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
Reposted by Miguel Ibarra
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)
October 29, 2025 at 2:57 PM
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)
Reposted by Miguel Ibarra
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.
October 29, 2025 at 3:45 PM
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.
Reposted by Miguel Ibarra
Big congratulations to @sabrinalewis.bsky.social on being awarded 2nd place for her talk at the Heidelberg Postdoc Symposium 🥳🎉
July 1, 2025 at 7:31 AM
Big congratulations to @sabrinalewis.bsky.social on being awarded 2nd place for her talk at the Heidelberg Postdoc Symposium 🥳🎉
Reposted by Miguel Ibarra
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!
July 1, 2025 at 9:52 AM
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!
Reposted by Miguel Ibarra
Great to see @miguelib.bsky.social attending the Medizin Informatik Initiative (MII) summer school 2025 at Kassel 👨💻💅
June 30, 2025 at 10:46 AM
Great to see @miguelib.bsky.social attending the Medizin Informatik Initiative (MII) summer school 2025 at Kassel 👨💻💅
Reposted by Miguel Ibarra
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...
www.nature.com
May 7, 2025 at 1:11 PM
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
Reposted by Miguel Ibarra
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
www.tanevskilab.org
May 7, 2025 at 1:11 PM
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...
Reposted by Miguel Ibarra
🚨 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...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
April 22, 2025 at 9:37 AM
🚨 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...
We present our new alignment framework TOAST www.biorxiv.org/content/10.1...
Reposted by Miguel Ibarra
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...
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...
April 15, 2025 at 3:50 PM
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...
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...
Reposted by Miguel Ibarra
🧵 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.
Congratulations to @miguelib.bsky.social and Lindsay Caprio for leading this project.
March 7, 2025 at 3:48 PM
🧵 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.
Congratulations to @miguelib.bsky.social and Lindsay Caprio for leading this project.
Reposted by Miguel Ibarra
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 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...
January 20, 2025 at 5:29 PM
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 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...
Reposted by Miguel Ibarra
Mind blowing science with 10x @10xgenomics.bsky.social #ESSB2024
December 12, 2024 at 12:09 PM
Mind blowing science with 10x @10xgenomics.bsky.social #ESSB2024
Thank you @denisschapiro.bsky.social and @schapirolab.bsky.social!! Happy to be here!
@miguelib.bsky.social from @schapirolab.bsky.social presenting #micronuclA (linktr.ee/micronuclAI) at #MII2024 despite double booking with #SpaceHack :)
December 10, 2024 at 1:44 PM
Thank you @denisschapiro.bsky.social and @schapirolab.bsky.social!! Happy to be here!
Reposted by Miguel Ibarra
@schapirolab.bsky.social mug #AdventCalendar courtesy of @margotch.bsky.social @chiaraschiller.bsky.social
December 6, 2024 at 12:19 PM
Reposted by Miguel Ibarra
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/index.php?ac...
Postdoc – Computational Tissue Analysis (m/f/d)
karriere.klinikum.uni-heidelberg.de
December 4, 2024 at 12:39 PM
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/index.php?ac...
Reposted by Miguel Ibarra
Reposted by Miguel Ibarra
📢 ¡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...
¡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
www.sanger.ac.uk
November 20, 2024 at 3:57 PM
📢 ¡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...
¡El premio Sanger está abierto! 👩🏽🔬🦠🧪🧫
Participa para ganar una #estancia de #investigación con #beca completa:
www.sanger.ac.uk/about/the-sa...
Reposted by Miguel Ibarra
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. 🧪☀️
November 18, 2024 at 10:18 PM
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. 🧪☀️
Reposted by Miguel Ibarra
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
November 19, 2024 at 5:04 PM
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
Reposted by Miguel Ibarra
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
November 19, 2024 at 1:55 PM
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
Reposted by Miguel Ibarra
🧵 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 our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
November 18, 2024 at 2:48 PM
🧵 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 our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
Reposted by Miguel Ibarra
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
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
November 13, 2024 at 6:56 PM
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
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
Reposted by Miguel Ibarra
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...
doi.org/10.1101/2024...
November 11, 2024 at 9:07 AM
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...
doi.org/10.1101/2024...
Reposted by Miguel Ibarra
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
elifesciences.org/articles/93161
November 24, 2023 at 10:25 AM
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
elifesciences.org/articles/93161