Sign in

Lukas Hatscher

@loggas.bsky.social
82 followers 126 following 30 posts

MD, PhD candidate in Institute of Computational Biomedicine - AG Schapiro, Interested in quantitative tissue analysis 💻 www.github.com/LukasHats

PostsRepliesMedia
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 16/02/2026
Happy (belated) Valentine's Day from our lab to yours 💕 Image credit: @loggas.bsky.social and Lisa Künstler
031
Reposted by Lukas Hatscher
Wissenschaft.Kunst.BW @handle.invalid · 24/11/2025
🔬🏥 Gesundheitsforschung für die Menschen im InnoLÄND! In der Health + Life Science Alliance Heidelberg Mannheim wird zu zentralen Gesundheitsfragen geforscht. Mit der Innovationscampus-Förderung ermöglichen wir Grundlagenforschung mit Potenzial für biomedizinische Durchbrüche. 🔗 youtu.be/LZN-Sx9wfVQ
youtu.be
THE InnoLÄND: Innovationscampus Health & Life Science Alliance Heidelberg Mannheim
YouTube video by Ministerium für Wissenschaft, Forschung und Kunst
054
Reposted by Lukas Hatscher
Marco Varrone @marcovarrone.bsky.social · 19/11/2025
I collected all of what I could find about the upcoming Illumina Spatial Transcriptomics technology, with some predictions about costs and sensitivity compared to 10x Genomics Visium HD www.batcheffect.com/p/the-giant-...
batcheffect.com
The giant wakes up: Illumina goes spatial
Predictions on the upcoming Illumina spatial transcriptomics technology
096
Reposted by Lukas Hatscher
Sabrina Lewis @sabrinalewis.bsky.social · 31/10/2025
Introducing Count COMET 🧛🧛‍♀️ Happy Halloween! 🎃
062
Reposted by Lukas Hatscher
Gregor Sturm @grst.bsky.social · 13/08/2025
Our benchmark + guidelines for atlas-level differential gene expression of single cells is online: academic.oup.com/bib/article/... Bottom line: Use pseudobulk + DESeq2 in simple and pseudobulk + DREAM in more complex settings. Collab w/ @leonhafner.bsky.social @itisalist.bsky.social
1156
Lukas Hatscher @loggas.bsky.social · 18/09/2025
This guy really dedicated his life to science: www.sciencedirect.com/science/arti... www.science.org/content/arti...
sciencedirect.com
Snake venom protection by a cocktail of varespladib and broadly neutralizing human antibodies
Snake envenomation is a neglected tropical disease, with 600 species causing over 100,000 deaths and 300,000 permanent disabilities in humans annually…
110
Lukas Hatscher @loggas.bsky.social · 13/09/2025
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...
biorxiv.org
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...
2125
Reposted by Lukas Hatscher
Ming Tommy Tang @tommytang.bsky.social · 03/08/2025
Nature Method: Temporal and spatial omics technologies for 4D profiling www.nature.com/articles/s4...
nature.com
Temporal and spatial omics technologies for 4D profiling
Nature Methods - This Perspective explores advances and future directions in spatiotemporal omics methods for four-dimensional profiling.
0103
Reposted by Lukas Hatscher
Marco Varrone @marcovarrone.bsky.social · 15/07/2025
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.
001
Reposted by Lukas Hatscher
Marco Varrone @marcovarrone.bsky.social · 15/07/2025
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.
111
Reposted by Lukas Hatscher
Marco Varrone @marcovarrone.bsky.social · 15/07/2025
RCS measures how large a cell niche (aka spatial domain aka spatial cluster) is compared to what would be normally expected. This pushed me to completely rewrite the system for generating and plotting boundaries for cell niches. The new system is now more efficient, consistent, and visually clear.
111
Reposted by Lukas Hatscher
Marco Varrone @marcovarrone.bsky.social · 15/07/2025
A few weeks ago, we released CellCharter v0.3.5. Among some bug fixes, we received our first contribution from an external contributor: @loggas.bsky.social ! He designed a new metric called Relative Component Size (RCS).
github.com
GitHub - CSOgroup/cellcharter: A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data. - CSOgroup/cellcharter
251
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 04/07/2025
Spotted: @loggas.bsky.social and @arojhada.bsky.social teaching phenotyping to our Advanced Systems Biology students
081
Reposted by Lukas Hatscher
Rob Patro @robp.bsky.social · 25/06/2025
🖥️🧬 I used to have to tell my students not to bother with differential expression analysis in a language outside of R. Recently, with pydeseq2 and now InMoose, this is changing! bmcbioinformatics.biomedcentral.com/articles/10....
bmcbioinformatics.biomedcentral.com
Differential expression analysis with inmoose, the integrated multi-omic open-source environment in Python - BMC Bioinformatics
Background Differential gene expression analysis is a prominent technique for the analysis of biomolecular data to identify genetic features associated with phenotypes. Limma—for microarray data –, an...
094
Reposted by Lukas Hatscher
Erik van Nimwegen @erikvannimwegen.bsky.social · 09/05/2025
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social. I'm so excited about this! www.biorxiv.org/content/10.1...
biorxiv.org
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
9335108
Reposted by Lukas Hatscher
Slavov Laboratory @slavovlab.bsky.social · 09/05/2025
An alternative to tSNE & UMAP for more accurate data visualization: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data. The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.
36614
Reposted by Lukas Hatscher
Joshua Bull @joshuabull.bsky.social · 01/05/2025
In addition to the two #SpatialBiology posts in the thread below, we're now also advertising for a Research Software Engineer #RSE to help us take #MuSpAn to the next level - come and join us! my.corehr.com/pls/uoxrecru... #academic #jobs #softwaredeveloper #compsci
my.corehr.com
Job Details
034
Reposted by Lukas Hatscher
napari @napari.fosstodon.org.ap.brid.gy · 01/05/2025
And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵
142
Reposted by Lukas Hatscher
Nextflow @nextflow.io · 17/04/2025
Big updates for the Nextflow @vscode.dev extension! 🚀 🔍 Workflow view – Visualize logical structure of pipelines ⚙️ Process view – See all processes in one place 🌐 Seqera view – Manage connected CEs directly in the IDE 📚 Resources view – Quickly access Copilot, AI tools & training
1125
Reposted by Lukas Hatscher
Cell Press @cellpress.bsky.social · 02/04/2025
Miso made in space tastes nuttier! Researchers successfully make miso at the #InternationalSpaceStation, confirming that making fermented foods in space is possible. www.cell.com/iscience/ful... @medialab.bsky.social Maggie Coblentz @novo-nordisk.bsky.social Joshua D. Evans @cp-cell.bsky.social
Sampling the space miso CREDIT Maggie CoblentzSampling three misos after fermentation CREDIT Maggie Coblentz
053
Reposted by Lukas Hatscher
Leeat Keren @leeat-keren.bsky.social · 26/03/2025
Super excited to finally see this published! Our new method to use combinatorial staining and deep learning to push the multiplexing boundaries of spatial proteomics!
43017
Reposted by Lukas Hatscher
Itai Yanai @itaiyanai.bsky.social · 07/03/2025
Science is an investment that pays enormous dividends. So if you’re business-minded, it’s an offer you can’t refuse! Here's my full speech from the Stand Up For Science rally in DC today: www.youtube.com/watch?v=eemj...
428461
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 07/03/2025
🧵 We are excited to share our new paper, showcasing micronuclAI, which leverages #AI and #ComputerVision to detect #chromosomal_instability #CIN #micronuclei Congratulations to @miguelib.bsky.social and Lindsay Caprio for leading this project.
1104
Reposted by Lukas Hatscher
Seth Thomas Scanlon @immunoeditor.bsky.social · 07/03/2025
The March issue is out! This week: TOX-inducible-KO 🐁show how #TOX maintains #exhausted CD8 #Tcell epigenetic fate; visualizing temporal & spatial #STING expression; & UVB-driven #mitochondrial Z-🧬complexed w ZBP1 fuels #autoimmune #photosensitivity via cGAS-STING! science.org/toc/sciimmunol/10/105
This month’s cover features a keratinocyte mitochondrion damaged by UVB radiation, which then releases reactive oxygen species (red spheres) and Z-DNA complexed with ZBP1 into the cytoplasm. (Credit: A. Fisher/Science Immunology)
0395
Reposted by Lukas Hatscher
Nature @nature.com · 06/03/2025
In an unprecedented move, the US National Institutes of Health has begun mass terminations of research grants that fund active scientific projects because they no longer meet “agency priorities”. go.nature.com/4bpG2It
go.nature.com
Exclusive: NIH to terminate hundreds of active research grants
Studies that touch on LGBT+ health, gender identity and DEI in the biomedical workforce could be terminated, according to documents obtained by Nature.
20342276
Reposted by Lukas Hatscher
Sabrina Lewis @sabrinalewis.bsky.social · 06/03/2025
One week to go!
001
Lukas Hatscher @loggas.bsky.social · 27/02/2025
Does anyone have a good universal membrane marker besides NaKATPase and CD98, that ideally stains epithelium/cancer similarly strong as stroma/immune cells? Antibody will be used for spatial proteomics (cyclic IF), goal is a good whole cell segmentation downstream
031
Reposted by Lukas Hatscher
Stephen Turner @stephenturner.us · 27/02/2025
Gemini Code Assist now free: blog.google/technology/d... VSCode: marketplace.visualstudio.com/items?itemNa... Positron: open-vsx.org/extension/Go... #Rstats
1278
Reposted by Lukas Hatscher
Nature Biotechnology @natbiotech.nature.com · 19/02/2025
Society, patients and clinicians welcome a much-needed non-opioid pain medication. Vertex’s first-in-class analgesic Journavx could soon be followed by a new generation of addiction-free pain drugs acting at NaV1.8 sodium channels www.nature.com/articles/s41...
nature.com
Vertex’s opioid-free drug for acute pain wins FDA approval - Nature Biotechnology
Society, patients and clinicians welcome a much-needed non-opioid pain medication. Vertex’s first-in-class analgesic Journavx could soon be followed by a new generation of addiction-free pain drugs ac...
0103
Reposted by Lukas Hatscher
Julio Saez-Rodriguez @juliosaezrod.bsky.social · 11/02/2025
Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com
Postdoctoral fellow - Saez-Rodriguez Group
Your group Saez-Rodriguez Research Group Your supervisor Julio Saez-Rodriguez Your role As a postdoctoral fellow in the Saez Rodriguez group, you will develop and apply computational methods and tools...
05846
Reposted by Lukas Hatscher
Heidelberg University Postdoc Network @heidelbergpostdoc.bsky.social · 11/02/2025
Are you a postdoc at @uniheidelberg.bsky.social? Don't forget to sign up!
heidelbergunipostd.wixsite.com
Kick off networking event (free)
Mar 13, 2025 at 5:00 PM – 8:00 PM
022
Reposted by Lukas Hatscher
Matthew Bernstein @matthew-bernstein.bsky.social · 26/01/2025
Much of my understanding came from his amazing video by 3Blue1Brown: www.youtube.com/watch?v=m2MI...
youtube.com
What's so special about Euler's number e? | Chapter 5, Essence of calculus
YouTube video by 3Blue1Brown
163
Reposted by Lukas Hatscher
Dead Neanderthals @deadneanderthals.bsky.social · 18/01/2025
2025 looking great so far!
520161
Reposted by Lukas Hatscher
Nature Portfolio @natureportfolio.nature.com · 30/12/2024
Huji Xu is a physician and researcher who took a chance on a revolutionary approach to treating autoimmune disease. Xu is part of Nature’s 10, a list of people who shaped science in 2024. 🧪
go.nature.com
The daring doctor behind a world-first treatment for autoimmune disease
Huji Xu is part of Nature’s 10, a list of people who shaped science in 2024.
04316
Reposted by Lukas Hatscher
Stephen Turner @stephenturner.us · 30/12/2024
Build common reference indexes with Nextflow @nf-co.re nf-core/references github.com/nf-core/references 🧬🖥️🧪
1185
Reposted by Lukas Hatscher
Sung Kim @sungkim.bsky.social · 21/12/2024
Any popular benchmark will become a target for AI companies. A chart of ARC-AGI scores for past five years of OpenAI models (updated w/ release dates), as provided by Riley Goodside.
2366
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 19/12/2024
Laser tag lab edition #happyholidays 🎄🎁🎅🏼
0103
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 13/12/2024
Schapiro lab does #ESSB 🔬🍷
0143
Reposted by Lukas Hatscher
Raza Ali Lab @hrazaalilab.bsky.social · 13/12/2024
Thank you to the organisers Anja Hauser, @denisschapiro.bsky.social, @schuerch.bsky.social and the wider team who have made the 1st #ESSB Symposium a reality! We have greatly enjoyed the meeting.
The 9 researchers of the  Ali Lab pose for a group picture at the ESSB conference hall
032
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 12/12/2024
@loggas.bsky.social - Poster 72
191
Reposted by Lukas Hatscher
Ajit Johnson Nirmal @ajitjohnson.com · 09/12/2024
Vision foundation models for microscopy from Lundberg lab - first proteome-wide hierarchical map of proteome organization that is learned from image data. #science 🧪 www.biorxiv.org/content/10.1...
1133
Reposted by Lukas Hatscher
Gregor Sturm @grst.bsky.social · 07/12/2024
Formulaic is the go-to way to specify design formulas in Python, e.g. ~treatment + timepoint. To compare sth, one needs to specify a contrast, e.g "on treatment vs baseline". To make this easier, we developed "formulaic-contrasts": formulaic-contrasts.readthedocs.io/en/latest/
# Define model with interaction term
model = MyModel(data, "~ treatment * timepoint")

# compare timepoints
contrast = model.cond(timepoint="on_treatment") - model.cond(timepoint="baseline")

# compare timepoints within drugA only
contrast = (
  model.cond(treatment="drugA", timepoint="on_treatment") - 
  model.cond(treatment="drugA", timepoint="baseline")
)

# compare interaction of timepoint with treatment 
# (= difference of changes between both treatments)
contrast = (
    mod.cond(treatment="drugB", timepoint="on_treatment")
    - mod.cond(treatment="drugB", timepoint="baseline")
) - (
    mod.cond(treatment="drugA", timepoint="on_treatment")
    - mod.cond(treatment="drugA", timepoint="baseline")
)
1186
Reposted by Lukas Hatscher
bioRxivpreprint @biorxivpreprint.bsky.social · 08/12/2024
MuSpAn: A Toolbox for Multiscale Spatial Analysis www.biorxiv.org/content/10.1101/202…
023
Reposted by Lukas Hatscher
Josh Moore @josh-moore.bsky.social · 09/12/2024
We’re thrilled to introduce MuSpAn! For researchers in biological imaging, MuSpAn provides tools for Multiscale Spatial Analysis with advanced mathematical methods. 🌟 For more information: www.muspan.co.uk 📝 Preprint: doi.org/10.1101/2024... We hope you find it as useful as we do! (Poster below)
A poster giving an overview of MuSpAn.
2228
Reposted by Lukas Hatscher
Rita Strack @ritastrack.bsky.social · 06/12/2024
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...
nature.com
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.
3614170
Reposted by Lukas Hatscher
Marco Varrone @marcovarrone.bsky.social · 05/12/2024
🔬 Spatial omics: revolutionary breakthrough or just incremental progress? In the third Batch Effect blog post, I compared this emerging technology to the historic hype around interferon therapy. Is this time going to be different? www.batcheffect.com/p/breakthrou...
batcheffect.com
Breakthrough or incremental progress?
Why spatial omics is revolutionary for biology and medicine
052
Reposted by Lukas Hatscher
Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8
bmcgenomics.biomedcentral.com
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
4244126
Reposted by Lukas Hatscher
Waggoner Lab @labwaggoner.bsky.social · 28/11/2024
Rather than immune suppression, CD206+ TAMs recruit a tumor-reactive network of CD8 T cells, cDC1s, and NK cells doi.org/10.1084/jem.... @maxkrummel.bsky.social @jexpmed.bsky.social
0248
Reposted by Lukas Hatscher
Malte Kuehl @maltekuehl.com · 04/12/2024
While we are all discussing sc/snRNAseq quality control metrics thanks to the recent BMC Genomics paper, I also want to take a moment to point to the related work by Zoe Clarke and Gary Bader. Preprint: www.biorxiv.org/content/10.1... Slides: f1000research.com/slides/13-1255
biorxiv.org
MALAT1 expression indicates cell quality in single-cell RNA sequencing data
Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cell types and tissues. However, empty droplets and poor quality cells are often captured in single cell genomics experim...
032
Reposted by Lukas Hatscher
Schapiro Lab @schapirolab.bsky.social · 04/12/2024
We are looking for a Postdoc with a strong computational background to join our team. Want to work on the development and application of computational methods in the field of translational spatial biology? Apply now! karriere.klinikum.uni-heidelberg.de/index.php?ac...
karriere.klinikum.uni-heidelberg.de
Postdoc – Computational Tissue Analysis (m/f/d)
01616