Lukas Hatscher
@loggas.bsky.social
MD, PhD candidate in Institute of Computational Biomedicine - AG Schapiro, Interested in quantitative tissue analysis 💻
www.github.com/LukasHats
www.github.com/LukasHats
Yes that’s exactly what I meant, I think it’s unique ;)
October 14, 2025 at 3:34 PM
Yes that’s exactly what I meant, I think it’s unique ;)
Entrance of this helix? Or should we meet at your poster?
October 14, 2025 at 3:21 PM
Entrance of this helix? Or should we meet at your poster?
Sounds good, how about tomorrows coffee break at 10:00?
October 14, 2025 at 1:30 PM
Sounds good, how about tomorrows coffee break at 10:00?
Would love to hear and talk about muspan and its integration into existing single cell data formats. When are you presenting your poster?
October 14, 2025 at 12:44 PM
Would love to hear and talk about muspan and its integration into existing single cell data formats. When are you presenting your poster?
Well this also depends on how we define the term hallucinations and the output an LLM is generating. I think it’s more terminology problem here. Which does not change the fact that a lot of people do not understand what an LLM is doing and how to proper interpret the outputs.
October 12, 2025 at 4:47 PM
Well this also depends on how we define the term hallucinations and the output an LLM is generating. I think it’s more terminology problem here. Which does not change the fact that a lot of people do not understand what an LLM is doing and how to proper interpret the outputs.
2 decades of self-injecting venom and hundreds of snake bites
September 18, 2025 at 6:48 AM
2 decades of self-injecting venom and hundreds of snake bites
And last but not least thanks a lot to @denisschapiro.bsky.social who established the collaboration and mentored me.
September 13, 2025 at 8:25 AM
And last but not least thanks a lot to @denisschapiro.bsky.social who established the collaboration and mentored me.
I am happy to have worked with my collaborators from NTNU (Ingrid and Therese) on this amazing project, as well as @chiaraschiller.bsky.social who developed COZi (www.biorxiv.org/content/10.1...). shout out to CellCharter developer @marcovarrone.bsky.social for his amazing method(and collaboration)
September 13, 2025 at 8:25 AM
I am happy to have worked with my collaborators from NTNU (Ingrid and Therese) on this amazing project, as well as @chiaraschiller.bsky.social who developed COZi (www.biorxiv.org/content/10.1...). shout out to CellCharter developer @marcovarrone.bsky.social for his amazing method(and collaboration)
The spatial analysis highlight is that we uncover this signal using 2 different spatial resolutions (cell and neighborhood level) and 2 independent methods (COZI and CellCharter). We hope that this will open up new research paths in Myeloma focusing on these cell interactions.
September 13, 2025 at 8:25 AM
The spatial analysis highlight is that we uncover this signal using 2 different spatial resolutions (cell and neighborhood level) and 2 independent methods (COZI and CellCharter). We hope that this will open up new research paths in Myeloma focusing on these cell interactions.
To our very surprise we find that increased “interaction” of PCs and a variety of immune cells, especially CD4+Tcells, is associated to increased risk of progression, which is contrary to many findings in other tumors where tumor immune interaction seem to generally be beneficial for patients.
September 13, 2025 at 8:25 AM
To our very surprise we find that increased “interaction” of PCs and a variety of immune cells, especially CD4+Tcells, is associated to increased risk of progression, which is contrary to many findings in other tumors where tumor immune interaction seem to generally be beneficial for patients.
Lastly we apply cell neighbor preference analysis with COZI (developed by @chiaraschiller.bsky.social ) and CellCharter’s neighborhood enrichment method and connect these findings to associated clinical metadata:
September 13, 2025 at 8:25 AM
Lastly we apply cell neighbor preference analysis with COZI (developed by @chiaraschiller.bsky.social ) and CellCharter’s neighborhood enrichment method and connect these findings to associated clinical metadata:
This questions the common belief that malignant PCs solely rely on glycolytic metabolism for cancer progression and niche establishment.
We further show that the aggregate size of the PC_OXPHOS neighborhood negatively correlates with immune infiltration
We further show that the aggregate size of the PC_OXPHOS neighborhood negatively correlates with immune infiltration
September 13, 2025 at 8:25 AM
This questions the common belief that malignant PCs solely rely on glycolytic metabolism for cancer progression and niche establishment.
We further show that the aggregate size of the PC_OXPHOS neighborhood negatively correlates with immune infiltration
We further show that the aggregate size of the PC_OXPHOS neighborhood negatively correlates with immune infiltration
This led to the finding of 2 different malignant PC neighborhoods: 1) PC_OXPHOS characterized by huge vascularized aggregates of PCs with increased oxidative phosphorylation and 2)PC_MYELOID, where PCs show glycolytic metabolism and are loosely scattered around including myeloid cells.
September 13, 2025 at 8:25 AM
This led to the finding of 2 different malignant PC neighborhoods: 1) PC_OXPHOS characterized by huge vascularized aggregates of PCs with increased oxidative phosphorylation and 2)PC_MYELOID, where PCs show glycolytic metabolism and are loosely scattered around including myeloid cells.
As our antibody panel focused on functional markers, we used a novel neighborhood algorithm CellCharter ( @marcovarrone.bsky.social ) to structure the tissue into neighborhoods driven by not only cell types but also functional state.
September 13, 2025 at 8:25 AM
As our antibody panel focused on functional markers, we used a novel neighborhood algorithm CellCharter ( @marcovarrone.bsky.social ) to structure the tissue into neighborhoods driven by not only cell types but also functional state.
We show that:
MM patients with bone disease (a frequent comorbidity) show an increased abundance of malignant Plasma Cells (PCs) in the vicinity of Osteoclasts and that PCs display a bone distance dependent expression of factors involved in bone degradation (IL32, HIF1A)
MM patients with bone disease (a frequent comorbidity) show an increased abundance of malignant Plasma Cells (PCs) in the vicinity of Osteoclasts and that PCs display a bone distance dependent expression of factors involved in bone degradation (IL32, HIF1A)
September 13, 2025 at 8:25 AM
We show that:
MM patients with bone disease (a frequent comorbidity) show an increased abundance of malignant Plasma Cells (PCs) in the vicinity of Osteoclasts and that PCs display a bone distance dependent expression of factors involved in bone degradation (IL32, HIF1A)
MM patients with bone disease (a frequent comorbidity) show an increased abundance of malignant Plasma Cells (PCs) in the vicinity of Osteoclasts and that PCs display a bone distance dependent expression of factors involved in bone degradation (IL32, HIF1A)
We apply IMC to biopsies from 65 MM patients, 6 SMM and 5 MGUS patients with an antibody panel focusing on immune, bone cells and metabolism. The dataset consists of roughly 1 million labeled cells including distance to the next bone surface for every image (soon on zenodo 10.5281/zenodo.17093203)
September 13, 2025 at 8:25 AM
We apply IMC to biopsies from 65 MM patients, 6 SMM and 5 MGUS patients with an antibody panel focusing on immune, bone cells and metabolism. The dataset consists of roughly 1 million labeled cells including distance to the next bone surface for every image (soon on zenodo 10.5281/zenodo.17093203)
Thanks @marcovarrone.bsky.social it was a pleasure, learnt a lot from the way you built your codebase. We have a paper coming up with a lot of cellcharter in there! Amazing method :)
July 16, 2025 at 6:56 PM
Thanks @marcovarrone.bsky.social it was a pleasure, learnt a lot from the way you built your codebase. We have a paper coming up with a lot of cellcharter in there! Amazing method :)
Reposted by Lukas Hatscher
And for anyone who has considered contributing to an open source package: don't be scared to propose changes.
Even if it's not a complete and perfect solution, whoever is maintaining the package will help you in get to the right solution and they will be incredibly grateful.
Even if it's not a complete and perfect solution, whoever is maintaining the package will help you in get to the right solution and they will be incredibly grateful.
July 15, 2025 at 1:31 PM
And for anyone who has considered contributing to an open source package: don't be scared to propose changes.
Even if it's not a complete and perfect solution, whoever is maintaining the package will help you in get to the right solution and they will be incredibly grateful.
Even if it's not a complete and perfect solution, whoever is maintaining the package will help you in get to the right solution and they will be incredibly grateful.
Reposted by Lukas Hatscher
For people like me who don't have a team behind a package like CellCharter, contributions like these mean a lot. So thank you Lukas :)
And congratulations, it's not always easy to jump into an existing codebase and propose changes.
And congratulations, it's not always easy to jump into an existing codebase and propose changes.
July 15, 2025 at 1:31 PM
For people like me who don't have a team behind a package like CellCharter, contributions like these mean a lot. So thank you Lukas :)
And congratulations, it's not always easy to jump into an existing codebase and propose changes.
And congratulations, it's not always easy to jump into an existing codebase and propose changes.