@RunningPhoton

I am a runner & data scientist at ZOMP (https://xitter.cf/t.co/lRvQQEWC4X). Previously postdoc with @KukuraLab (@KavliOxford) and PhD with @RainerHeintzmann (@Leibniz_IPHT).

 Cambridge, England
researchgate.net/profile/Jan_Becker17
Joined November 2019
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We demonstrate our method on biological samples with a range of RIs, including a whole fly brain 🧠 (imaged in < 3 min⚡) and > 1 cm long mouse bone 🐭🦴 (🧵 5/6).
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Pre-Christmas Fun! Look what some of our researchers got up to today. Huge congrats to the winning team. Well deserved guys! #tugofwar
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Single-protein optical holography biorxiv.org/cgi/content/shor… #biorxiv_biophys
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Our work related to simulating mass photometry is now available @ACSPhotonics: pubs.acs.org/doi/10.1021/acs… @KavliOxford | @OxfordChemistry | @UZH_en
The protein rendering was done by Dan Loewenthal in Blender using the Molecular Nodes plugin: Brady Johnston, Yinying Yao, wjm41, Johannes Elferich, Olivier Laprevote, Thibault Tubiana, Domenico Marson, Jessica A. Nash, & kimjoyc. (2023). BradyAJohnston/MolecularNodes: BETA: v2.7.1 for Blender 3.5+ (v2.7.1_beta). Zenodo. https://doi.org/10.5281/zenodo.7979024; https://github.com/BradyAJohnston/MolecularNodes (accessed 01st June 2023) The glass coverslip was taken from the Laboratory Glassware Pack 1 created by Dr. Joseph G. Manion, while the image background is freely available at: https://www.freepik.com/free-vector/matrix-style-binary-code-digital-background-with-falling-numbers_8289995.htm (accessed 1st June 2023)

ALT The protein rendering was done by Dan Loewenthal in Blender using the Molecular Nodes plugin: Brady Johnston, Yinying Yao, wjm41, Johannes Elferich, Olivier Laprevote, Thibault Tubiana, Domenico Marson, Jessica A. Nash, & kimjoyc. (2023). BradyAJohnston/MolecularNodes: BETA: v2.7.1 for Blender 3.5+ (v2.7.1_beta). Zenodo. https://doi.org/10.5281/zenodo.7979024; https://github.com/BradyAJohnston/MolecularNodes (accessed 01st June 2023) The glass coverslip was taken from the Laboratory Glassware Pack 1 created by Dr. Joseph G. Manion, while the image background is freely available at: https://www.freepik.com/free-vector/matrix-style-binary-code-digital-background-with-falling-numbers_8289995.htm (accessed 1st June 2023)

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A nice tweetorial from @KukuraLab can be found here: xitter.cf/KukuraLab/status/16431…
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A yellow photon running through the forrest ... moving at a speed v << c 😅
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(my twitter handle is @RunningPhoton 😉 )
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Enjoying day 2 of #FOM2023🔬with lots of light-sheet talks. Visit poster P1-G/3 to learn more about dual-view oblique plane microscopy (dOPM) and its application to high-content imaging of 3D cancer organoid models as part of the @MACH3Cancer CRUK Accelerator. – at Oporto, Portugal
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Any idea what this animation could represent? #FOM2023 | @FOMconferences | @KavliOxford | @OxfordChemistry Come to my poster (P2-F / 11) in the "Various Topics" poster session on Tuesday to find out. 🔬💻👩‍🔬
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Further work from my PhD out in @SciReports : nature.com/articles/s41598-0… With Hugh Sparks, @liliana_brito91 , Ken MacLeod, @sian_harding, and Chris Dunsby Many thanks to @ImperialPhysics @impchemistry @icbcdt @NHLI @EPSRC @TheBHF A mini-tweetorial (1/6):
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Our preprint on the principles & limitations on inferring mass from optical signals is out today. biorxiv.org/content/10.1101/… Many thanks to @KukuraLab at @KavliOxford | @OxfordChemistry and the Schuler lab @UZH_en (1/2)

A quantitative description for optical mass measurement of single biomolecules

Label-free detection of single biomolecules in solution has been achieved using a variety of experimental approaches over the past decade. Yet, our understanding of the magnitude of the optical...

biorxiv.org
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This study involves the simulation of the interferometric nature of the detected signal, a quantification of the effects of glass roughness and protein shape/orientation ... and many more. (2/2)
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Study from my PhD work recently out: doi.org/10.3389/fphys.2023.1… With Hugh Sparks, Ken MacLeod and Chris Dunsby (1/2)
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Out today: As it turns out, imaging using a full pupil is not always the best one can do. Instead split the information & computationally recombine! opg.optica.org/optica/fullte… Many thanks to: @TakahiroDeguch1, @AlexanderJugler, Ronny Förster, Uwe Hübner, @JonasRies, @HeintzmannLab
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Really enjoyed the Heraeus-Seminar on "Advanced Microscopy & Spectroscopy Methods in Medicine" at the Physikzentrum in Bad Honnef. After greeting Albert every morning, we covered a wide spectral range, with me comfortably staying in the visible but looking at unlabeled proteins.
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Thanks to just-received funding from @royalsociety & @MRC_LMB, @Mad_Lancaster and I are looking to recruit a PhD student (see below). The deadline is very soon (1 Dec), so please email [email protected] if you don't think you'll make it and we'll work something out.
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We're hiring - two Postdoctoral Research Associate positions in @OxfordChemistry @KavliOxford 1) single-molecule glycan imaging via scanning probe microscopy together with @ESIBDLab 2) hydrogen-deuterium exchange mass spectrometry of virus glycoprotein assemblies🦠 Links below!
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Already 3 months since my PhD defense - time flies!🎓 Thesis is now online at doi.org/10.25560/99343 🔬🫀
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New publication by #KavliOxford's @PhilippKukura, @WestonStruwe, @HundtNikolas, #MaxHantke, and #DanielCole Available here: doi.org/10.1126/sciadv.abm79…

Direct observation of the molecular mechanism underlying protein polymerization

The mechanism of actin polymerization is revealed by quantifying the full range of intermediates during filament formation.

science.org
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At which iteration would you stop this image restoration? Comment below.🤔🔬 me, @microRussell, @JamesDManton, @AndrewGYork had an idea, which I am going to present at #FOM2022 | @FOMconferences on Tuesday at 13:25 (CET) in "Image Analysis Methods"
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Of course there are still many aspects that we need to explore ... (experimental data?, regularizers?, ...) Many thanks to @microRussell, @JamesDManton & @AndrewGYork for their contributions in this "pandemic-born" project. 🙏
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Interestingly, early stopping acts as a very efficient regularizer! See below: instead of choosing to regularize + many iterations, it often makes sense to simply stop the restoration at the optimum point. Finding this optimum, however, is the tricky part.
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