Maciej Dobrzynski (@macdobry) profile picture

Maciej Dobrzynski

@macdobry

computational biologist | data scientist | biophysicist | modeller

 Berne, Switzerland
macdobry.net
Joined September 2010
  • Tweets487
  • Following166
  • Followers217
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Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)Photo by Maciej Dobrzynski (@macdobry)
Code an image classifier from scratch using numpy only. Watch the network train on a nano dataset. github.com/dmattek/tutorial-… #MachineLearning #NeuralNetworks #tutorial #Python
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A step-by-step tutorial for detecting collective phenomena in time-lapse images in a new #OpenAccess article in Methods in Microscopy from @degruyter_brill @benigraedel @paoloarmando83 @PertzL, doi.org/10.1515/mim-2024-000…
Image from Maciej Dobrzynski (@macdobry)
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John Bogovic (@BogovicJohn) profile picture
John Bogovic@BogovicJohn15 Sep 2023
Replying to @david_legland
@david_legland blows the minds of students and teachers alike. Do NOT measure a shape's perimeter by counting pixels! See @ahklemm and @cmci_'s reactions at #EMBOBioImage
Image from John Bogovic (@BogovicJohn)
Image from John Bogovic (@BogovicJohn)
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Our training at #EMBOBioImage @EMBLEvents Feels like I’ve stepped into NASA’s Mission Control. 🚀👩‍🚀 Expecting a countdown for Ctrl+Alt+Delete any moment now. 🤓
Image from Maciej Dobrzynski (@macdobry)
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Maciej Dobrzynski retweeted
Robert Haase (@haesleinhuepf) profile picture
Robert Haase@haesleinhuepf10 Sep 2023
#EMBOBioImage poster session @EMBOevents in full swing 🔬🖥️🤯
Image from Robert Haase (@haesleinhuepf)
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Catching up with the pre-course material for the Advanced Bioimaging Analysis training in Heidelberg. Looking forward to networking and learning all the latest in #bioimageanalysis @EMBLEvents #EMBOBioImage
Image from Maciej Dobrzynski (@macdobry)
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A dream software/hardware stack for smart #microscopy developed by our fantastic PhD student @lhinderling
Lucien Hinderling (@lhinderling) profile pictureLucien Hinderling@lhinderling11 Aug 2023
What if you could talk to your microscope? Honoured to present our work @PertzL on real-time image processing and smart microscopy! Video shows @manager_micro control using #OmegaAgent by @loicaroyer
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Finally out! Quantify collective phenomena with our computational tool ARCOS.
Journal of Cell Biology (@JCellBiol) profile pictureJournal of Cell Biology@JCellBiol27 Jul 2023
.@paoloarmando83, @benigraedel et al. develop ARCOS, a method to detect & quantify collective signaling in cell collectives. Open-source and user-friendly, w/ R & Python packages, and a @napari_imaging plugin: bit.ly/47kXefR @lhinderling @PascalEnder @PertzL @macdobry
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Great to see ARCOS (doi.org/10.1083/jcb.20220704…) applied to such a beautiful phenomenon 👍🏻
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Fund a project that will democratize microfabrication by using cheap, off-the-shelf components #crowdfunding #opensource #Science #technology
Lucien Hinderling (@lhinderling) profile pictureLucien Hinderling@lhinderling19 Jun 2023
How to 3D-print any microfluidic device or stamp for micropatterning? Quick iteration times, from design idea to seeding cells in one day, no clean room required. Short thread on a method we’re working on in the lab!
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Maciej Dobrzynski retweeted
Peyman Milanfar (@docmilanfar) profile picture
Peyman Milanfar
@docmilanfar12 Jun 2023
don’t be misled by low-order statistics
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DL@MBL: Deep Learning for Microscopy Image Analysis (#DLatMBL) Course Dates: August 21 – September 5, 2023 Application Deadline: May 18, 2023 mbl.edu/education/advanced-r…

AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory

The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks...

mbl.edu
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Fantastic collaborative spirit at 2023 @NEUBIAS_ training and symposium. We need to create sustainable support for the amazing #bioimaging #opensource software and prevent the infamous code rot. Interesting to see @ChanZuckerberg financing so many projects. Thank you all!
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Strong Swiss representation at @NEUBIAS_ symposium in Porto🇨🇭💪🏻 @SwissBIAS #ImageAnalysis #MachineLearning #DeepLearning
Image from Maciej Dobrzynski (@macdobry)
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Michael Baym (@baym) profile picture
Michael Baym@baym10 May 2023
<chefs kiss> arxiv.org/abs/2304.01393
Every Author as First Author

Every Author as First Author

We propose a new standard for writing author names on papers and in bibliographies, which places every author as a first author -- superimposed. This approach enables authors to write papers as...

arxiv.org
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Are you a grad student, postdoc, or early-career PI and passionate about teaching and learning #bioimageanalysis? So passionate you want to talk about it for 4 days next February with an AMAZING group of folks (see next)? If so, please apply to our @Co_Biologists workshop! 1/3
Image from Beth Cimini Lab 🔬💻 📊 (@CiminiLab)
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Maciej Dobrzynski retweeted
Kota Miura (@cmci_) profile picture
Kota Miura@cmci_10 May 2023
Daniel Sage insisting us to estimate the CO2 consumption for the computation we use for each bioimage analysis project by a python library offered at codecarbon.io/ : NEUBIAS Porto 2023

Code Carbon

Open tools to measure the environmental footprint of computing and AI — CodeCarbon for local compute, EcoLogits for GenAI APIs.

codecarbon.io
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Maciej Dobrzynski retweeted
Kota Miura (@cmci_) profile picture
Kota Miura@cmci_9 May 2023
NEUBIAS training school Porto: people working on data they brought with them. Tracking to identify movement patterns, counting spots, profiling mitochondria shapes…
Image from Kota Miura (@cmci_)
Image from Kota Miura (@cmci_)
Image from Kota Miura (@cmci_)
Image from Kota Miura (@cmci_)
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I have written code like this... 😬
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PertzLab (@PertzL) profile picture
PertzLab@PertzL15 Sep 2022
Our latest work ! authors.elsevier.com/a/1floh…. We show how simple self-organization rules in MAPK signaling allows to shape a simple epithelial cyst - a breast acinus.
Image from PertzLab (@PertzL)
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