James Manton

@jamesdmanton.bsky.social

Applied physicist & microscopist/microscopologist

Yey, I figured out how to display 3D movie stacks in #ChimeraX, thanks to @dabiophysicist.bsky.social for the suggestion. My original tiff was not ome-tiff so you'll need to convert it first (do this with #Python), then adjust voxelsize in ChimeraX so the image isn't flat, record, and voila!

Anh Hoang Le, PhD 🏳️‍🌈@anhhle2702.bsky.social · 2w ago

One drawback tho and unless I'm not aware of an alternative, it seems if you want to display a time series stack, you have to save each time frame as a separate stack before loading them into #ChimeraX. If you don't, it will superimpose all timepoints into 1 single 3D stack. This, #napari is better!

New preprint! Using multiscale ExM/OPM/ASLM, we show that oncogenic drivers leave distinct 3D architectural fingerprints in intact liver tissue: NRAS primarily remodels cell shape, whereas CTNNB1 shifts mitochondrial architecture toward a pericentral-like state. tinyurl.com/kepy33m6

Deciphering the Multiscale Morphology of Somatic Oncogenic Alterations in Hepatocellular Carcinoma

Somatic oncogenic mutations are typically defined by their molecular alterations, yet how they reorganize cellular architecture within intact tissues remain largely unknown. Here, we demonstrate that ...

biorxiv.org

We've updated our cleared-tissue direct-view oblique plane microscopy preprint to include our latest resolution-enhancing results. Now the Nyquist sampling of our camera is no longer a limitation and so we obtain a diffraction-limited 2 μm lateral resolution! www.biorxiv.org/content/10.6...

An panel of three images showing 1) raw data, 2) bicubic interpolated data on a two-fold finer grid, 3) properly upsampled data on a two-fold finer grid, for two parallel neuronal filaments that can only be resolved as separate entities in the upsampled image.
James Manton@jamesdmanton.bsky.social · 2mo ago

We present: Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution www.biorxiv.org/content/10.6...

Image of first two pages of manuscript.

In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn

Waves of laser light coming from four different directions and meeting in the middle brightly inside the cavity of the laser phase plate

It's not every day you set up a new website and have it blocked by the Government Communications Headquarters (GCHQ), an intelligence service so secretive the UK government didn't formally acknowledge its existence until 1994, 75 years after it was founded...

A web warning from the National Cyber Security Centre, a part of GCHQ, stating:

"This site may be associated with malicious activity or malware.

Access to this site has been blocked by the Protective DNS Service

Site: www.ctdvopm.org

Please contact your local Network Administrator or IT support if you require further assistance"

🔬 UK researchers - funding is available to access world-class bioimaging facilities! The UK Bioimaging User Access Fund offers up to £5K for bioimaging or £2K for image analysis at 6 UK sites Open to PhD students, postdocs, technicians & PIs 📅 Next deadline: 31 Jul '26 👉https://shorturl.at/M2ckv

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I have been unreasonably fortunate to work with some extremely clever and notably kind people during my career so far. Katerina is a prime example of such. Whilst I obviously cannot guarantee the outcome of any endeavour, I'll be damned if I don't recommend this PhD opportunity most wholeheartedly!

IMPRS for Living Matter@imprs-lm.bsky.social · 5mo ago

📣 Physicists and engineers: apply your experimental skills to biology! Join the group of Katerina Naydenova @imprs-lm.bsky.social for a #PhD to develop new technologies that enable answering fundamental biological questions. Apply NOW!

Myself and @immunoah.bsky.social are looking to hire a postdoctoral scientist to build a next-generation high-throughput high-resolution light sheet microscope for imaging entire cleared organs/tissues and to further develop live & fixed tissue clearing methods. www.nature.com/naturecareer...

MRC Laboratory of Molecular Biology@mrclmb.ac.uk · 5mo ago

Interested in instrument development & optical microscopy? Join @immunoah.bsky.social & @jamesdmanton.bsky.social developing high-throughput light sheet microscopy to image entire tissues & progressing tissue clearing methods www.nature.com/naturecareer... Closes 07 APR #PostdocJobs #neuroimmunology

Microscopy image taken by a light sheet microscope showing an optically cleared lung in blue.

📣🧠 We're looking for someone to join the Lancaster Lab family as a Research Support Officer (maternity cover). You'll be studying the origins of human brain specialisations using brain organoids, as part of a great team at one of the world's great research environments. mrc.tal.net/vx/mobile-0/...

Research Support Officer - Cell Biology - Dr Madeline Lancaster - LMB 2788 - Medical Research Council

Location: Cambridge. Vacancy: Research Support Officer - Cell Biology - Dr Madeline Lancaster - LMB 2788. Closing Date: 25/03/2026, 23:55

mrc.tal.net

We are excited to be recruiting a new tenure track group leader in the Structural Studies Division at MRC LMB! It is an amazing place to start your own lab. @mrclmb.bsky.social Please get in touch if you have any questions. www.nature.com/naturecareer...

Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Cambridge, Cambridgeshire (GB) job with MRC Laboratory of Molecular Biology (LMB) | 12854636

Research Group Leader Tenure Track Starting Salary £67,979 to £76,868 per annum MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laborato...

nature.com

Sjors Scheres@sjorsscheres.bsky.social · 6mo ago

Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. 🥳 mrc.tal.net/vx/mobile-0/...