James Manton

James Manton

@jamesdmanton.bsky.social

Applied physicist & microscopist/microscopologist

1.4K followers602 following418 posts

James Manton
@jamesdmanton.bsky.social

I've been steadily developing our image compression software over the past month and now you can try it out in your browser, without needing to install anything, thanks to the magic of WebAssembly! beryl.mrc-lmb.cam.ac.uk/radelta/ No data is uploaded anywhere, it all stays on your computer.

beryl.mrc-lmb.cam.ac.ukRadelta — microscopy image compressionLocal compression and decoding of microscopy image volumes using Radelta.
James Manton@jamesdmanton.bsky.social

I've been working on a fast, high-ratio image compressor to try and alleviate the data storage issues myself and some of my colleagues have recently been facing. Before I 'release' version 1, it'd be great to gain some feedback regarding performance and missing features. github.com/jdmanton/rad...

github.comGitHub - jdmanton/radeltaContribute to jdmanton/radelta development by creating an account on GitHub.

James Manton reposted

MRC Laboratory of Molecular Biology
@mrclmb.ac.uk

Lead the next discovery at the LMB. We’re recruiting Group Leaders to join our Structural Studies and @cellbiol-mrclmb.bsky.social Divisions. Benefit from long-term support, access to outstanding core-facilities and a collaborative environment where science thrives. ➡️ mrclmb.ac.uk/research-lea...

mrclmb.ac.ukCurious about how life works? | MRC Laboratory of Molecular BiologyThe LMB's Structural Studies and Cell Biology Divisions are each looking for a new Group Leader, at tenured or tenure-track level, to help solve the pu ...

James Manton reposted

Rob Campbell
@raacampbell.com

Preprint is out! Our BakingTray software turns a 2-photon microscope into a serial-section tomography system for automated whole-organ imaging. ~€35k to convert an existing scope. 11 systems worldwide, >7,000 samples at SWC alone #neuroskyence #microscopy www.biorxiv.org/content/10.6...

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James Manton
@jamesdmanton.bsky.social

For now there are sources and binaries for Windows, Mac and Linux, along with a universal ImageJ plugin. Napari is an obvious next target for support, but I'd like to know what you'd want developed. Both HDF5 and Zarr support are in the works.

James Manton
@jamesdmanton.bsky.social

A key design goal was to exceed the bandwidth of a saturated sCMOS camera (0.7813 GiB/s) without needing a GPU. Current benchmarking suggests my office PC should be able to handle 3. Another goal was high compression ratio: JPEG-XL lossless (effort 9) beats us by 3.7%, but we're ~1000× faster.

James Manton
@jamesdmanton.bsky.social

Blosc2 bitshuffle + Zstd-5 beats us on speed (approximately double encode and decode), but produces files about a third larger. Nevertheless, if speed is the ultimate concern, this is probably the way to go.

James Manton
@jamesdmanton.bsky.social

I very much enjoyed Lisa Cuneo's talk at FOM2026 on a new approach to deconvolution, so it's great to see the preprint is now out: www.biorxiv.org/content/10.6... @vicidominilab.bsky.social

biorxiv.orgIndependent noise realizations enable morphologically agnostic image reconstruction in single-photon-sensitive microscopyAdvances in single-photon sensitive detectors are rapidly expanding the adoption of photon-counting fluorescence microscopy. Under the Poisson photon-counting statistics, iterative Richardson-Lucy (RL...

James Manton reposted

Nils Norlin
@nilsnorlin.bsky.social

I am looking for postdoc candidates for two opportunities in my lab at Lund University. 1. Co-application for a two-year postdoc scholarship on method development in 3D spatial biology, with applications in lung physiology, cancer and neuroscience.

James Manton reposted

Sjors Scheres
@sjorsscheres.bsky.social

Michel Goedert and myself are looking for two postdocs to work on #cryoEM and #masspec of #alphasynuclein filaments from neurodegenerative disease. Come join our bubbly and friendly team at the @mrclmb.ac.uk in lovely Cambridge, UK. www.nature.com/naturecareer...

nature.comPostdoctoral Scientist | Neurobiology | Dr Michel Goedert | LMB 2842 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12864505Postdoctoral Scientist Salary £42,694 per annum Fixed term, 3 years MRC Laboratory of Molecular Biology, Cambridge, UK To work in the group of Dr M...

James Manton reposted

Lara Krüger
@lara-kruger.bsky.social

📢 We are looking for a Junior Group Leader to join us at @institutcurie.bsky.social! Having joined the department just over a year ago, I can honestly say that it is an exceptionally stimulating and supportive scientific environment, filled with outstanding colleagues — all in the heart of Paris.

James Manton
@jamesdmanton.bsky.social

GCHQ strikes again and deems knowledge of our new approach to tissue clearing too dangerous for public consumption! We're still working on the information included on the website, so hopefully we're unblocked by the time we've finished. If you never hear from me again you know what's happened...

James Manton@jamesdmanton.bsky.social

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...

James Manton reposted

Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳
@anhhle2702.bsky.social

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

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!

James Manton reposted

Kevin Dean
@kevin-dean.bsky.social

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

biorxiv.orgDeciphering the Multiscale Morphology of Somatic Oncogenic Alterations in Hepatocellular CarcinomaSomatic 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 ...
James Manton
@jamesdmanton.bsky.social

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...

James Manton@jamesdmanton.bsky.social

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

James Manton
@jamesdmanton.bsky.social

To achieve this, we integrated a beam shifting device into the optical path and acquired four frames for every slice of the z stack. Between frames, the image is shifted by half a pixel in a 2×2 xy grid. Then, a simple algorithm based on the Richardson–Lucy iteration reconstructs the full image.

James Manton reposted

Biohub
@biohub.org

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

James Manton
@jamesdmanton.bsky.social

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...

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James Manton
@jamesdmanton.bsky.social

We anticipate that this implementation of direct-view oblique plane microscopy will provide both a practical platform for volumetric cleared-tissue imaging and an extensible basis for further improvements in imaging performance. If you'd like to give it a try please contact me and we can host you!

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James Manton
@jamesdmanton.bsky.social

As well as producing samples ourselves, we worked with friends and colleagues from the LMB and Imperial College London to put the system through its paces, imaging samples cleared with iDISCO (n = 1.56), MACS/ECi (n = 1.56), Ce3D (n = 1.50), OptiMuS-prime (n = 1.49) and ExM (n = 1.33).

James Manton
@jamesdmanton.bsky.social

ExM is great for clearing tissues, but the 64-fold (or larger!) volume increase prohibits imaging some samples, even with our extended FOV. So, we also developed our own tissue clearing method (REPLICA), with water as the index-matching liquid, which will soon be fully described in its own preprint.

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James Manton
@jamesdmanton.bsky.social

Furthermore, by careful use of optomechanics and 3D printed parts, the detection system is inherently alignment-free, drastically simplifying construction. The light sheet launch is similarly simple, with changes in refractive index requiring only the insertion of a chock to change incidence angle.

James Manton
@jamesdmanton.bsky.social

Through a careful reanalysis of the optical theory of remote refocussing, we realised that the detection system could be unaltered over the range n = 1.33–1.56, as diffraction-limited imaging performance is maintained. Only the processing needs to change, to account for a slight volume compression.

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James Manton
@jamesdmanton.bsky.social

While existing OPM systems can be tricky to align due to their multiple objective lenses and relay systems, our CtDvOPM instrument uses a single detection lens. By using a commercially available bi-telecentric lens (designed for parts inspection), we boost field-of-view while maintaining resolution.

James Manton
@jamesdmanton.bsky.social

Compared with the closest magnification microscope objective (Olympus 1.25× 0.04 NA), we maintain the same FOV but increase resolution more than three-fold. Alternatively, compared with the closest resolution microscope objective (Nikon 4× 0.13 NA) we obtain an almost eight-fold larger imaging area.

James Manton
@jamesdmanton.bsky.social

We introduce cleared-tissue direct-view oblique plane microscopy (CtDvOPM), which enables optically sectioned subcellular resolution imaging of centimetre-scale tissues at high-throughput over the full range of clearing media refractive indices (n = 1.33–1.56).

James Manton
@jamesdmanton.bsky.social

CtDvOPM can image conventionally-mounted expanded, aqueous or non-aqueous cleared tissue samples at up to 2 μm lateral by 14 μm axial resolution over a 10 mm × 10 mm × 25 mm sample volume without image tiling, at up to 400 million voxels per second.

James Manton
@jamesdmanton.bsky.social

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...

James Manton
@jamesdmanton.bsky.social

It's not clear if this is because GCHQ thinks our new microscope "is the bomb", a "cleared and well-presented danger" or because, as microscopists, we "look after the small things and [so] the big ones will take care of themselves".

James Manton
@jamesdmanton.bsky.social

A new direct-view oblique plane microscope is released into the wild, taking the number of lenses that need to be aligned down from four to two, all while maintaining the field-of-view and resolution!

Kevin Dean@kevin-dean.bsky.social

Altair Direct View OPM Preprint! We built a simplified direct-view oblique-plane microscope for imaging big, optically accessible specimens with a single-objective light-sheet geometry. Delivers... • ~5.4 mm field of view • ~2.6 μm, ~3.4 μm, and ~17.8 μm resolution in X/Y/Z