Arrate Munoz-Barrutia
@arratemunoz.bsky.social
Reposted by Arrate Munoz-Barrutia
#EPFL has an open faculty position - tenure track or tenured!! - in AI driven biophysics. Deadline is Nov 15th. Please spread the word!
www.epfl.ch/about/workin...
www.epfl.ch/about/workin...
Assistant/associate Professor of AI-assisted Biophysics at the Ecole polytechnique fédérale de Lausanne (EPFL) and Group Leader at the Paul Scherrer Institute (PSI)
The School of Basic Sciences (Physics, Chemistry and Mathematics) at EPFL and the Paul Scherrer Institute (PSI) jointly seek to appoint a Tenure Track Assistant or tenured Associate Professor in AI-As...
www.epfl.ch
October 28, 2025 at 2:56 AM
#EPFL has an open faculty position - tenure track or tenured!! - in AI driven biophysics. Deadline is Nov 15th. Please spread the word!
www.epfl.ch/about/workin...
www.epfl.ch/about/workin...
Reposted by Arrate Munoz-Barrutia
I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗
beta.ideas.lego.com/product-idea...
beta.ideas.lego.com/product-idea...
Biological Laboratory | LEGO® Ideas
This is a two-floor realistic Biological Laboratory building. In this design, I try to tell stories about biologists, introduce biology concepts to general publ…
beta.ideas.lego.com
October 16, 2025 at 8:07 AM
I just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗
beta.ideas.lego.com/product-idea...
beta.ideas.lego.com/product-idea...
Reposted by Arrate Munoz-Barrutia
❗The official application call for our PhD position has already started:
www.ehu.eus/es/web/ikerk...
Since most of the application is in either Spanish or Basque, I have prepared a document in English 👇
drive.google.com/file/d/1q0mH...
Looking forward to receiving applications! 🤩
www.ehu.eus/es/web/ikerk...
Since most of the application is in either Spanish or Basque, I have prepared a document in English 👇
drive.google.com/file/d/1q0mH...
Looking forward to receiving applications! 🤩
October 14, 2025 at 7:57 AM
❗The official application call for our PhD position has already started:
www.ehu.eus/es/web/ikerk...
Since most of the application is in either Spanish or Basque, I have prepared a document in English 👇
drive.google.com/file/d/1q0mH...
Looking forward to receiving applications! 🤩
www.ehu.eus/es/web/ikerk...
Since most of the application is in either Spanish or Basque, I have prepared a document in English 👇
drive.google.com/file/d/1q0mH...
Looking forward to receiving applications! 🤩
Reposted by Arrate Munoz-Barrutia
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Reposted by Arrate Munoz-Barrutia
‼️ Raúl Rabadán será el nuevo director del CNIO tras la destitución de Maria Blasco
Raúl Rabadán será el nuevo director del CNIO tras la destitución de Maria Blasco
Catedrático en la Universidad de Columbia y experto en genómica del cáncer, Rabadán ha sido elegido por unanimidad; el pasado enero el patronato cesó a Blasco y al gerente en un proceso que convulsion...
www.eldiario.es
September 4, 2025 at 10:04 AM
‼️ Raúl Rabadán será el nuevo director del CNIO tras la destitución de Maria Blasco
Reposted by Arrate Munoz-Barrutia
Our latest article is online @natcancer.nature.com describing the application of #nanotechnology in #immuno-oncology. A great effort led by Adam Grippin, our star Holman resident and soon to be Physician Scientist. @bettykimmdphd.bsky.social @mdanderson.bsky.social @eileenparkes.bsky.social
Nanotechnology for immuno-oncology - Nature Cancer
Kim and colleagues provide an overview of the current state of the art of nanomaterials and their application in immuno-oncology, discussing preclinical development and the clinical landscape.
www.nature.com
August 7, 2025 at 10:49 AM
Our latest article is online @natcancer.nature.com describing the application of #nanotechnology in #immuno-oncology. A great effort led by Adam Grippin, our star Holman resident and soon to be Physician Scientist. @bettykimmdphd.bsky.social @mdanderson.bsky.social @eileenparkes.bsky.social
Reposted by Arrate Munoz-Barrutia
⛴️ BiaPy just reached version 3.6.1 💫 (latest release)!
github.com/BiaPyX/BiaPy...
➡️ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs 🐞
Let me tell you a bit about what's new 👇
github.com/BiaPyX/BiaPy...
➡️ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs 🐞
Let me tell you a bit about what's new 👇
Release Version 3.6.1 · BiaPyX/BiaPy
Minor:
Disable painting matching instances by default as it takes a lot of time, i.e. TEST.MATCHING_STATS_THS_COLORED_IMG to [] (#135)
Refine DA notebook
Update notebooks to install BiaPy v3.6.0
...
github.com
July 15, 2025 at 2:58 PM
⛴️ BiaPy just reached version 3.6.1 💫 (latest release)!
github.com/BiaPyX/BiaPy...
➡️ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs 🐞
Let me tell you a bit about what's new 👇
github.com/BiaPyX/BiaPy...
➡️ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs 🐞
Let me tell you a bit about what's new 👇
Reposted by Arrate Munoz-Barrutia
In the meantime, we have more than 46 pretrained models from ⛴️ BiaPy available now in the 🦒 Bioimage Model Zoo 🫶 @ai4life.bsky.social
🔗 Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI 🖥️, Colab notebooks 📔 and our API 🤓
🔗 Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI 🖥️, Colab notebooks 📔 and our API 🤓
BioImage.IO - Model Zoo
BioImage Model Zoo - A community-driven, open resource for sharing standardized AI models for bioimage analysis
bioimage.io
July 15, 2025 at 2:58 PM
In the meantime, we have more than 46 pretrained models from ⛴️ BiaPy available now in the 🦒 Bioimage Model Zoo 🫶 @ai4life.bsky.social
🔗 Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI 🖥️, Colab notebooks 📔 and our API 🤓
🔗 Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI 🖥️, Colab notebooks 📔 and our API 🤓
Reposted by Arrate Munoz-Barrutia
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
June 17, 2025 at 8:16 AM
🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource
@ai4life.bsky.social & @eu-openscreen.bsky.social link highlighted in the isciii eu infrastructures for health event
June 17, 2025 at 9:03 AM
@ai4life.bsky.social & @eu-openscreen.bsky.social link highlighted in the isciii eu infrastructures for health event
Reposted by Arrate Munoz-Barrutia
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
June 16, 2025 at 3:53 PM
We released version 1.6 of micro_sam:
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
- Improvements for automatic tracking.
- A new experimental mode for object classification.
- **New versions of the LM and EM models**
The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
Reposted by Arrate Munoz-Barrutia
InterpolAI is an optical flow tool to restore and replace input images for enhanced 3D imaging.
Here is a mouse lung where 6 out of 7 light-sheet images were missing or photobleached. We used InterpolAI to reconstruct.
More about InterpolaAI here: www.nature.com/articles/s41...
Here is a mouse lung where 6 out of 7 light-sheet images were missing or photobleached. We used InterpolAI to reconstruct.
More about InterpolaAI here: www.nature.com/articles/s41...
June 10, 2025 at 2:46 PM
InterpolAI is an optical flow tool to restore and replace input images for enhanced 3D imaging.
Here is a mouse lung where 6 out of 7 light-sheet images were missing or photobleached. We used InterpolAI to reconstruct.
More about InterpolaAI here: www.nature.com/articles/s41...
Here is a mouse lung where 6 out of 7 light-sheet images were missing or photobleached. We used InterpolAI to reconstruct.
More about InterpolaAI here: www.nature.com/articles/s41...
Reposted by Arrate Munoz-Barrutia
A nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression - Nature Methods
Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in both iST and live imag...
www.nature.com
June 6, 2025 at 5:29 PM
A nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...
Reposted by Arrate Munoz-Barrutia
Delighted to share that I will start a five-year K. Albin Johansson Research Professorship next year. I am deeply honored to have been selected for this position. Many thanks to the Finnish Cancer Institute and the K. Albin Johansson Foundation 🙏
www.syopainstituutti.com/researcher-p...
www.syopainstituutti.com/researcher-p...
Researcher Positions
Currently, the Finnish Cancer Institute has nine researcher positions funded by the Cancer Foundation Finland and the K. Albin Johansson Foundation. The Finnish Cancer Institute handles the selection ...
www.syopainstituutti.com
June 6, 2025 at 4:23 PM
Delighted to share that I will start a five-year K. Albin Johansson Research Professorship next year. I am deeply honored to have been selected for this position. Many thanks to the Finnish Cancer Institute and the K. Albin Johansson Foundation 🙏
www.syopainstituutti.com/researcher-p...
www.syopainstituutti.com/researcher-p...
Reposted by Arrate Munoz-Barrutia
Segment any MRI, CTscan, histology, transcriptomic image using CODA using Prof. Kiemen's CODAvision.
CODAvision enhances the usability of the CODA algorithm to automatically generating quantitative results and comprehensive reports.
More here: www.biorxiv.org/content/10.1...
CODAvision enhances the usability of the CODA algorithm to automatically generating quantitative results and comprehensive reports.
More here: www.biorxiv.org/content/10.1...
June 7, 2025 at 4:46 PM
Segment any MRI, CTscan, histology, transcriptomic image using CODA using Prof. Kiemen's CODAvision.
CODAvision enhances the usability of the CODA algorithm to automatically generating quantitative results and comprehensive reports.
More here: www.biorxiv.org/content/10.1...
CODAvision enhances the usability of the CODA algorithm to automatically generating quantitative results and comprehensive reports.
More here: www.biorxiv.org/content/10.1...
Reposted by Arrate Munoz-Barrutia
InterpolaAI, based on deep learning-based optical flow, restores and interpolates sparse image stacks.
This first example is a stack of histological images of a human pancreatic duct.
6 out of 7 images were missing or defective, all now generated.
Download here: www.nature.com/articles/s41...
This first example is a stack of histological images of a human pancreatic duct.
6 out of 7 images were missing or defective, all now generated.
Download here: www.nature.com/articles/s41...
June 7, 2025 at 5:43 PM
InterpolaAI, based on deep learning-based optical flow, restores and interpolates sparse image stacks.
This first example is a stack of histological images of a human pancreatic duct.
6 out of 7 images were missing or defective, all now generated.
Download here: www.nature.com/articles/s41...
This first example is a stack of histological images of a human pancreatic duct.
6 out of 7 images were missing or defective, all now generated.
Download here: www.nature.com/articles/s41...
Reposted by Arrate Munoz-Barrutia
Can you go from protein sequence to a generated image of protein localization? New work from the Uhler lab says yes, and it is generalizable to unseen proteins and more than one cell type. I'm excited for work moving us toward virtual cell models.
PUPS - prediction of unseen proteins' subcellular localization - uses machine learning models to predict the localization of unseen proteins in unseen cell lines from sequence and cellular images.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
June 3, 2025 at 7:59 PM
Can you go from protein sequence to a generated image of protein localization? New work from the Uhler lab says yes, and it is generalizable to unseen proteins and more than one cell type. I'm excited for work moving us toward virtual cell models.
Reposted by Arrate Munoz-Barrutia
Inauguramos el Hospital Universitario de Melilla con 265 camas, cirugía robótica, resonancia, cámara hiperbárica, hemodinámica y UCI pediátrica. La mayor dotación de personal de la sanidad melillense: 1.100 profesionales que contarán con los medios y las condiciones que merecen.
June 2, 2025 at 12:26 PM
Inauguramos el Hospital Universitario de Melilla con 265 camas, cirugía robótica, resonancia, cámara hiperbárica, hemodinámica y UCI pediátrica. La mayor dotación de personal de la sanidad melillense: 1.100 profesionales que contarán con los medios y las condiciones que merecen.
My office for the day… Quite an honor I must say…
June 2, 2025 at 12:45 PM
My office for the day… Quite an honor I must say…
This work is part of the results from my sabbatical stay at Prof. Denis Wirtz’s lab at Johns Hopkins during the 2022–2023 academic year. Very grateful to have been part of this exciting collaboration—congrats to the team on the Nature Methods publication!
To fix input images in a stack for 3D imaging, use InterpolAI.
InterpolAI removes tissue tears and stitching + photobleaching artifacts in stacks of ssTEM, MRI, light-sheet, or histological images (CODA).
Read it here: www.nature.com/articles/s41...
Download it here: github.com/sjoshi17jhu/...
InterpolAI removes tissue tears and stitching + photobleaching artifacts in stacks of ssTEM, MRI, light-sheet, or histological images (CODA).
Read it here: www.nature.com/articles/s41...
Download it here: github.com/sjoshi17jhu/...
June 1, 2025 at 7:19 PM
This work is part of the results from my sabbatical stay at Prof. Denis Wirtz’s lab at Johns Hopkins during the 2022–2023 academic year. Very grateful to have been part of this exciting collaboration—congrats to the team on the Nature Methods publication!
Prou (ex-)supervisor & (always) mentor of @ai4life.bsky.social @egomezm.bsky.social Teresa Zulueta Coarasa; @danifranco93.bsky.social @cfusterbarcelo.bsky.social Carlos Garcia Lopez de Haro @uc3m @cienciauc3m
May 29, 2025 at 1:57 PM
Prou (ex-)supervisor & (always) mentor of @ai4life.bsky.social @egomezm.bsky.social Teresa Zulueta Coarasa; @danifranco93.bsky.social @cfusterbarcelo.bsky.social Carlos Garcia Lopez de Haro @uc3m @cienciauc3m
Reposted by Arrate Munoz-Barrutia
InterpolAI accurately generates synthetic images between real image pairs to help restore tissue damage and reduce stitching artifacts across different imaging modalities. Shows that deep learning can understand data to intelligently fill in the gaps.
Scientific research, working for everyone.
Scientific research, working for everyone.
Dream Police alert: InterpolAI for enhanced 3D imaging (CODA, MRI, EM, confocal).
Read about and InterpolAI here: www.nature.com/articles/s41...
Read about and InterpolAI here: www.nature.com/articles/s41...
InterpolAI: deep learning-based optical flow interpolation and restoration of biomedical images for improved 3D tissue mapping
Nature Methods - InterpolAI leverages optimal flow-based artificial intelligence to produce synthetic images between pairs of images for diverse three-dimensional image types. InterpolAI is more...
www.nature.com
May 28, 2025 at 6:48 PM
InterpolAI accurately generates synthetic images between real image pairs to help restore tissue damage and reduce stitching artifacts across different imaging modalities. Shows that deep learning can understand data to intelligently fill in the gaps.
Scientific research, working for everyone.
Scientific research, working for everyone.
Reposted by Arrate Munoz-Barrutia
Dream Police alert: InterpolAI for enhanced 3D imaging (CODA, MRI, EM, confocal).
Read about and InterpolAI here: www.nature.com/articles/s41...
Read about and InterpolAI here: www.nature.com/articles/s41...
InterpolAI: deep learning-based optical flow interpolation and restoration of biomedical images for improved 3D tissue mapping
Nature Methods - InterpolAI leverages optimal flow-based artificial intelligence to produce synthetic images between pairs of images for diverse three-dimensional image types. InterpolAI is more...
www.nature.com
May 28, 2025 at 11:42 AM
Dream Police alert: InterpolAI for enhanced 3D imaging (CODA, MRI, EM, confocal).
Read about and InterpolAI here: www.nature.com/articles/s41...
Read about and InterpolAI here: www.nature.com/articles/s41...
Reposted by Arrate Munoz-Barrutia
Very excited about this paper that came online today! InterpolAI can predict missing image data from light microscopy to H&E to MRI for improved volumetric imaging and image analysis.
Can a deep learning model know your data well enough to predict missing parts? InterpolAI accurately interpolates synthetic images between pairs of authentic images to “repair” tissue damage and reduce stitching artifacts across diverse modalities. @deniswirtz.bsky.social bit.ly/453o1i1
May 28, 2025 at 6:22 PM
Very excited about this paper that came online today! InterpolAI can predict missing image data from light microscopy to H&E to MRI for improved volumetric imaging and image analysis.