What if we could map every cell in the body, revealing its location and molecular identity? In this @NatureMethods perspective, we discuss the new era of 3D-omics by tissue clearing and AI, called Deep 3D Histology: PDF: 🧵👇🏼 rdcu.be/dNBe8
bit.ly/3WaD0QU
2- Tissue clearing techniques are evolving to enable imaging of intact specimens at cellular resolution. Learn how these methods, combined with light-sheet microscopy, are pushing the boundaries of 3D imaging from mouse embryos to entire human organs.

Very excited to share that our DELiVR method is now open access published @NatureMethods. We created a simple, brain-wide cell analysis deep learning tool, no coding needed! Fiji Plugin makes it accessible to all.
by @Dorie00 @Rami96614090 @moritz_negwer nature.com/articles/s4159…
2/n DELiVR is a robust deep-learning pipeline for whole-brain cell mapping. It operates through a user-friendly Fiji plugin. Re-trainable on custom data, DELiVR simplifies and streamlines brain cell analysis.

Exciting🥳 Our new study in Cell shows that our skull is a gateway for diagnosing & potentially treating brain diseases such as Alzheimer's & stroke. Imagine a future where a portable sensor on the skull can monitor brain health! @CellCellPress 🧵👇🏼with🔈 https://t.co/VrzVSra4lKcell.com/cell/fulltext/…
2/n Background: Neuroinflammation, the brain's immune system reaction common in disorders like stroke and dementia, can be like a fire damaging a house. Controlling it is tough as the brain isn't easily accessible.

Want to use deep learning for image analysis but lack the coding skills? We introduce DELiVR, a game-changer in brain-wide cell analysis. No coding required, our Fiji Plug-in does the magic. Hats off to @Dorie00, @Rami96614090, @moritz_negwer! 🧵👇🏼 1/n biorxiv.org/content/10.110… twitter.com/i/web/status/1… 2. What makes DELiVR stand out? It's a robust deep-learning pipeline for mapping cFos+ cells in whole brains. Combining tissue clearing, light-sheet microscopy, VR annotation & deep learning, it comes in an easy-to-use FIJI plugin and docker container! biorxiv.org/content/10.110…

4/n Finding 1)
Along with many organs, we discovered spike accumulations in the skull marrow niches and recently discovered skull-meninges connections (SMCs), revealing a new route of pathogens into the brain. 5/n Finding 2)
Critically, we found the spike protein also in the skull bone marrow niches, and meninges of people who died from COVID-19.

😮~60% of us who had COVID still might have lingering viral spikes in our heads! Our new study reveals SARS-CoV-2 spike accumulation in the skull-meninges-brain axis & its implications in long COVID. By @zhouyi_rong @HongchengM @Sakethkapoor🔬🧠🦠🧵👇 biorxiv.org/content/10.110… 2/n Summary:
We found SARS-CoV-2 spike protein in the skull-meninges-brain axis in mouse models and human post-mortem tissues long after their COVID, which was associated with vascular and inflammatory changes in the brain along with neuronal damage.

Imagine you could stain whole adult mice with standard IgG antibodies. What you couldn't do! We present wildDISCO technology for this🤗, creating the first whole body vascular, lymphatic, and nerve atlases. By @HongchengM @jieluo692 biorxiv.org/content/10.110… 🧵👇🏼(turn on the sound) 2/n Summary:
wildDISCO is a new tissue chemistry enabling uniform staining of whole bodies with conventional (150 kDa size) IgG antibodies. It reveals the first whole mouse body cellular & structural maps similar to Allen Brain Atlas only that main them at the whole mouse level.

Spatial-omics goes 3D🤗! Out at Cell @CellCellPress 👉🏼 We developed DISCO-MS with @labs_mann, a spatial proteomics technology for specimens fully imaged in 3D. DISCO-MS is aided by robotics and enables the study of diseases at their early stages. cell.com/cell/fulltext/…🧵👇 Summary:
DISCO-MS is a spatial proteomics technology: it enables proteomics analysis of cleared tissues imaged in 3D. DISCO-MS is aided by AI and robotics and yields proteome similar to fresh or fixed samples.
Have questions? Add them below👇 we will answer📖

We are very excited to share our SHANEL method making the intact human organs transparent, just published at Cell. cell.com/cell/fulltext/… by @shan_heather et al.
See short tweetorial for details:
#clearing #imaging #3D #deeplearning #AI @CellCellPress Mapping the human brain or other organs is a crucial step forward deciphering how they function in health and disease.

I am excited to share our publication of vDISCO technology: a whole mouse body clearing & imaging method nature.com/articles/s4159…. The thread below presents details of vDISCO and its biological findings. @NatureNeuro @nature. Happy New Year all! 1/12 2 years ago, we published uDISCO to clear and image intact adult mouse body with light-sheet microscopy. However, neuronal details were mostly invisible through intact bones, skin and highly autofluorescent muscles. nature.com/articles/nmeth…. 2/12