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Siân Culley @superresolusian.bsky.social · 9d

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

Bioimage Analysis Specialist | King's College London

www.kcl.ac.uk

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Siân Culley @superresolusian.bsky.social · Aug 22

Thanks Uri (for both the complement and being rigorous in your benchmarking)!

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Siân Culley @superresolusian.bsky.social · Aug 12

This is suuuuper cool! Quantitative modelling of structures in fluorescence microscopy images across several orders of magnitude 👀

Susan Cox @micoxscopy.bsky.social · Aug 12

How do you quantify cell structures which are deformed between different observations? Our preprint shows how to perform Simultaneous QUAntification of Structure and Structural Heterogeneity (SQUASSH) on 3D fluorescence microscopy data. (1/5)
www.biorxiv.org/content/10.1...

Extracting biological structure and heterogeneity from the nano to the macro scale

Fluorescence microscopy is an essential tool in biology. It has revealed great variability at multiple scales, in macromolecular complexes, cells, and organisms. Understanding this variability will re...

www.biorxiv.org

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Siân Culley @superresolusian.bsky.social · Aug 7

This is the result of a super fun collaboration with Andrew Gunawan from @locusj.bsky.social and Erik Meijering's groups at UNSW (there aren't many collaborators I'd brave a 9-11 hour time difference for, but these guys are great 🦘) and @micoxscopy.bsky.social a bit closer to home! (5/5)

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Siân Culley @superresolusian.bsky.social · Aug 7

For giggles, we also discovered that you can deliberately force images to be structurally wacky while still getting high scores on quality metrics (please don't try this at home) (4/5)

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Siân Culley @superresolusian.bsky.social · Aug 7

Most alarmingly, it turns out that sometimes these metrics tell you that your image has got better after image processing, even when your downstream biological analysis gets worse as a result ☹️ (3/5)

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Siân Culley @superresolusian.bsky.social · Aug 7

We show that PSNR and SSIM fundamentally suck (technical scientific term there) for fluorescence microscopy in general. They also love processed images - even if those processed images don't look all that great. (2/5)

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Siân Culley @superresolusian.bsky.social · Aug 7

Hello! Very excited to share our latest preprint, which is great news for us but terrible news for any diehard fans of PSNR and SSIM as image quality metrics in microscopy... (1/5)
www.biorxiv.org/content/10.1...

Image quality metrics fail to accurately represent biological information in fluorescence microscopy

Image processing methods offer the potential to improve the quality of fluorescence microscopy data, allowing for image acquisition at lower, less phototoxic illumination doses. The training and evalu...

www.biorxiv.org

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Siân Culley @superresolusian.bsky.social · Jul 30

Had a great time teaching on #SOMC25, including my first ever field trip and resultant microscope-based exposure therapy to try and cure myself of my irrational crustacean phobia

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Siân Culley @superresolusian.bsky.social · Dec 25

Haha definitely! Also I'm not sure how hot Great Uncle Donald's Russian was 😂 I do enjoy the apparent mismatch of energies though

Siân Culley @superresolusian.bsky.social · Dec 25

It's simply too complex for my tiny woman brain to comprehend, Dave

Siân Culley @superresolusian.bsky.social · Dec 25

I love everything about this relic I just found at my parents' house. My great uncle Donald met Valentina Tereshkova! Look how happy he is! Look how unimpressed she is with Concorde when she has been into been into actual literal space! Look how mansplainy the caption is!

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Siân Culley @superresolusian.bsky.social · Dec 10

London microscopy folk - does anyone have an old-school SIM (rather than an iSIM/Sora/Airyscan) that we could have a look at some expanded samples on? Our STED is dead (which rhymes but is also sad) so we're hunting for another system 👀

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Siân Culley @superresolusian.bsky.social · Dec 3

Okay this worked!!!! I now have a .zarr that I can open in BigDataViewer, which is the biggest achievement in the last two hours/half a packet of biscuits. Thank you! 💕

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Siân Culley @superresolusian.bsky.social · Dec 3

Yes chef! 👩‍🍳

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Siân Culley @superresolusian.bsky.social · Dec 3

👋 all aboard the struggle bus! 🚌 (a) was the first thing we tried, (b) I don't understand what this means (I am an idiot who mainly only understands tiff files), (c) I'm in the middle of composing a image.sc post so I'll see you over there 🫡

Image.sc Forum

Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).

image.sc

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Siân Culley @superresolusian.bsky.social · Dec 3

I have tried 😀 I have failed 😩
This threw an error for our test image (18215x18215 pixels, 3 channels) - I tried massaging the chunk size with no joy. Happy to share the error if it's helpful, but I'm 99% sure that the problem is that I am an idiot and failing to understand something fundamental

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Siân Culley @superresolusian.bsky.social · Dec 3

This is our first ever attempt to use zarr and the one image we have converted from .nd2 to .zarr as a test seems to have had the effect of opening a portal to actual hell 😂

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Siân Culley @superresolusian.bsky.social · Dec 3

Putting the AAAAARRRRRRGGGGHHHH into OME-Zarr

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Siân Culley @superresolusian.bsky.social · Dec 2

Gently sobbing into microscopes with a weak smile on my face since 2009

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Siân Culley @superresolusian.bsky.social · Dec 2

My actual life

https://www.instagram.com/p/DDE5b69tGOA/?igsh=YjhleW0yaW10Z2d5

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Siân Culley @superresolusian.bsky.social · Nov 29

Turns out that it's even easier to apply if you have the correct link to follow 🤠
CORRECT LINK: www.jobs.ac.uk/job/DKU906/p...

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Siân Culley @superresolusian.bsky.social · Nov 29

It's even more fun and collaborative when it's the correct link to apply: www.jobs.ac.uk/job/DKU906/p...

Postdoctoral Research Associate in the Department of Randall Cell & Molecular Biophysics at King's College London

Apply for the Postdoctoral Research Associate in the Department of Randall Cell & Molecular Biophysics role on jobs.ac.uk, the top job board for academic positions in higher education. View details an...

www.jobs.ac.uk

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Siân Culley @superresolusian.bsky.social · Nov 29

There's a good chance we'll be able to extend the post beyond the advertised end date 🤠
Please don't hesitate to drop me a line if you want a chat about the position or are thinking of applying!

Siân Culley @superresolusian.bsky.social · Nov 29

An early Christmas present if you like Fluorescence Lifetime Imaging Microscopy, data analysis and pho-ho-ho-tons (sorry not sorry) - another postdoc position open in my group! Deadline 16th December -> www.kcl.ac.uk/jobs/100785-...
Part of a super fun and collaborative Wellcome Bioimaging project 🔬

www.kcl.ac.uk

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