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-...
Thanks Uri (for both the complement and being rigorous in your benchmarking)!
This is suuuuper cool! Quantitative modelling of structures in fluorescence microscopy images across several orders of magnitude 👀
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)
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)
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)
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)
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...
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
Haha definitely! Also I'm not sure how hot Great Uncle Donald's Russian was 😂 I do enjoy the apparent mismatch of energies though
It's simply too complex for my tiny woman brain to comprehend, Dave
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!
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 👀
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! 💕
Yes chef! 👩🍳
👋 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 🫡
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
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 😂
Putting the AAAAARRRRRRGGGGHHHH into OME-Zarr
Gently sobbing into microscopes with a weak smile on my face since 2009
https://www.instagram.com/p/DDE5b69tGOA/?igsh=YjhleW0yaW10Z2d5
My actual life
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...
It's even more fun and collaborative when it's the correct link to apply: www.jobs.ac.uk/job/DKU906/p...
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!
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 🔬
I am of course delighted to be here.
