ayakimovich.bsky.social's Avatar

ayakimovich.bsky.social

@ayakimovich.bsky.social

I am a group leader at Helmholtz in GΓΆrlitz, 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

843 Followers  |  522 Following  |  83 Posts  |  Joined: 03.02.2024  |  1.815

Latest posts by ayakimovich.bsky.social on Bluesky

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 πŸŽ‚, policy is more than insurance πŸ“ƒ, proteins and training don't just mean gym πŸ‹οΈ to you. DM if interested.

01.11.2025 11:47 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

This year for Halloween I will be the Schienenersatzverkehr πŸ‘»

30.10.2025 09:20 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Preview
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

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 πŸ§ͺ

17.10.2025 13:09 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

had a great time talking about #GenAI for improving microscopy at the #FoB @hzdr.bsky.social @casusscience.bsky.social

01.10.2025 15:46 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

Always great to be back to #Basel, you might think that staying in hotel 2.7182.. is irrational, but the night rates are quite natural! #FoB here we go!

01.10.2025 08:45 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Preview
Register for Festival of Biologics Basel 2025 | 30 September - 2 October, 2025 Europe's largest biologics event.

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

23.09.2025 07:06 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

looking forward to talking about #Microscopy, #GenAI, and virological plaques at the 8th International Symposium on Systems Biology of Microbial Infection in beautiful Jena!

18.09.2025 11:56 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

#BuildingBridges in Dresden! Excited to talk about #GenAI for #Microscopy tomorrow! @casusscience.bsky.social @hzdr.bsky.social

11.09.2025 16:17 β€” πŸ‘ 3    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
Post image

Had a blast discussing #microscopy and #AI at BNMI in beautiful Gothenburg!

21.08.2025 11:10 β€” πŸ‘ 3    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
Preview
mSphere Board of Editors Members of the mSphere Editorial Board

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

11.07.2025 07:04 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

German railways maintain an unmatched level of backward compatibility! πŸ§‘β€πŸ’»

03.07.2025 16:52 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 2    πŸ“Œ 0
Post image

Drop me a line if you're in sunny 😎 Manchester today/tomorrow @casusscience.bsky.social

30.06.2025 10:43 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

Maybe it is time to rethink the big conferences... #AI

29.06.2025 12:25 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

After #fluorescencefriday comes #superresolutionsaturday if you still can spell it!

28.06.2025 19:47 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Event β€” Effectively publishing data-rich science – CASUS – Center for Advanced Systems Understanding Andrew Hufton, Ph.D., Editor-in-Chief Patterns, Cell Press, Munich (Germany)

Iβ€˜m looking forward to visiting the Center for Advanced Systems Understanding (#CASUS) tomorrow in GΓΆrlitz!

I will be giving a talk to CASUS and other @hzdr.bsky.social researchers at 14:00. Details: www.casus.science?page_id=15608

24.06.2025 10:19 β€” πŸ‘ 2    πŸ” 1    πŸ’¬ 0    πŸ“Œ 1
Post image

Had a blast talking about #BioMed #AI at the International Urogynecological Association (IUGA) conference in beautiful Barcelona @hzdr.bsky.social @casusscience.bsky.social

19.06.2025 08:05 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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...

πŸ”₯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...

08.06.2025 09:44 β€” πŸ‘ 3    πŸ” 2    πŸ’¬ 0    πŸ“Œ 0
Preview
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 ...

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! πŸ§ͺ @mosaicgroup.bsky.social @hzdr.bsky.social @mpi-cbg.de @casusscience.bsky.social onlinelibrary.wiley.com/doi/10.1002/...

06.06.2025 16:45 β€” πŸ‘ 6    πŸ” 3    πŸ’¬ 0    πŸ“Œ 1
Preview
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

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. πŸ§ͺ@casusscience.bsky.social @hzdr.bsky.social www.nature.com/articles/s41...

28.05.2025 13:34 β€” πŸ‘ 2    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
Post image

Oh hello there @embl.org

21.05.2025 14:38 β€” πŸ‘ 3    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
Post image

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 β˜• #AI4Science @casusscience.bsky.social @hzdr.bsky.social πŸ§ͺ

15.05.2025 08:12 β€” πŸ‘ 5    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
Preview
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

Conceived by FΓ©lix 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... πŸ§ͺ

01.05.2025 06:57 β€” πŸ‘ 4    πŸ” 2    πŸ’¬ 0    πŸ“Œ 0
Post image

Was amazing to speak at the good old @uzh-ch.bsky.social

22.04.2025 20:25 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Preview
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.

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 πŸ§ͺ @natureportfolio.nature.com
@casusscience.bsky.social

@hzdr.bsky.social

10.04.2025 11:47 β€” πŸ‘ 14    πŸ” 7    πŸ’¬ 0    πŸ“Œ 0
Post image

Down the memory lane giving a talk at the Crick AI club today! πŸ§ͺ

28.03.2025 20:32 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

Helmholtz-ELLIS Workshop on Foundation Models in Science

18.03.2025 08:51 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image

When you cross the Atlantic and accidentally time travel presenting your phone's AI with a good old fashioned paradox 🀯

04.03.2025 16:12 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Preview
From handicap to asset: AI approach leverages optics phenomenon to produce better images - Helmholtz-Zentrum Dresden-Rossendorf, HZDR Quantitative phase imaging (QPI) is a microscopy technique widely used to investigate cells and tissues. Even though first biomedical applications based on QPI have been developed, both acquisition sp...

Our new press release is out! www.hzdr.de/db/Cms?pOid=... @hzdr.bsky.social @hzdr.bsky.social @helmholtzai.bsky.social πŸ§ͺ

28.02.2025 20:25 β€” πŸ‘ 8    πŸ” 2    πŸ’¬ 0    πŸ“Œ 1
Post image

Come check out the poster 100 at #ICLR

28.02.2025 18:04 β€” πŸ‘ 0    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
Post image Post image Post image

The one and only Andrew Ng at #AAAI!

28.02.2025 13:34 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

@ayakimovich is following 19 prominent accounts