iiinova — where your digital self keeps evolving

Simon Cleary @simoncleary.bsky.social · 09/10/2026

Nikon have made the right choice and an important discussion has been started on acceptable use of AI in microscopy. Look at this weird little guy (now 5th place, a sea slug captured by Igor Adameyko)!!

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Simon Cleary @simoncleary.bsky.social · 01/10/2026

This stood out in the Nature news coverage. I don't think that we will ever get to see the underlying data.

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Simon Cleary @simoncleary.bsky.social · 24/09/2026

Sounds sensible as Nikon comms do not seem to understand. The winner's responses have made people even angrier, but I think it is important to remember that this is a young scientist who also doesn't seem to understand the upset, and pile-ons can be harmful. Wrote this on Linkedin:

Screenshot of Linkedin comment response to Ning Xu - "Ning - I want to add that the greyscale images in your preprint look excellent and you shouldn't feel discouraged from research by how other scientists have reacted to your submission to this contest. People are upset about use of AI to generate images here because doing this gives the false and potentially harmful impressions that airways look like this (images from this competition get used a lot in education and science communication) and that we can already image them like this (it is important to be open about limitations of current approaches so that research funders understand the need to continue to support research). "

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Simon Cleary @simoncleary.bsky.social · 24/09/2026

Even if it were ok to add AI-generated details in the lower half of the movie, what we are now told is a section of one ciliated cell is way too wide to be based on real images of one cell.

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Simon Cleary @simoncleary.bsky.social · 23/09/2026

In the original version of this piece the person/people writing for the Nikon competition also removed a mention of AI by the winner:

Original paragraph reads:
'His advice to other researchers considering entering the competition is straightforward: “Take care of the sample, use as little light as possible when working with living cells, and most importantly, keep recording. The best moment usually appears right after you decide to stop.”'

New paragraph has added section on AI: 'His advice to other researchers considering entering the competition is straightforward: “Take care of the sample, use as little light as possible when working with living cells, and embrace AI to reveal the hidden beauty in your data. Most importantly, keep recording. The best moment usually appears right after you decide to stop.”'

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Simon Cleary @simoncleary.bsky.social · 22/09/2026

Some upset regarding the Nikon Small World in Motion winner this year so wanted to highlight that the beautiful image that won the Small World competition in 2022 was the initial inspiration for our project:

Embryonic hand of a Madagascar giant day gecko (Phelsuma grandis) stained for collagen and beta tubulin, from Grigorii Timin and Michel Milinkovitch https://doi.org/10.1016/j.isci.2023.106452

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Simon Cleary @simoncleary.bsky.social · 21/09/2026

Grateful for any feedback or questions. Thanks to @acmedsci.bsky.social @balrcommunity.bsky.social @britpharmsoc.bsky.social @bioimaginguk.bsky.social for funding that enabled this work - a result of the summer projects of talented undergraduate students Amy Rivers and Mahhum Saqib!

Co-authors Amy Rivers (left) and Mahhum Saqib (right) in the lab.

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Simon Cleary @simoncleary.bsky.social · 21/09/2026

First preprint from the lab! We found that fluorescence imaging of fibrillar collagen with fast green FCF is useful for imaging pulmonary fibrosis: doi.org/10.64898/202...

Two images showing fast green FCF staining of fibrillar collagen in magenta. An image of a fibrotic sample on the right shows higher intensity and prevalence of staining compared to a healthy control sample on the left.

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Simon Cleary @simoncleary.bsky.social · 18/09/2026

You can see the nice (label-free) images that this microscope modality produces in this preprint: doi.org/10.48550/arX... Not sure how you would get from this to the prize-winning image (with very long anenome-like cilia) without genAI shenanigans...

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Simon Cleary @simoncleary.bsky.social · 05/08/2026

The AJP-Lung editorial fellowship is inviting applications for a new round: ow.ly/rUAN50Zq10K I really enjoyed and benefitted from participating - more info in this article from previous fellows: doi.org/10.1152/ajplung.00251.2026

Flyer promoting the AJP-Lung Editorial Fellowship Program with QR code linking to information on applications: ow.ly/rUAN50Zq10K

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Simon Cleary @simoncleary.bsky.social · 22/06/2026

Read about how research into lymphatic function is changing our understanding of immune regulation in the lungs in our review: doi.org/10.1016/j.co... Congratulations to co-authors Amy Rivers and Camila Migues Ramirez!

Immunofluorescence staining for lymphatic endothelial cells (green) and smooth muscle (white) in a mouse lung. Image credit: Yurim Seo

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Simon Cleary @simoncleary.bsky.social · 05/03/2026

Few but mighty - check out this cool study implicating gamma delta T cells in controlling macrophage responses in lung cancer!

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Simon Cleary @simoncleary.bsky.social · 16/02/2026

Cool to see data backing up an anecdote I have been told - that short (1 hour) formaldehyde fixation can be better than longer (6 hours+) fixation for staining some antigens:

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Simon Cleary @simoncleary.bsky.social · 15/01/2026

Nice evidence for a role for the ectonucleotidase CD39 in limiting pulmonary thromboembolism in sickle cell disease with striking footage of this process!

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Simon Cleary @simoncleary.bsky.social · 09/01/2026

Thanks, odd decisions being made at a company with a focus on preventing plagiarism.

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Simon Cleary @simoncleary.bsky.social · 22/12/2025

This is cool stuff - imaging covalent drug biodistribution using tissue clearing methods

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Simon Cleary @simoncleary.bsky.social · 25/11/2025

Looking forward to chairing a session with @doreenlau.bsky.social at the British Society for Immunology Congress next week! Great line-up of speakers. Send an email if you would like to meet at or around the conference.

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Simon Cleary @simoncleary.bsky.social · 19/08/2025

PhD opportunity: please contact me if you know someone with a strong interest in respiratory science who would like to apply for a Sir David Jack PhD scholarship. Details here: www.bps.ac.uk/membership-a... Course fee waivers possible for outstanding international students.

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Simon Cleary @simoncleary.bsky.social · 23/06/2025

Interested in new ways to study interactions between cancers and the immune system? If yes, have a read of this article on mine and Longhui Qiu's recent work, featured in Nature Reviews Cancer's Tools of the Trade series: rdcu.be/er3Iq

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Simon Cleary @simoncleary.bsky.social · 27/01/2025

A role for the druggable kinase TNIK in promoting vascular leak in inflammation! Grateful to have had the opportunity to contribute to this study: science.org/doi/10.1126/sciadv.adk6583

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Simon Cleary @simoncleary.bsky.social · 09/01/2025

Congrats to Farsh Moussavi-Harami for discovering that deficiencies in SHP-1 (Ptpn6) lead to vasculitis and inflammatory bleeding in lung infections, and that increasing SHP-1 activity might be a useful way to suppress harmful neutrophil responses!

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