1/7 Want to know which spatial patterns correlate with your disease of interest? Check out our preprint introducing GraphCompass, a Python-based framework for the differential analysis of spatial organization across conditions! bioRxiv: biorxiv.org/content/10.110…

Wow what a paper by Justin Crocker and colleagues ! Massive tracking data to show drastic effects of agro toxins at sublethal dose.

A few thoughts on the recent comparison paper for imaging-based #spatialtranscriptomics (iST) methods from the Rahul Satija:
biorxiv.org/content/10.110…

Important points regarding QC metrics in spatial transcriptomics!

Cells live and interact in 3D tissues but pathology and spatial omics typically rely on 2D sections...

Excited to share our latest efforts in Nikolaus Rajewsky lab to generate a 3D, multimodal atlas of a human tumor!

Find out what we learned: video + 🧵!
🔗 bit.ly/3D_lung_cancer

Excited to share our lessons we took from the Preprint Club - Immunology. Learn how it works, the benefits of it, its weaknesses and how you can start your own preprint club hub. Get involved in #preprint #PeerReview . ASAPbio Review Commons PREreview #PreprintJC

Exciting New Year's release of #BigStitcher ! It now supports:
1) efficient blocked processing, meaning large, tiled acquisitions are fused blazingly fast (second/minutes instead of hours)!
2) Export of ZARR/N5/HDF5 thanks to the N5-API
Check it out, just update Fiji!

Leider öffentlich gar nicht diskutiert: Ende des Jahres endet ein extrem effektives Tool zur Unterstützung von NachwuchswissenschaftlerInnen mit Kindern in DFG public | @[email protected]-Verbünden. 1/n

Are you looking for an opportunity to combine #singlecell #spatialtranscriptomics and clinical data? Join my new group in Computational Oncology at Charité as a PhD student! 💻🔬🩺 bit.ly/3FgnqLe Please RT and/or apply! #cancer #jobs Charité - Universitätsmedizin Berlin Berlin Institute of Health

Glow Worms Chenshu Liu We built Friedrich Preußer 's WormObservers for ~$150 / piece including a 7' touchscreen, wireless keyboard and mouse, and use them both for worm tracking and for general basic imaging
github.com/Fritze/WormObs…

RS-FISH is out as open access article in Nature Methods
Great collaboration with @bellonet Laura Breimann Marwan Zouinkhi Kyle Harrington Timothée Lionnet from HHMI | Janelia MDC-BIMSB Max Delbrück Center NYU Langone Health

github.com/PreibischLab/R…
github.com/PreibischLab/R…
nature.com/articles/s4159…

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 Sten Linnarsson simone codeluppi Alejandro Mossi Camiel Mannens @jokubasj3

#Tweetorial of our recent Blood Cancer Discovery paper:

We used 1.3 billion #SingleCell images from 390 #BloodCancer samples to train a #CNN . Our ‘mCNN’ could recognize malignant and healthy cells based on morphology, while immunofluorescence markers were only used as training labels. 1/7

We build on the excellent work of others, perhaps most recently that of Stephan Preibisch which I also strongly recommend for the novice microscopist scholar.google.com/citations?view…

Together with Ronen Zaidel-Bar and Zhirong Bao we attempt a gentle introduction to imaging resources and experimental design for the newcomer to microscopy focused on C. elegans applications

Great opportunity!