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!
Downtown Seattle at sunset
Mount Rainier at sunset
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...
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...
This workflow is very nice for organoids, where you want to take your time to pick and choose which organoids you re-image at sub-cellular resolution.
LUMI - light-sheet microscope control software main user interface. Both low resolution and high resolution camera feeds are simultaneously displayed on the right. Scan bounds, estimated scan time, laser control, and other control features are on the left of the screen.
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!
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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!
Shoutout to #napari and #kdenlive for making video creation and editing with ~200Gb light-sheet images super easy
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...
I like the 3Di from Alpenglow Biosciences. It makes it easy to load 10 brains to scans at a time and has simultaneous high and low resolution imaging paths. www.alpenglowbiosciences.com/aurora-3d-sp... Disclaimer: they sign my paychecks
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
Sunrise
From Maple Leaf
I teach a lot less on the industry side now, but I still rely on resources from ecology for helping new engineers/data scientists with spatial analysis. We use mostly python, CytoMAP, and a little R. Every once in a while we use Aivia as well.
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?
For commercial software we use Aivia or Imaris, which both have free versions if you are only rendering the images. We use Napari for viewing data when we are doing custom analysis in python. The image analysis forum, forum.image.sc, is a great resource for getting started
Very cool work! I really like the videos showing off the segmentation
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!
