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

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)

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

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 😂

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

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!