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Dr. Caleb Stoltzfus

@cstoltzfus.com
376 followers 2K following 26 posts

Optics | Microscopy | Physics | Image Analysis | Anything with lasers and data science

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Dr. Caleb Stoltzfus @cstoltzfus.com · 05/05/2026
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
alpenglowbiosciences.com
Summit AI | Multimodal 3D tissue analysis platform — Alpenglow Biosciences
Summit AI combines multimodal data and full-sample 3D tissue imaging through an AI foundation model to generate quantitative tissue signatures for digital pathology.
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Reposted by Dr. Caleb Stoltzfus
Dave Barry @david-j-barry.bsky.social · 25/03/2026
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/...
Image analysis. (A) Pie chart shows the % of facilities with dedicated image analysis support. Yes (blue), no (orange). (B) Violin plot shows the distribution of # FTE providing that support. Mean and standard deviation are included. (C) Pie chart shows the % of facilities providing bespoke image analysis. Yes (blue), no (orange). (D) Pie chart shows the sources of cost recovery of bespoke image analysis support. Uncharged (blue), charged by the hour (orange), project fee (green), staff salary contribution (sky blue). (E) Pie chart shows the % of facilities that support commercial image analysis software. Yes (blue), no (orange). (F) Pie chart shows the sources of funding to maintain commercial analysis software. Mix of all sources (blue), on an annual basis from user charges (orange), institutional support (green), grant funding (sky blue), on an ad hoc basis from user charges (magenta).

https://onlinelibrary.wiley.com/doi/10.1111/jmi.70079
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Dr. Caleb Stoltzfus @cstoltzfus.com · 09/03/2026
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...
alpenglowbiosciences.com
3rd Annual 3D Spatial Biology Summit | Discover 3D Insights – Join Now — Alpenglow Biosciences
Join the 3rd Annual 3D Spatial Biology Summit to explore ground-truth 3D tissue imaging, spatial omics, and predictive workflows. Connect with leaders in imaging, computation, and translational resear...
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Tanja Stadler @tanjastadler.bsky.social · 20/02/2026
We have an open Assistant Professor position (tenure track) @ethz.ch in Computational Immunology - ethz.ch/en/the-eth-z... Please apply / share!
ethz.ch
Assistant Professor (Tenure Track) of Computational Immunology
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Dr. Caleb Stoltzfus @cstoltzfus.com · 31/12/2025
When it stops raining for a minute Seattle is beautiful
Downtown Seattle at sunsetMount Rainier at sunset
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Ali Maximilian Erturk @erturklab.bsky.social · 06/12/2025
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...
linkedin.com
#histopathology #tissueclearing #lightsheetmicroscopy #postdoc #sciencecareers #munich | Ali Maximilian Ertürk
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. ...
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Kevin Dean @kevin-dean.bsky.social · 11/11/2025
A game changer in our hands... www.nature.com/articles/s41...
nature.com
Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
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Dr. Caleb Stoltzfus @cstoltzfus.com · 07/11/2025
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.
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Denis Wirtz @deniswirtz.bsky.social · 09/06/2025
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...
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voigtvision.bsky.social @voigtvision.bsky.social · 27/05/2025
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...
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Adam Glaser @adamkglaser.bsky.social · 19/05/2025
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!
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allen institute @alleninstitute.org · 05/05/2025
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...
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Reposted by Dr. Caleb Stoltzfus
Adam Glaser @adamkglaser.bsky.social · 02/05/2025
To look into: a Python alternative to ZEMAX... github.com/HarrisonKram...
github.com
GitHub - HarrisonKramer/optiland: Comprehensive optical design, optimization, and analysis in Python, including GPU-accelerated and differentiable ray tracing via PyTorch.
Comprehensive optical design, optimization, and analysis in Python, including GPU-accelerated and differentiable ray tracing via PyTorch. - HarrisonKramer/optiland
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Dr. Caleb Stoltzfus @cstoltzfus.com · 21/03/2025
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.
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Dr. Caleb Stoltzfus @cstoltzfus.com · 21/03/2025
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!
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.
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Constantin Pape @cppape.bsky.social · 12/02/2025
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...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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Philip Hubbard @philiphubbard.bsky.social · 20/12/2024
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!
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Dr. Caleb Stoltzfus @cstoltzfus.com · 20/12/2024
Shoutout to #napari and #kdenlive for making video creation and editing with ~200Gb light-sheet images super easy
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Dr. Caleb Stoltzfus @cstoltzfus.com · 20/12/2024
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
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Dr. Caleb Stoltzfus @cstoltzfus.com · 18/12/2024
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...
wrfseattle.org
Washington Research Foundation awards 12 three-year postdoctoral fellowships - Washington Research Foundation
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Dr. Caleb Stoltzfus @cstoltzfus.com · 06/12/2024
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
alpenglowbiosciences.com
3D Tissue Imaging — Alpenglow Biosciences
Alpenglow is pioneering a new frontier in digital 3D spatial biology, integrating proprietary 3D imaging technology with cloud computing and AI-powered analysis. This high-throughput, digital approach...
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Dr. Caleb Stoltzfus @cstoltzfus.com · 06/12/2024
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
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Dr. Caleb Stoltzfus @cstoltzfus.com · 06/12/2024
From Maple Leaf
Sunrise
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Dr. Caleb Stoltzfus @cstoltzfus.com · 29/11/2024
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.
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Lucy Dornan @lucygdornan.bsky.social · 27/11/2024
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?
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Dr. Caleb Stoltzfus @cstoltzfus.com · 27/11/2024
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
forum.image.sc
Image.sc Forum
Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).
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Dr. Caleb Stoltzfus @cstoltzfus.com · 27/11/2024
Very cool work! I really like the videos showing off the segmentation
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Dr. Caleb Stoltzfus @cstoltzfus.com · 27/11/2024
Come check out the work we have been doing on 3D morphometrics using #light-sheet #microscopy!
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Hao Yin @haoyin.bsky.social · 26/11/2024
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/...
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Dr. Caleb Stoltzfus @cstoltzfus.com · 22/11/2024
Here is a murine heart video we imaged with the Red-Horse lab for #FluorescenceFriday.
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Jose Maldonado, PhD @josemald.bsky.social · 20/11/2024
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!
youtu.be
Marmoset brain hemisphere imaged with lightsheet
YouTube video by Neurovisualization Lab
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Dr. Caleb Stoltzfus @cstoltzfus.com · 21/11/2024
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Dr. Caleb Stoltzfus @cstoltzfus.com · 21/11/2024
There are some really cool supplemental videos
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Dr. Caleb Stoltzfus @cstoltzfus.com · 21/11/2024
Whoa! Visualization of RNA gene expression in intact rodent brains using TRISCO clearing and light-sheet #microscopy. www.science.org/doi/10.1126/...
science.org
Whole-brain spatial transcriptional analysis at cellular resolution
Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context acr...
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Dr. Caleb Stoltzfus @cstoltzfus.com · 18/11/2024
It's this a rebuttal to the famous chicken paper? www.researchgate.net/publication/...
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Daniel von Wangenheim @dvonwangenheim.bsky.social · 16/11/2024
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...
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Dr. Caleb Stoltzfus @cstoltzfus.com · 17/11/2024
This is the best one I've found this fall
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Dr. Caleb Stoltzfus @cstoltzfus.com · 17/11/2024
Brutal!
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Dr. Caleb Stoltzfus @cstoltzfus.com · 17/11/2024
The motorized stage crushing the objective.
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Dr. Caleb Stoltzfus @cstoltzfus.com · 15/11/2024
Change indexing to start at 1.
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Dr. Caleb Stoltzfus @cstoltzfus.com · 14/11/2024
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.
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