iiinova — where your digital self keeps evolving

Pradeep Rajasekhar @pradeepr.bsky.social · 10/09/2026

Shoutout to @dpshepherd.bsky.social as well for OPMv2 library and support!

Pradeep Rajasekhar @pradeepr.bsky.social · 10/09/2026

Really proud to see napari-lattice out! Developing the pipeline is one thing, but making it something genuinely usable by others was a lot of work. Grateful for the support @drlachie.bsky.social @krogersiooi.bsky.social @niallgeoghegan.bsky.social. Thankful to the OSS community!

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DrLachie @drlachie.bsky.social · 10/09/2026

We mostly use the LLSz for cellular imaging and we made the observation that in a field of view full of cells, more often than not, the cells are actually all independent measurements. If they don't interact, (or move much), why are we processing the whole image? Most of the image is empty!

Maximum intensity projection of a relatively sparse field of cells.

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DrLachie @drlachie.bsky.social · 10/09/2026

When we purchased our Zeiss Lattice Light Sheet all the problems we thought we knew from previously building our own were amplified by how much data it could acquire quickly. LLS data needs to be deskewed before viewing or analysis, if you want to add deconvolution – GPUs start catching fire

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DrLachie @drlachie.bsky.social · 10/09/2026

Proud to present the publication of napari-lattice – our solution to the immense computational requirements of Lattice Light Sheet and Oblique Plane Microscopy. onlinelibrary.wiley.com/doi/10.1111/... Before I get into the thread, the important part is on github: github.com/BioimageAnal... (1/n)

onlinelibrary.wiley.com

napari‐lattice: A user‐friendly image processing tool for lattice light‐sheet microscopy data

Lattice light-sheet microscopy (LLSM) enables researchers to capture high-speed 3D videos of living cells with high definition and minimal damage. However, this technology generates terabytes of data....

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DrLachie @drlachie.bsky.social · 10/09/2026

Thanks for indulging me. This is the first publication entirely driven by the Bioimage Analysis Core at @wehi-research.bsky.social and I can't thank everyone involved, but know that you're all appreciated and I wish all your lattice data be manageable! We can help with that!

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DrLachie @drlachie.bsky.social · 10/09/2026

Thanks also to all the authors for the contributions. And mostly to lead author @pradeepr.bsky.social – who has never stopped thinking of improvements and passion for OSS has ensured that napari-lattice has become a useful piece of software for the community, not just a pipeline that only we can use

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DrLachie @drlachie.bsky.social · 10/09/2026

Finally (nothing is ever final), I want to thank everyone involved. Of course @krogersiooi.bsky.social our fearless leader, @niallgeoghegan.bsky.social wizard of the lattice, @haesleinhuepf.bsky.social for his GPU libraries. Michael Milton for wrangling our spaghetti code into a modern structure.

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DrLachie @drlachie.bsky.social · 10/09/2026

But @DrLachie I hear you say – what if your cells move! Well I'm glad you asked (kind of), we've toyed with a workaround and are looking at integrating tracking data into our pipeline – so keep an eye on the github for new features as we develop them!

A moving cell is tracked across the field by an ROI drawn at each timepoint.

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DrLachie @drlachie.bsky.social · 10/09/2026

But why do one-by-one when you can do ALL AT ONCE! As a part of the development, we built in flexibility to parallelise over any parameter. ROI was the obvious one, but you could also do by time point, channel, even Z-range if you really wanted. All HPC enabled!

ANALYSE ALL THE THINGS! (Apologies to Hyperbole and a Half)

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DrLachie @drlachie.bsky.social · 10/09/2026

So, we (mostly @pradeepr.bsky.social ), started developing a pipeline that would take ROIs extract and only process those one-by-one - rather than the whole image Around here we also got a small development grant from @chanzuckerberg.bsky.social to make it into a @napari.org plugin.

napari-lattice - A napari plugin for processing Lattice Light Sheet or other Oblique Plane Microscopy data

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Australian BioImage Analysts' Society @ausbias.org · 03/08/2026

In a talk out of left field for us, this Month's AusBIAS meeting was @pradeepr.bsky.social taking us back to Ancient Rome to investigate whether image anlaysis can help read scrolls that haven't been read for nearly two thousand years. www.youtube.com/watch?v=mPtS...

youtube.com

AusBIAS July 2026 - Pradeep Rajasekhar

YouTube video by AusBIAS

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Johannes Soltwedel @jo-soltwedel.bsky.social · 17/06/2025

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging Let's have a look 👇🧪💻🔬

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Matt Lycas @lycasworks.bsky.social · 01/04/2025

Expansion microscopy of a tardigrade

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Cristobal Uauy @cristobaluauy.bsky.social · 07/01/2025

1/10 We are thrilled to share our preprint on spatial transcriptomics in wheat spikes led by the amazing @katielong.bsky.social and Ashleigh Lister. We resolved expression of 200 genes to cellular resolution. Pre-print👉 tinyurl.com/c7t3kncf., @johninnescentre.bsky.social @earlhaminst.bsky.social

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Wallace Marshall @wallaceucsf.bsky.social · 23/12/2024

Mitochondria consist of networks of cylindrical tubes, right? Not necessarily! - in our new preprint, @gavsturm.bsky.social investigates how mitochondria transiently adopt a beads-on-a-string morphology www.biorxiv.org/content/10.1...

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haesleinhuepf-bot.bsky.social @haesleinhuepf-bot.bsky.social · 16/12/2024

Exciting work by Schmidt et al.! Dive into BioImage Data Management & OMERO insights on Zenodo! 📊🔬 #BioImaging doi.org/10.5281/zenodo.13861026

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DrLachie @drlachie.bsky.social · 05/12/2024

I sound like a broken record when advising researchers about filenaming, my favourite line is "It's a filename, not a password" when discouraging special characters. I've got a new frontrunner for the worst I've seen. And they're only a single character.

Screenshot of three filenames that use just single characters D or E with weird accents that I've never even seen, let alone know how to type.

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Joachim Goedhart @joachimgoedhart.bsky.social · 21/11/2024

Nice work from Yasushi Okada and colleagues on the development of fluorescence lifetime biosensors for ATP, cAMP, citrate, and glucose using mTurquoise2 www.cell.com/cell-reports...

Construction, characterization, and validation of qmTQ2-ATP biosensor

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Nicolas Chiaruttini @nkiaru.bsky.social · 20/11/2024

Direct streaming of an #OMERO dataset in #BigDataViewer from the public server omero-tim.gerbi-gmb.de (dataset from the Workshop 35). Thank you Tom and @gerbi.bsky.social !

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DrLachie @drlachie.bsky.social · 19/10/2023

Running our first QuPath workshop today with @pradeepr.bsky.social, who doesn't love multiplex slide analysis on a Friday?

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