We are launching our set of 3D image segmentation and analysis tools! I am nervous and excited to see how something that has worked well internally can help our collaborators segment and understand their own large cohorts of 3D image data: www.alpenglowbiosciences.com/summit-ai

Little bit surprised to see most microscopy facilities now have dedicated image analysis support, but 1.0 FTE on average is nowhere near enough. And more than half don't charge for analysis services?!? 🤨 onlinelibrary.wiley.com/doi/10.1111/...

If you are in San Francisco this week stop by and check out Alpenglow Biosciences 3rd annual 3D spatial biology symposium: www.alpenglowbiosciences.com/3d-spatial-b...

We have an open Assistant Professor position (tenure track) @ethz.ch in Computational Immunology - ethz.ch/en/the-eth-z... Please apply / share!

When it stops raining for a minute Seattle is beautiful

Hiring: PostDoc in Tissue Clearing & 3D Histopathology 🧪🖥️ My lab at Helmholtz Munich is seeking a highly motivated PostDoc/Scientist to strengthen our efforts in advanced imaging of cancer tissues. More info: www.linkedin.com/posts/ali-ma...

A game changer in our hands... www.nature.com/articles/s41...

If you are at #SITC2025 stop by poster #1117 today from 12–2. Chat with Paula Andrea Rotger Gonzalez about Exploring Ovarian Cancer Subtypes with AlpenInsight 3D: A Scalable Workflow for 3D Tissue Classification Using Texture-Based Features and Light-Sheet Microscopy.

3D spatial multi-omic assessment of tumors is not a luxury, it is necessary. 2D assessments of tumors are simply insufficient. The whole field of spatial omics needs to move to 3D. Read about this here: www.cell.com/action/showP...

The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more! www.biorxiv.org/content/10.1...

We are excited to share our development of a new 10X lens with NA=0.50 over a 7.2 mm FOV and a 35 mm working distance (water), fully corrected from 400-850 nm. This lens will power our upcoming ExA-SPIM "2" and is available for dissemination - please get in touch if interested!

Are you a visionary leader in quantitative cellular imaging? We're looking for a Director of Quantitative Cellular Imaging. This role is pivotal in our mission to demystify multicellular morphogenesis through innovative imaging assays and data analysis. 🔗 alleninstitute.org/careers/jobs...

To look into: a Python alternative to ZEMAX... github.com/HarrisonKram...

The team published LUMI v2.0! The best new feature defines ROIs on low-res 3D scout scans! Scan your whole tissue at low resolution Define a bounding box using something like BigStitcher Import and scan the ROI Take your time finding and defining an ROI without worrying about photobleaching!

After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...

I used VVD Viewer for this #FluorescenceFriday video: 141 volumes from the #HHMIJanelia FlyLight Split-GAL4 #Drosophila driver collection. The animation comes from a high-level description processed by neuVid. Such a rapid tour of the data has questionable scientific value, but it's fun to watch!

I hope I never get tired of how amazing cells look in 3D. Happy Holidays and Happy #FluorescenceFriday! Here are CD45+ cells in a skin biopsy. The segmented cells and nerves at the end of the video kind of look like strings of lights

The Washington Research Foundation announced the next cohort of 12 postdoctoral fellowships! Congratulations to the fellows! I can't wait to see what they accomplish. www.wrfseattle.org/news/washing...

For #fluorescencefriday here is a mouse brain stained with Eosin and To-PRO-3 showing a segmented Glioblastoma in yellow. While this whole brain computational H&E staining is cool, I think I prefer TH staining for the dendrites. Imaged on Alpenglow Bioscience's 3Di #light-sheet #microscopy

Microscopy/live imaging people! Need your help 😅 I’ve only just recently started working with large time series files (1,000+ slices) and don’t know where to start when it comes to rendering and exporting them. What software(s) do you use?

Come check out the work we have been doing on 3D morphometrics using #light-sheet #microscopy!

TRISCO A solid step closer to 3D #SpatialTranscriptomics 😎 Optimized probe-based 3D RNA imaging in whole organs isHCR Tris 500 mM 4'C Validated probe list in Table S1 Brain Heart Lung Kidney @peruhlen.bsky.social @science.org 2024 www.science.org/doi/10.1126/...

Here is a murine heart video we imaged with the Red-Horse lab for #FluorescenceFriday.

Let’s see how well bsky does with external media. 🧪 #Vanderbilt Neurovisualization Lab is among the first to clear, label and image an intact NHP hemisphere. Please set your player to 4K! #lightsheet #microscopy #science #brain. If your lab wants to add lightsheet to your work we can help!

Whoa! Visualization of RNA gene expression in intact rodent brains using TRISCO clearing and light-sheet #microscopy. www.science.org/doi/10.1126/...

Axially Swept Light-Sheet Microscopy (#ASLM) synchronizes the camera’s rolling shutter with axial remote focusing (sweeping) of the light sheet. This enables 3D imaging with a thin optical section and isotropic resolution across large FOVs. Ideal for imaging cleared tissue! doi.org/10.1016/j.bp...

Lets start this off with some 3D imaging of human placenta. Samples from Mira Moufarrej and the lab of Kristy Red Horse at Stanford. Imaged at Alpenglow Biosciences in Seattle by our amazing team of scientists and engineers.