ayakimovich.bsky.social
@ayakimovich.bsky.social
I am a group leader at Helmholtz in Görlitz, Germany and an Associate Prof of CS at Uni Wroclaw, Poland. My group is working on Machine Learning for Infection and Disease. Personal account and opinions. Website: ayakimovich.github.io / www.casus.science
There's a fully funded postdoc position available in my group starting next year. Prerequisites: you know that python is not just a snake 🐍, pi is not just a dessert 🎂, policy is more than insurance 📃, proteins and training don't just mean gym 🏋️ to you. DM if interested.
November 1, 2025 at 11:47 AM
There's a fully funded postdoc position available in my group starting next year. Prerequisites: you know that python is not just a snake 🐍, pi is not just a dessert 🎂, policy is more than insurance 📃, proteins and training don't just mean gym 🏋️ to you. DM if interested.
This year for Halloween I will be the Schienenersatzverkehr 👻
October 30, 2025 at 9:20 AM
This year for Halloween I will be the Schienenersatzverkehr 👻
Sometimes you just need the flexibility of a #Python library! We present the "Pandas for clonal phenotypes", #PyPlaque aims to do just that! www.nature.com/articles/s41... @hzdr.bsky.social @casusscience.bsky.social 🧪
PyPlaque is an open-source python package for phenotypic analysis of virus plaque assays - Scientific Reports
Scientific Reports - PyPlaque is an open-source python package for phenotypic analysis of virus plaque assays
www.nature.com
October 17, 2025 at 1:09 PM
Sometimes you just need the flexibility of a #Python library! We present the "Pandas for clonal phenotypes", #PyPlaque aims to do just that! www.nature.com/articles/s41... @hzdr.bsky.social @casusscience.bsky.social 🧪
had a great time talking about #GenAI for improving microscopy at the #FoB @hzdr.bsky.social @casusscience.bsky.social
October 1, 2025 at 3:46 PM
had a great time talking about #GenAI for improving microscopy at the #FoB @hzdr.bsky.social @casusscience.bsky.social
I'll be speaking at the Festival of Biologics 2025 in Basel next week. If you're interested, pass by and please pick up one of my FREE passes: i.snoball.it/p/IGqAE/l/7
#FestivalOfBiologics @hzdr.bsky.social @casusscience.bsky.social
#FestivalOfBiologics @hzdr.bsky.social @casusscience.bsky.social
Register for Festival of Biologics Basel 2025 | 30 September - 2 October, 2025
Europe's largest biologics event.
i.snoball.it
September 23, 2025 at 7:06 AM
I'll be speaking at the Festival of Biologics 2025 in Basel next week. If you're interested, pass by and please pick up one of my FREE passes: i.snoball.it/p/IGqAE/l/7
#FestivalOfBiologics @hzdr.bsky.social @casusscience.bsky.social
#FestivalOfBiologics @hzdr.bsky.social @casusscience.bsky.social
looking forward to talking about #Microscopy, #GenAI, and virological plaques at the 8th International Symposium on Systems Biology of Microbial Infection in beautiful Jena!
September 18, 2025 at 11:56 AM
looking forward to talking about #Microscopy, #GenAI, and virological plaques at the 8th International Symposium on Systems Biology of Microbial Infection in beautiful Jena!
#BuildingBridges in Dresden! Excited to talk about #GenAI for #Microscopy tomorrow! @casusscience.bsky.social @hzdr.bsky.social
September 11, 2025 at 4:18 PM
#BuildingBridges in Dresden! Excited to talk about #GenAI for #Microscopy tomorrow! @casusscience.bsky.social @hzdr.bsky.social
Had a blast discussing #microscopy and #AI at BNMI in beautiful Gothenburg!
August 21, 2025 at 11:10 AM
Had a blast discussing #microscopy and #AI at BNMI in beautiful Gothenburg!
I am happy to share that I have recently been invited and joined the editorial board of mSphere - a journal of the @asm.org journals.asm.org/journal/msph... @casusscience.bsky.social @hzdr.bsky.social
mSphere Board of Editors
Members of the mSphere Editorial Board
journals.asm.org
July 11, 2025 at 7:04 AM
I am happy to share that I have recently been invited and joined the editorial board of mSphere - a journal of the @asm.org journals.asm.org/journal/msph... @casusscience.bsky.social @hzdr.bsky.social
German railways maintain an unmatched level of backward compatibility! 🧑💻
July 3, 2025 at 4:52 PM
German railways maintain an unmatched level of backward compatibility! 🧑💻
Drop me a line if you're in sunny 😎 Manchester today/tomorrow @casusscience.bsky.social
June 30, 2025 at 10:44 AM
Drop me a line if you're in sunny 😎 Manchester today/tomorrow @casusscience.bsky.social
After #fluorescencefriday comes #superresolutionsaturday if you still can spell it!
June 28, 2025 at 7:47 PM
After #fluorescencefriday comes #superresolutionsaturday if you still can spell it!
Reposted by ayakimovich.bsky.social
I‘m looking forward to visiting the Center for Advanced Systems Understanding (#CASUS) tomorrow in Görlitz!
I will be giving a talk to CASUS and other @hzdr.bsky.social researchers at 14:00. Details: www.casus.science?page_id=15608
I will be giving a talk to CASUS and other @hzdr.bsky.social researchers at 14:00. Details: www.casus.science?page_id=15608
Event — Effectively publishing data-rich science – CASUS – Center for Advanced Systems Understanding
Andrew Hufton, Ph.D., Editor-in-Chief Patterns, Cell Press, Munich (Germany)
www.casus.science
June 24, 2025 at 10:19 AM
I‘m looking forward to visiting the Center for Advanced Systems Understanding (#CASUS) tomorrow in Görlitz!
I will be giving a talk to CASUS and other @hzdr.bsky.social researchers at 14:00. Details: www.casus.science?page_id=15608
I will be giving a talk to CASUS and other @hzdr.bsky.social researchers at 14:00. Details: www.casus.science?page_id=15608
Had a blast talking about #BioMed #AI at the International Urogynecological Association (IUGA) conference in beautiful Barcelona @hzdr.bsky.social @casusscience.bsky.social
June 19, 2025 at 8:06 AM
Had a blast talking about #BioMed #AI at the International Urogynecological Association (IUGA) conference in beautiful Barcelona @hzdr.bsky.social @casusscience.bsky.social
Reposted by ayakimovich.bsky.social
🔥Just out @EGPGV’25: Parallel visualization of distributed volume data for non-convex decompositions! @csbdresden.bsky.social @tudresden.bsky.social @mpi-cbg.de And the best: code is contributed upstream 🤩 diglib.eg.org/items/3aed38...
A Transparent and Efficient Extension of IceT for Parallel Compositing on Non-Convex Volume Domain Decompositions
The IceT library is widely used for parallel compositing but does not support non-convex volume domain decompositions. We provide a backward-compatible extension of IceT to handle non-convex domain de...
diglib.eg.org
June 8, 2025 at 9:44 AM
🔥Just out @EGPGV’25: Parallel visualization of distributed volume data for non-convex decompositions! @csbdresden.bsky.social @tudresden.bsky.social @mpi-cbg.de And the best: code is contributed upstream 🤩 diglib.eg.org/items/3aed38...
It never ceases to amaze me how much information we can get just by looking at the gradients in #BioImageAnalysis #AI #GenAI Kudos Ivo F. Sbalzarini and the group! 🧪 @mosaicgroup.bsky.social @hzdr.bsky.social @mpi-cbg.de @casusscience.bsky.social onlinelibrary.wiley.com/doi/10.1002/...
Regularized Gradient Statistics Improve Generative Deep Learning Models of Super Resolution Microscopy
A generative AI model for super-resolution microscopy images is presented. Super-resolution microscopy provides high spatial detail at the expense of lower time resolution. Using it for live samples ...
onlinelibrary.wiley.com
June 6, 2025 at 4:45 PM
It never ceases to amaze me how much information we can get just by looking at the gradients in #BioImageAnalysis #AI #GenAI Kudos Ivo F. Sbalzarini and the group! 🧪 @mosaicgroup.bsky.social @hzdr.bsky.social @mpi-cbg.de @casusscience.bsky.social onlinelibrary.wiley.com/doi/10.1002/...
Generation of a new #fluorescent reporter #virus could often take years! Here, we propose to use #AI #VirtualStaining to detect infection, by providing a #baseline and a #benchmark for #RV, #HAdV, #IAV, #HSV and #VACV. 🧪@casusscience.bsky.social @hzdr.bsky.social www.nature.com/articles/s41...
A Benchmark for Virus Infection Reporter Virtual Staining in Fluorescence and Brightfield Microscopy - Scientific Data
Scientific Data - A Benchmark for Virus Infection Reporter Virtual Staining in Fluorescence and Brightfield Microscopy
www.nature.com
May 28, 2025 at 1:34 PM
Generation of a new #fluorescent reporter #virus could often take years! Here, we propose to use #AI #VirtualStaining to detect infection, by providing a #baseline and a #benchmark for #RV, #HAdV, #IAV, #HSV and #VACV. 🧪@casusscience.bsky.social @hzdr.bsky.social www.nature.com/articles/s41...
I'll be giving a talk and taking part in a panel at @embl.org Heidelberg next Wednesday. Drop me a line if you have time for a ☕ #AI4Science @casusscience.bsky.social @hzdr.bsky.social 🧪
May 15, 2025 at 8:12 AM
I'll be giving a talk and taking part in a panel at @embl.org Heidelberg next Wednesday. Drop me a line if you have time for a ☕ #AI4Science @casusscience.bsky.social @hzdr.bsky.social 🧪
Conceived by Félix d’Herelle, plaque assay remains the cornerstone of #Virology and #Microbiology. In our recent work, we bring it to the era of #AI by collating mobile photos benchmark and proposing an e2e baseline @casusscience.bsky.social @hzdr.bsky.social www.nature.com/articles/s41... 🧪
A digital photography dataset for Vaccinia Virus plaque quantification using Deep Learning - Scientific Data
Scientific Data - A digital photography dataset for Vaccinia Virus plaque quantification using Deep Learning
www.nature.com
May 1, 2025 at 6:58 AM
Conceived by Félix d’Herelle, plaque assay remains the cornerstone of #Virology and #Microbiology. In our recent work, we bring it to the era of #AI by collating mobile photos benchmark and proposing an e2e baseline @casusscience.bsky.social @hzdr.bsky.social www.nature.com/articles/s41... 🧪
Was amazing to speak at the good old @uzh-ch.bsky.social
April 22, 2025 at 8:26 PM
Was amazing to speak at the good old @uzh-ch.bsky.social
The lack of high-quality annotated #datasets is hampering applications of #AI in Optical #Microscopy. Let's change this together! I'm honored to be serving as the collection's Guest Editor. More in: go.nature.com/4hyDnNK 🧪 @natureportfolio.nature.com
@casusscience.bsky.social
@hzdr.bsky.social
@casusscience.bsky.social
@hzdr.bsky.social
Annotated Optical Microscopy Datasets
This Scientific Data Collection of articles focuses on datasets of annotated microscopy images from a variety of cell types and tissues.
go.nature.com
April 10, 2025 at 11:47 AM
The lack of high-quality annotated #datasets is hampering applications of #AI in Optical #Microscopy. Let's change this together! I'm honored to be serving as the collection's Guest Editor. More in: go.nature.com/4hyDnNK 🧪 @natureportfolio.nature.com
@casusscience.bsky.social
@hzdr.bsky.social
@casusscience.bsky.social
@hzdr.bsky.social
Down the memory lane giving a talk at the Crick AI club today! 🧪
March 28, 2025 at 8:32 PM
Down the memory lane giving a talk at the Crick AI club today! 🧪