Lightnews — Scholar-powered news

Reposted by John Lock

Siân Culley @superresolusian.bsky.social · 11d

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

80 60

Reposted by John Lock

Clausen Lab @clausenlab.bsky.social · Aug 21

big one! a decade in the making. nadler & team develop tools to track lipid transport in living cells at single-species resolution. turns out non-vesicular, asymmetry-driven transport is the main architect of organelle identity. feels like the dawn of a golden era for lipid biology. rdcu.be/eBGJv

Quantitative imaging of lipid transport in mammalian cells

Nature - Directional, non-vesicular lipid transport is responsible for fast, species-selective lipid sorting into organelle membranes.

rdcu.be

1 21 58

John Lock @locusj.bsky.social · Aug 11

As old mate said: "the mind is not a vessel to be filled, but a fire to be kindled". Glad to see it burning brightly, & likely to spread further.

John Lock @locusj.bsky.social · Aug 11

This is also a lot more than an article for me. @felkohdigital.bsky.social is a PhD student in my team, & these are ideas he & I & we as a team discuss a lot; not so much the analogies (though sometimes). It's a beautiful thing to read it in his words, & to see his passion for the ideas.

1

John Lock @locusj.bsky.social · Aug 11

@felkohdigital.bsky.social wrote a beautiful popular science piece about how #AI is advancing the inference of molecular function from analysis of cellular form, i.e. image-based phenotyping. If you want to explain your #HCS project to a friend, this might help! #Microscopy tinyurl.com/4ne8vcaj

Imaging in the age of AI: form and function, computed at scale — Cancer Systems Microscopy Lab

From 17th-century microscopes to AI-powered imaging, discover how technology is transforming our ability to study cancer cell form and function at scale.

tinyurl.com

1 2 3

Reposted by John Lock

Rita Strack @ritastrack.bsky.social · Aug 8

Microscopy most especially. To be the first human to ever lay eyes on something. What a feeling.

RedPen/BlackPen @redpenblackpen.bsky.social · Aug 8

Really just had something like this feeling this afternoon. It’s the high that keeps you coming back for more

Cartoon of a scientist peering through a microscope saying "Whoaah!!!". Title says "The best part of Science is knowing, for a moment, something that nobody else in the world knows."

5 23 140

Reposted by John Lock

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)

1 8

Reposted by John Lock

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)

1 2 9

Reposted by John Lock

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)

1 2 7

Reposted by John Lock

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)

1 2 7

Reposted by John Lock

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

3 24 76

John Lock @locusj.bsky.social · Aug 8

Yes, a wonderful collaboration! Fantastic vision from @superresolusian.bsky.social, Andrew Gunawan & @micoxscopy.bsky.social challenging IQM dogma re what a 'good' #FluorescenceMicroscopy image is. Important ideas for our field, always with good humour, regardless of the hour (or pet behaviour) :)

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)

1

John Lock @locusj.bsky.social · Jul 31

Our #Extensible_Immunofluorescence (ExIF) technique is a bit like #AI doing #origami. From some starting information (raw images = sheets of paper), AI can re-fold many alternatives (virtual images = alternate origami), capturing more #single-cell biology. Check out: www.nature.com/articles/s41...

1 1 1

Reposted by John Lock

John Lock @locusj.bsky.social · Jul 30

Amazing new collab with & led by @kriskilian.bsky.social showing brief capillary constriction drives cancer stem cell traits & tumorgenicity in a PIEZO (i.e. mechanosensitive) manner. Blood-borne CTCs get an 'aggressiveness boost' from squeezing through small vessels. www.biorxiv.org/content/10.1...

Capillary constrictions prime cancer cell tumorigenicity through PIEZO1

Metastasis is a hallmark of cancer and is responsible for the majority of cancer-related deaths. Evidence suggests that even a single cancer cell can spread and seed a secondary tumour. However, not a...

www.biorxiv.org

1 1

John Lock @locusj.bsky.social · Jul 30

Not just noise! Single-cell quantitative imaging reveals that epithelial-mesenchymal #EMT cell state pre-determines different magnitudes, kinetics & intracellular spatial routing of EGF-induced phospho-signalling. Great work @felkohdigital.bsky.social & collab team! www.biorxiv.org/content/10.1...

Epithelial–mesenchymal cell state heterogeneity predetermines differential phospho-signaling responses to EGF stimulation

Understanding why isogenic cancer cells respond differently to equivalent oncogenic stimuli is vital for optimizing anticancer therapies. Emerging evidence suggests that pre-existing differences in ce...

www.biorxiv.org

John Lock @locusj.bsky.social · Jul 30

Amazing new collab with & led by @kriskilian.bsky.social showing brief capillary constriction drives cancer stem cell traits & tumorgenicity in a PIEZO (i.e. mechanosensitive) manner. Blood-borne CTCs get an 'aggressiveness boost' from squeezing through small vessels. www.biorxiv.org/content/10.1...

Capillary constrictions prime cancer cell tumorigenicity through PIEZO1

Metastasis is a hallmark of cancer and is responsible for the majority of cancer-related deaths. Evidence suggests that even a single cancer cell can spread and seed a secondary tumour. However, not a...

www.biorxiv.org

1 1

Reposted by John Lock

IMAGE Lab @labphan.bsky.social · Jun 26

Christine Chaffer, @skummerf.bsky.social at @garvaninstitute.bsky.social, Smita Krishnaswamy at Yale et al present AAnet a neural network for nonlinear archetype analysis that more accurately captures cell plasticity & learns the spatial organisation of the archetypes. What is the advance? 1/3

AAnet resolves a continuum of spatially-localized cell states to unveil intratumoral heterogeneity

Abstract. Identifying functionally important cell states and structure within heterogeneous tumors remains a significant biological and computational challenge. Current clustering or trajectory-based ...

aacrjournals.org

1 2 7

Reposted by John Lock

Elizabeth McKenna @elizsmckenna.bsky.social · Jun 24

Now online in Cancer Discovery: AAnet Resolves a Continuum of Spatially-Localized Cell States to Unveil Intratumoral Heterogeneity - by Aarthi Venkat, Scott Youlten, Beatriz San Juan, Smita Krishnaswamy, Christine Chaffer, and colleagues doi.org/10.1158/2159...

1 5 10

John Lock @locusj.bsky.social · Jul 15

Follow-up stories coming soon on our next-generation beyond #Extensible_Immunofluorescence (i.e. microscopy image data augmentation with Generative AI) & on #EMT definition + dynamics & on E/M state-dependent computation across diverse stimuli + signalling. Watch this #Systems_Microscopy space 🔬👍

John Lock @locusj.bsky.social · Jul 15

For those interested in the regression / ML-based #Computational_Multiplexing strategy used by @felkohdigital.bsky.social here, it builds on DL-based #Extensible_Immunofluorescence we demo in www.nature.com/articles/s41.... You can build multiplexed IF data from standard IF with either method.

Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data - Nature Communications

Gunawan et al. propose an Extensible Immunofluorescence (ExIF) strategy that integrates distinct 4-plex image panels from routine fluorescence microscopy into multiplexed datasets enabling q...

www.nature.com

1

John Lock @locusj.bsky.social · Jul 15

The first, first-author story www.biorxiv.org/content/10.1... from @felkohdigital.bsky.social & www.cancersystemsmicroscopylab.com exploring how the epithelial-mesenchymal (E/M) state landscape pre-determines EGF signalling responses. An analytical tour-de-force, with more to come on this theme!

1 3 4

John Lock @locusj.bsky.social · May 27

🔬 PostDoc Alert! Our liquid biopsy collaborators Cancer & Inflammation Lab seek talented PostDoc to develop personalized cancer diagnostics. Focus: DDR & immune biomarkers in prostate/lung/GI cancers. Be part of the #precision_medicine revolution! #PostDoc #CancerResearch
Apply@ tinyurl.com/yps8nwdf

Postdoctoral Research Fellow - Medical Oncology Job in Liverpool, Sydney NSW - SEEK

Seeking a talented Postdoctoral Research Fellow to join the Cancer and Inflammation Research Group at the Ingham institute, Liverpool.

tinyurl.com

1

John Lock @locusj.bsky.social · May 20

Our #AI #research @natcomms.nature.com uses #multiomics data integration concepts to fuse 4-channel imaging data into unlimitedly multiplexed image datasets via generative deep learning to interrogate complex cell biology, like #EMT. Multiplexing made easy! rdcu.be/emtBc @singmolsci.bsky.social

Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data

Nature Communications - Gunawan et al. propose an Extensible Immunofluorescence (ExIF) strategy that integrates distinct 4-plex image panels from routine fluorescence microscopy into multiplexed...

rdcu.be

1 7 9

John Lock @locusj.bsky.social · Sep 9

I'm developing a new onboarding, orientation & support pack for postdocs & professional staff #UNSW School of Biomedical Sciences. What's the #1 thing you wish someone had told you when you arrived at your institution, to help you connect, contribute & launch your career?

2