ai/en/opportunities#/job-description/110906
April 26, 2025 at 11:00 AM
Our new call for VIB.AI group leaders is online! Junior and senior positions available to develop innovative ML methods in biology. With professorship at CS or Medical Faculty. Deadline 14th June. DM for more info.
Reposted by Denis Schapiro
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Ever wondered how to best quantify cell-cell neighbor preferences in tissues?
We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨
Read more: doi.org/10.1101/2025...
Ever wondered how to best quantify cell-cell neighbor preferences in tissues?
We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨
Read more: doi.org/10.1101/2025...
April 15, 2025 at 3:50 PM
1/
Ever wondered how to best quantify cell-cell neighbor preferences in tissues?
We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨
Read more: doi.org/10.1101/2025...
Ever wondered how to best quantify cell-cell neighbor preferences in tissues?
We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨
Read more: doi.org/10.1101/2025...
Reposted by Denis Schapiro
Laser tag lab edition #happyholidays 🎄🎁🎅🏼
December 19, 2024 at 9:16 AM
Laser tag lab edition #happyholidays 🎄🎁🎅🏼
Reposted by Denis Schapiro
We are searching for a highly motivated and talented computational postdoc with an interest in translational spatial omics to join our team in Heidelberg. Apply now!
karriere.klinikum.uni-heidelberg.de/index.php?ac...
karriere.klinikum.uni-heidelberg.de/index.php?ac...
Postdoc – Computational Tissue Analysis (m/f/d)
karriere.klinikum.uni-heidelberg.de
January 30, 2025 at 10:23 AM
We are searching for a highly motivated and talented computational postdoc with an interest in translational spatial omics to join our team in Heidelberg. Apply now!
karriere.klinikum.uni-heidelberg.de/index.php?ac...
karriere.klinikum.uni-heidelberg.de/index.php?ac...
Reposted by Denis Schapiro
✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
2024 SpatialData Workshop – Bioconductor community blog
R/Bioconductor developers participating in the 1st scverse SpatialData Workshop
buff.ly
January 9, 2025 at 12:11 PM
✍️ New Bioconductor blog post on the SpatialData hackathon and workshop, organized by https://buff.ly/4j1UidT with Bioconductor participation. Check it out: https://buff.ly/4fM1qrH
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
Thanks @arturmansl.bsky.social !
#Bioconductor #SpatialData #scverse #Bioinformatics #OpenScience #RStats
Reposted by Denis Schapiro
Interested in our research? We've created a starter pack so you can now follow our current lab members and alumni. Be sure to check it out! 🥳
December 18, 2024 at 5:21 PM
Interested in our research? We've created a starter pack so you can now follow our current lab members and alumni. Be sure to check it out! 🥳
Reposted by Denis Schapiro
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
Reposted by Denis Schapiro
We are excited to be in Berlin for the Inaugural Conference of the European Society of Spatial Biology (#ESSB). We sure to checkout our posters tonight! 🧵
December 12, 2024 at 1:00 PM
We are excited to be in Berlin for the Inaugural Conference of the European Society of Spatial Biology (#ESSB). We sure to checkout our posters tonight! 🧵