petrakovavladka.bsky.social
Scientist excited about plasmons, DNA origami and microscopy. Group leader at the Heyrovsky Institute in Prague, Czexpats co-founder, Humboldt Foundation alumni, mother of 4.
petrakova-group.eu
16 posts
300 followers
327 following
Conversation Starter
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We will be happy to collaborate with developers of SMLM software on implementing the method and bringing it to the users! Please, reach out to us!
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A „behind the scene” note: The method was designed and implemented by Mirek, who came to work on microscopy after his tenure in the radar industry. To me, it is a beautiful example of how inspiration from one field leads to progress in another and that it is worth taking the risk.
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Congratulations to all authors, Mirek Hekrdla, Niklas Hansen @niklasha.bsky.social, David Roesel, Soumya Frederick, and Khalilullah Umar from
Heyrovsky Institute Prague. Big thanks to reviewers and editors from @naturecomms.bsky.social
for an exceptionally constructive review process.
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We tested the method on simulated data, experimental data, and data from SMLM challenge (it is wonderful that it exists, big thanks to those who made and maintain it!). The method is computationally efficient and easy to implement using standard Python libraries.
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Second, we implemented probabilistic thresholding, where the level of false positive probability sets the detection threshold and minimizes false negative detections. To enhance robustness against varying background, we set the threshold adaptively.
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How did we solve it? By combining two steps. First, we derived a theoretically optimal filter for Poisson noise prevalent in microscopy, Poisson Matched Filter, and used it as a performance benchmark for other filters used in SMLM, setting Matched Filter as a desired option.
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Why is this important? Detection of molecules is an essential first step in Single Molecule Localization Microscopy. Yet, it currently lacks quantification of detection errors resulting in artifacts and affecting further analysis. Furthermore, it is unduly complex.
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Inspired by radars and astronomy, we used signal detection theory to design an optimal filter for microscopy and implement probabilistic thresholding that allows to control the level of false positive detections.
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I actually enjoyed reading it! It is a letter to editor and so obviously satire that I don't think it deserves the ridicule... As I witnessed non-ethical behavior from doctors when my mom was seriously ill, I am glad it raises important questions in a very entertaining and attention grabbing way.
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👏 Thank you for making the list! Would love to take part 🧬
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This is my dream!! Leading a lab alone is a lot of pressure to be good at everything - innovative ideas, knowledge, networking, mentorship, communication, running the lab, admin, service,... Which is impossible for me... I would love to have someone to complement and combine our skills and talents!
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@jordanovaan.bsky.social
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👏🖐️🔬
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so please if you are (or know of) a Czech scientist or a student living abroad, I would love to hear from you!