Lars Borm
@LarsBorm
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Postdoc at Stein Aerts lab, smFISH of the non-swimming kind. Building and tinkering.
Leuven, Belgium
Joined October 2017
Very happy that our EEL method for large scale, high resolution spatial transcriptome profiling is out now! Thanks to all who contributed to this fun project! Especially @slinnarsson @SimoneCodeluppi @MossiAlejandro @CamielMannens @jokubasj3
Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH https://t.co/JBoLgGIN0h
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๐ Excited to share scPortrait! Led by Sophia Mรคdler & Niklas Schmacke w/ the Mann lab โ a new @scverse tool for standardized single-cell image data. Enables ML-ready extraction, >1B cell processing, cross-omics, & cancer macrophage insights. ๐ https://t.co/VXHrCBgdDh
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This light-sheet microscopy three-dimensional rendering shows a first-of-its-kind mouse whole-brain mRNA analysis at single-cell resolution. Learn more in this weekโs issue: https://t.co/TC95lPspFC
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We are thrilled to share that our first paper from my new lab, Spateo ( https://t.co/s5ZlWWwbML) for spatiotemporal modeling of molecular holograms, is now online in Cell: https://t.co/rmVeqy3drK. Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal
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Do you want to learn more about Spatial Omics data analysis? Please join our course 21-24Jan in Lausanne! Link below.
Come join us for a 1w @ISBSIB spatial omics workshop in beautiful Lausanne ๐จ๐ญ > https://t.co/O9EAifjBne < featuring @LarsBorm @ahmedElkoussy @markrobinsonca @YvanSaeys @RaSaghaleyn @AnnaCSchaar @MarcoVarrone & more - deadline: Nov 1st.
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STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging | bioRxiv โฆ@DrJasPlummerโฉ โฆ@hoheynโฉ โฆ@pascual_reguantโฉ โฆ@eliseinsingโฉ โฆ@cnag_euโฉ โฆ@ACEpigeneticsโฉ โฆ@StJudeResearchโฉ
biorxiv.org
We introduce Single-Cell Transcriptomics Analysis and Multimodal Profiling (STAMP), a scalable profiling approach of individual cells. Leveraging transcriptomics and proteomics imaging platforms,...
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Thrilled to report Patho-DBiT, just published in Cell ๐. It allows us to directly โseeโ all kinds of RNA species on the same clinical FFPE tissue slide, including mRNA, miRNA, snRNA, snoRNA, tRNA, etc, and splicing isoforms, genetic alterations (SNV, CNV, etc). Really a fun,
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our work on vitessce is out in @naturemethods!
Out today from the Gehlenborg lab! Vitessce is an interactive web-based visualization framework for exploration of multimodal and spatially resolved single-cell data. https://t.co/oLpprMx3I4
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7 years ago, I met a junior fellow named @JD_Buenrostro who blew me away with a vision of futuristic genomic technologies Today, we (@ajaylabade31, @carolinecomenho) are excited to share our first steps into that future: Expansion in situ genome sequencing 1/
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Long awaited (thanks @JamesDManton for posting the patent application!) and now out in @ScienceMagazine: Using absorption to look deeper by @HongNeuroTech - they achieved approx. 3 mm depth using the food dye tartrazine: #Microscopy
https://t.co/FkhBiQ1wDT
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Our paper โWhole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesisโ is now on biorxiv! We introduce weMERFISH, a platform for profiling gene expression in entire embryos at subcellular resolution. Here is๐งต https://t.co/U6eGtbvF0g (1/12)
biorxiv.org
Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in single-cell genomics, mapping these patterns across whole embryos with comprehensive gene coverage and at high...
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Interested in navigating #metabolism in space and time? Meet uMAIA (the Unified Mass Imaging Analyzer) - a framework developed in collaboration with @Gio_Dangel0 & @OatesLab @epflSV led by @HSchede & @Leila_Alieh
#omics #lipidtime #MALDI
https://t.co/Z0mp9P7A6J 1/N
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๐จ๐๐ ๐๐๐ job opportunity @UCSF ๐จ: I'm hiring TWO postdocs - an experimentalist and a computational biologist. Join us to use cutting-edge single-cell and spatial technologies to unravel the mysteries of human tissues. https://t.co/QJqxMmrxGi
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๐ Exciting news! Our latest work is now published in @Dev_journal! The open-source solution for RNA-targeted in situ sequencing provides an accessible and efficient method for spatially resolved gene expression analysis and spatial multi-omics. ๐
journals.biologists.com
Summary: We describe an improved open-source, flexible and customizable method and complete computational workflow for high-throughput multiplexed in situ transcriptomics, readily applicable to a...
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๐ The Segment Anything Model (SAM) has been upgraded to SAM2, featuring an efficient image encoder for segmenting images and videos. But does SAM2 outperform SAM1 in medical image and video segmentation? We're thrilled to present our paper "Segment Anything in Medical Images
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๐บ Introducing Nova-ST, a new open-source platform for high-resolution spatial transcriptomics! โก Developed in the @steinaerts lab, Nova-ST will make large-scale, high-resolution spatial tissue analysis more accessible and affordable. Find out more โก๏ธ https://t.co/vyoqbUAyEc
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Happy to see our work, Nova-ST, a new open-source platform for high-resolution spatial transcriptomics published in @CellCellPress @CellRepMethods
https://t.co/436up3a4CV ๐
cell.com
Poovathingal etย al. develop Nova-ST, a low-cost, whole-transcriptome spatial workflow based on Illumina NovaSeq flow cells. The nano-patterned structure allows high-resolution, single-cell spatial...
๐บ Introducing Nova-ST, a new open-source platform for high-resolution spatial transcriptomics! โก Developed in the @steinaerts lab, Nova-ST will make large-scale, high-resolution spatial tissue analysis more accessible and affordable. Find out more โก๏ธ https://t.co/vyoqbUAyEc
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Cool evolution of spectral barcoding for RNA in situ:
biorxiv.org
To resolve many RNA species in situ, cyclic reactions are typically necessary to increase the multiplexity since conventional fluorescence microscopy is often limited to five channels. Therefore,...
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Systematic comparison of sequencing-based spatial transcriptomic methods | Nature Methods
nature.com
Nature Methods - This analysis presents a systematic comparison of 11 sequencing-based spatial transcriptomics methods using well-characterized references, which offers insights into performance...
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A great DIY guide for image-based spatial transcriptomic from Florian Mueller and team at @institutpasteur
biorxiv.org
Spatial RNA profiling methods provide insight to the cellular heterogeneity and spatial architecture of complex, multi-cellular systems. Combining molecular and spatial information provides important...
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Come and join us! Lots of cool psatial data and interesting questions to drive our knowledge on duchenne therapies
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