So happy to see that spage2vec works so well to find cell niches from spatially multiplexed single cell data! Congrats @lesolorzanova (and all others) for this very interesting work!
...and the first paper using spage2vec for finding cell niches in tissue: biorxiv.org/content/10.1101/…
Super-neat approach for fluorescence decoding of MERFISH, SeqFISH, ISS and any other image-based spatial transcriptomics technology!
ISTDECO: In Situ Transcriptomics Decoding by Deconvolution biorxiv.org/cgi/content/shor… #bioRxiv
Gabriele Partel retweeted
The latest version of umap-learn is now out. Version 0.5 includes some major new features, including ParametricUMAP, DensMAP, AlignedUMAP, model composition, and model updating. Thank you to everyone who contributed! 1/14
Gabriele Partel retweeted
Excited to share our data&model zoo sfaira: We provide 233 data sets, 55 organs, 3.1M annotated cells together with 8 pre-trained model classes, to replace manual workflows, facilitate method benchmarking & extension w private data. biorxiv.org/content/10.1101/… github.com/theislab/sfaira
Gabriele Partel retweeted
#CoMIR: Contrastive Multimodal Image Representation for Registration @ #NeurIPS2020 – solving your #multimodal #imageRegistration needs by first translating images to a shared virtual modality where the task is easier: github.com/MIDA-group/CoMIR
proceedings.neurips.cc/paper…
#MIDAgroup
Gabriele Partel retweeted
If you missed today's talk for in-situ RNA sequencing by @MatsNilssonLab
youtu.be/aQSSTr9E61M
co-organized by @RongFan8
Gabriele Partel retweeted
Come by my poster at #I2K2020 if you want to learn about how to visualize millions of in situ sequencing gene expression points and how you can use them to learn more about your cell types and spatial compartments! @Vi2UU @CarolinaWahlby @gapartel
Gabriele Partel retweeted
I'm super proud to announce that our fantastic PhD students won the AI Sweden 'Adipocyte Cell Imaging Challenge': ai.se/en/news/ai-sweden-init…
#PhDdone ;)
Proud of @gapartel presenting his dissertation at @Vi2UU. Image and data analysis for spatial resolved transcriptomics. Extremely powerful, bleeding edge technology for exploring the very thing we are all made of. We thank the great opponent Roland Eils @CaptainSysBio
Great collaboration with @M_Hilscher and @MatsNilssonLab! Take a look at the brain regions in our interactive viewer for spatial gene expression tissuumaps.research.it.uu.se…
@CarolinaWahlby @lesolorzanova @ahklemm @milli_giorgia
Out now: automated, unsupervised and unbiased annotation of spatial compartments from in situ sequencing data. rdcu.be/b8LxB @gapartel @CarolinaWahlby @M_Hilscher
Gabriele Partel retweeted
Hybridization-based in situ sequencing is now out on @NAR_Open! Fantastic work guys! @dgyllborg @XiaoyanQian @M_Hilscher academic.oup.com/nar/advance…
Gabriele Partel retweeted
🔬 Different microscopes output different image file formats making it challenging for scientists to compare. That's why we developed an #openscience software to help level the playfield. #microscopy
alleninstitute.org/what-we-d…
Gabriele Partel retweeted
Our #TissUUmaps applications note is out! and it's Open access! We thank @OUPBioinfo for a friendly process, the reviewers for their kind comments and constructive criticism, @UppsalaUniLib for the OA agreements and @ERC_Research for the funding. @CarolinaWahlby @GabrielePartel
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Gabriele Partel retweeted
A scalable embedding algorithm that clusters scRNA-seq data by optimizing a clustering objective function and enables batch effects removal, from @DrMingyaoLi @UPennDBEI @KSusztak
go.nature.com/35ZuhXt
Gabriele Partel retweeted
Phew, so much work! But finally submitted another paper. If you want to hear me embarrassing myself speaking english go to
tissuumaps.research.it.uu.se…
You can also visit if you are curious about our work! #TissUUmaps #geneExpression #spatialTranscriptomics
Gabriele Partel retweeted
L’unità e il lavoro di squadra sono da sempre i principi su cui si fonda la nostra Forza Armata e, in questo momento più che mai, sono fondamentali.
Ed allora, come fanno da sempre le @FrecceTricolori ‘facciamo squadra’ 💪🏻, uniamo le forze 🏋🏻, insieme ce la faremo 🇮🇹!
Gabriele Partel retweeted
Teaching online the next few weeks? Check out this Coding & Vision 101 Educational Lecture Series includes 12 videos produced by the Allen Institute for Brain Science to serve as an educational resource for the community.
youtube.com/playlist?list=PL…
Gabriele Partel retweeted
Two open positions (senior + postdoc) in digital image processing with life science applications in my lab at Uppsala University and SciLifeLab:
uu.se/en/about-uu/join-us/de…
uu.se/en/about-uu/join-us/de…
#WahlbyLab #SciLifeLab
Gabriele Partel retweeted
Dear friends, may I suggest you follow the one and only, @CarolinaWahlby .
@joakim_lindblad @BoSoxBioBeth @HenriquesLab @0x00B1 @ahklemm @MatsNilssonLab @M_Hilscher @PhilipJHarriso1 @GabrielePartel @petebankhead @npielawski @scilifelab @Prof_Lundberg @rita_strack @CellProfiler
Gabriele Partel retweeted
Next iteration of in situ sequencing is now out as a preprint @biorxivpreprint. We show improved robustness and flexibility of Hybridization-based in situ sequencing (HybISS) on human brain sections with goals towards a spatial human cell atlas.🧠🔬🧬 disq.us/t/3lupqeo