We're excited to be at GloBIAS 2025 in Kobe Japan! Come say hi to @arojhada.bsky.social (presenting cell phenotyping) and @miguelib.bsky.social (presenting micronuclAI)
Miguel Ibarra
@miguelib.bsky.social
🇲🇽 PhD. Candidate in Schapirolab at Uni Heidelberg. Deep leaning, computer vision, spatial omics and neighborhood analysis. Photography, sci-fi, music. Bachelor: @LCGUNAM masters: @UniBonn
Last week our lab came together for our annual lab retreat, kindly hosted by @hlsalliance.bsky.social! We exchanged ideas about our research, spatial omics, and took part in some fun (albeit slightly competitive) activities.
Big congratulations to @sabrinalewis.bsky.social on being awarded 2nd place for her talk at the Heidelberg Postdoc Symposium 🥳🎉
We're excited to be at the Kick Off Heidelberg Spatial-Omics Lunch Seminar Series with our very own @chiaraschiller.bsky.social presenting some of her PhD work!
Great to see @miguelib.bsky.social attending the Medizin Informatik Initiative (MII) summer school 2025 at Kassel 👨💻💅
The latest version of the Kasumi manuscript is now published in Nature Comms www.nature.com/articles/s41... Kasumi identifies patterns in tissue patches, enabling analysis of disease progression and treatment response while providing insights into spatial coordination at cell-type or marker level
Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications
Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...
nature.com
Kasumi is a joint effort led by @tanevski.bsky.social (www.tanevskilab.org) with the support from @lvulliard.bsky.social, @miguelib.bsky.social, @denisschapiro.bsky.social, Felix Hartmann and supervision of @juliosaezrod.bsky.social. An R package is freely available at github.com/jtanevski/ka...
Tanevski Lab | Computational biomedical discovery | Spatial omics | Heidelberg
Tanevski Lab - Computational biomedical discovery. Machine learning / Artificial intelligence methods for analysis of spatial omics data in Heidelberg
tanevskilab.org
🚨 New preprint: Topography Aware Optimal Transport for Alignment of Spatial Omics Data We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
1/ Ever wondered how to best quantify cell-cell neighbor preferences in tissues? We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨ Read more: doi.org/10.1101/2025...
🧵 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.
Communications Biology@commsbio.nature.com · last yr.@arojhada.bsky.social, @miguelib.bsky.social, @denisschapiro.bsky.social, @schapirolab.bsky.social
Quentin Blampey, Lotte Pollaris, @clarencemah.me Laurens Lehner @chiaraschiller.bsky.social @miguelib.bsky.social We worked on easing the learning curve of the SpatialData framework by improving the documentation and APIs. We prepared new beginner-friendly notebooks and introduced a new more...
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...
Postdoc – Computational Tissue Analysis (m/f/d)
karriere.klinikum.uni-heidelberg.de
📢 ¡Atención estudiantes de licenciatura! ¿Vives en un país en desarrollo ("low- and middle-income country) como México o muchos otros en Latinoamérica? ¡El premio Sanger está abierto! 👩🏽🔬🦠🧪🧫 Participa para ganar una #estancia de #investigación con #beca completa: www.sanger.ac.uk/about/the-sa...
The Sanger Prize Competition 2025
Sanger Prize competiton 2025 for undergraduates interested in genomics, who are from low- and middle-income countries
sanger.ac.uk
This is a great demonstration for anyone who does visual data analysis. There are 12 black dots – but you'll have trouble seeing more than one or two at a time. The human visual system is not an especially reliable way to process images or extract features from out-of-the-ordinary visual fields. 🧪☀️
Interested in #singlecell and #spatial #metabolomics? Then book your calendar for December 10th! – Our online, free event will summarize major achievements of the field in 2024. #metabolism #omics #MALDI #EPFL With Giovanni D'Angelo and our #PhD students we prepared for you a fantastic lineup. 🧵 1/5
DeepCellTypes from Van Valen Lab, a new language-informed vision model, leverages the power of AI to accurately identify cell types in spatial proteomics data across diverse datasets and imaging platforms. 🧪https://www.biorxiv.org/content/10.1101/2024.11.02.621624v2.full.pdf+html
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices. In our latest paper, we advocate for improving software quality in bioinformatics through teamwork. academic.oup.com/bioinformati...
In this 2 min 📽️ I talk about "posts" from Starter Packs on #BlueSky that allow you to catch up with a subset of people you might be following. Aka feel free to follow as many accounts as you want without fear of missing posts from people you are interested in! 🙌🏽 #AcademicSky youtu.be/dYrMR8v4LCQ
[2024-11-13] Bluesky: starter packs "posts" feature
YouTube video by Leonardo Collado Torres
youtu.be
What are the key disrupted multicellular processes in heart failure? In our new work we combine 23 years of molecular data with recent single-cell atlases to draw a cross-study patient map doi.org/10.1101/2024...
Explore disease at a multicellular level, capturing variations in patient samples across cell types, tissue features, studies, and technologies with Multicellular Factor Analysis, peer-reviewed by Review Commons and now published @elife.bsky.social elifesciences.org/articles/93161
People potentially interested in a career in academic research are increasingly aware of the precarious contract situations and poor long-term career prospects in academia (seeimg also the situation of older postdocs) and choose alternative routes.
Takeaway from the Challenges deep dive discussion during AI In(Sci)de Out conference. @EMBL. "Clusters don't make Class" by Alexandra Albu. Don't over interpret your UMAPs! #AcademicSky #MLSky
Very happy to see that our review on gene regulatory networks is being featured by Nature Reviews Genetics and that it inspired its cover! 🥳 doi.org/10.1038/s415...
