Excited to see direct streaming of @openmicroscopy.org @zarr.dev datasets in #syGlass!
Exploring huge images without upfront download is just what we’ve been working toward with cloud-optimized formats.
Great to have tools connecting the ecosystem of imaging repositories, now including VR 🙌
syGlass reads image data from many file formats: some open, some proprietary. Few are as exciting and dynamic as OME-Zarr, and direct streaming of these files is only the beginning of what's possible. More on our support for OME-Zarr in syGlass v2.6.0 below.
Segmenting image volumes has long been a feature of syGlass, but our latest release adds the ability to segment surfaces as well. A nice ~45 second demo of this below!
The first syGlass feature release of the year is here! Meet syGlass v2.6.0:
🖥️ Spatial Reality Display support
🛜 Stream/read OME-Zarr directly
🖌️ Partition surfaces via 3D brush
⌨️ Enter text via in-VR keyboards
www.syglass.io/blog/syglass...
For rapid creation of immersive narrative content from 3D image data, there is no more capable tool than syGlass.
Narrations like these can be viewed in fully immersive VR; as 2D, stereo-3D, or 360 video; or as an anaglyph scene for viewing with red/cyan 3D glasses.
Create once & deploy anywhere!
Running TotalSegmentator inside #syGlass for #3DThursday! 🔬 Automated segmentation needs strong clinical data for training and benchmarking, plus models that generalize. Mayo Clinic Low Dose CT Grand Challenge + #TotalSegmentator by Jakob Wasserthal are great examples.
#MedicalImaging #3DImaging
The Allen Mouse Brain Atlas is a cornerstone of #neuroscience: a standardized, high-resolution map of brain anatomy built to keep experiments comparable across labs. 🧠 Here’s a 3D walk through its anatomical meshes in #syGlass!
@alleninstitute.org
#3DThursday #DataViz #VR
For #3DThursday, a skeleton shrimp imaged on a Flamingo light sheet microscope — a modular, traveling #LSFM built to bring the microscope to the biology.🔬🦩Fast 3D imaging, low phototoxicity.
🥼: Carsten Wolff @carsten-wolff.bsky.social
📝: huiskenlab.com/flamingo/
🏛️: @morgridgeinstitute.bsky.social
🪰 For #3DThursday, this #microCT scan of an adult #Drosphila (Schoborg et al.) captures the entire fly intact. Using #VR, we can teach anatomy by labeling the 3D fly from a 2D diagram. Spatial context changes everything. #SciComm
🔬: Bruker SkyScan 1172
🏛️: UWyoming
🎬: #syGlass, v2.5.0
Label-free #holotomography for #3DThursday! This imaging technique lets you follow the same living organoid in 4D with no dyes or phototoxicity.
🔬: @tomocube.bsky.social, HT-X1
🧫: Mouse Intestinal #Organoid
🏛️: Institut Pasteur Workshop, Pushing the Frontiers of Dynamic Imaging
🎬: #syGlass, v2.5.0
#syGlass v2.5.0 is out! 🎉
New depth-aware colormaps, expanded file formats (NRRD/MRC/TCF/OME-Zarr v3), better #VR segmentation tools, and upgraded narration workflows — all focused on making #3Ddata easier to explore and share.
Blog: www.syglass.io/blog/syglass...
#Microscopy #Imaging #3DThursday
Stereoscopic visualization can be achieved in a variety of ways, each with their own advantages. One of the many strengths of syGlass is its ability to seamlessly switch between them: immersive virtual reality, anaglyph (red/cyan) rendering, and now Sony's glasses-free 3D displays.
For #3DThursday we’re introducing Dynamic Depth color mapping! It encodes distance with smooth depth-aware gradients so layered structures pop without losing context.
🔬 #MicroCT of a P1 mouse
🥼 Hsu Lab, Baylor, @cwloganhsu.bsky.social
🎬 syGlass.io
#Microscopy #SciComm #3DVisualization #syGlass
💧 A male water flea (#Daphnia magna) for #3DThursday! Yellow 🟨 is musculature, magenta/gray 🟪 shows autofluorescence of its outer cuticle.
🔬: Fluorescence Microscopy
🥼: Carsten Wolff
🏛️: Marine Bio Lab @mblscience.bsky.social
🎬: syGlass.io
#EnvironmentalScience #MBL #SciComm #Microscopy #syGlass
🍺 It’s Oktoberfest, so let's look inside beer foam! Non-destructive imaging like this is key for food science and helps us understand how structure and stability affect things like aroma and taste.
🔬: TESCAN DynaTOM #microCT
🥼: Wesley De Boever
🎬: syGlass.io
#Oktoberfest #3DThursday #Microscopy
👀 #3DThursday: Cross your eyes to see this super res pollen dataset in 3D! Good old fashioned stereo pairs in #syGlass bringing science to life. 🌿✨
🔬: Zeiss LSM 980 with Airyscan 2
🥼: Nat Prunet, @nat-prunet.bsky.social
🏛️: UNC Biological Microscopy Core: tarheels.live/biologymicro...
🎬: syGlass.io
Non-destructive testing for #3DThursday!🥽 Apple Vision Pro vs MetaQuest in a microCT.
🔬: Lumafield @lumafield.bsky.social microCT
🎬: syGlass.io, loading two projects at once
3D imaging like this is used to validate design, catch flaws, and build smarter devices.
#MicroCT #syGlass #VR #SciComm
Pollen diversity #3DThursday!🌼🌾 Thanks to Nat Prunet's careful microscopy, we see ridges, spikes & pores that reveal how plants spread & survive.
🔬: @zeiss-microscopy.bsky.social LSM 980, Airyscan 2
🥼: @nat-prunet.bsky.social
🏛️: UNC Biological Microscopy Core
🎬: syGlass.io v2.4.0 #syGlass
Chicken balancing for #3DThursday!🐔 These utricle hair cells sense gravity & straight-line motion. We segmented them with #CellposeSAM in #syGlass.
🥼: Stefan Heller Group
🏛️: Stanford @stanfordmedicine.bsky.social
🎬: syGlass.io v2.4.0, out now!
#Neuroanatomy #Microscopy #3DVisualization #SciComm
It's #MicroscopyMonday! Today we have a very special confocal dataset that HIGH SCHOOL students were able to label and image themselves at the MBL.
🐟: #Zebrafish
🔬: Nipam Patel, High School Science Discovery Programs
🏛️: @mblscience.bsky.social
🎬: syGlass.io
#NESM #Confocal #SciComm #ScienceEd
4D bread baking inside a microCT for #3DThursday?!🍞
🔬: TESCAN DynaTOM
🏛️: TESCAN, thanks to Marijn Boone for the data!
🎬: syGlass.io
Total scan time: 22m8s
Time for 1 scan: 10 seconds
Total scans: 124 volumes
#4DImaging #MicroCT #DynamicImaging #FoodScience #syGlass #VRVisualization #ScientificVR
Automated Segmentation by Cellpose-SAM using syGlass for #3DThursday! This took about 30 minutes to run on one of the gaming laptops. Crazy.
🔬: Synchrotron #MicroCT
🥼: Keith Cheng, MD, PhD, @pennstateuniv.bsky.social
📝: #CellposeSAM www.biorxiv.org/content/10.1...
🥽: syGlass.io v2.4.0 -- out soon!
I love this for #3DThursday -- Zebrafish, but make it four and layer them!
🥼: Arnim Jenett
🏛️: TEFOR tefor.net/en/
🔬: #Lightsheet
🎬: syGlass in colorblind mode, #syGlass
Check it out for yourself with their resource "The Larval Standard Brain":
zebrafish.tefor.net#/home?_k=fz1...
A #microscopy mystery for #3DThursday!🌾 What is this? 🔍 Things that I know: it is a #plant, it was imaged on a Lumafield #microCT, and the color is a LUT (look up table) that I applied in #syGlass and has nothing to do with the organism (microCT comes in as grayscale). Help! #SciComm
Happy 4th for #3DThursday! 🎉 Do I occasionally forget and then remember ecstatically that we have a confetti cannon in the syGlass room? Yes, yes, I do ...
#syGlass #VRScience #Microscopy #SciComm
Finally plants for #3DThursday!🌽 A maize root tip, imaged using #microCT, from the Topp Roots Lab.
🔬: @zeiss-microscopy.bsky.social Versa 520 XRM
🥼: Keith Duncan @cygnusplantxray.bsky.social
🏛️: Danforth Center @danforthcenter.bsky.social
📝: academic.oup.com/plphys/artic...
🎬: syGlass.io #syGlass
Get your 3D glasses out for #3DThursday! And click the link below to see syGlass on the really big screen at the @mit.edu MIT Museum last week. (guys it's my first syGlass blog ...)
📝: www.syglass.io/blog/a-night...
🥼: Kory Evans @sternarchella.bsky.social , Rice University
🎥: syGlass.io #syGlass
LIVE sea urchin larvae for #3DThursday! Catch me at the MIT Museum tonight at AfterDark and see it in person.
🔬: @brukercorporation.bsky.social TruLive3D
🥼: Amro Hamdoun @hamdounlab.bsky.social , Tzer Han Tan's @tzerhan29.bsky.social group at UCSD
🌌: Painted Sea Urchin
🎥: syGlass.io #syGlass
Up in Acadia at the @mdibiolab.bsky.social for #LSFM25! Here's a cleared whole mouse head on the SmartSPIM, 3.6X objective for #3DThursday.
🔎 @jtakatoh.bsky.social, now at @stonybrooku.bsky.social
🔬 LifeCanvas Technologies, lifecanvastech.com/products/sma...
🥽 syGlass.io
@lsfm-na.bsky.social
✨ Heading to @mdibiolab.bsky.social next week for the LSFM course! Here’s some stunning lightsheet data from @erturklab.bsky.social
🔬: Blaze Ultramicroscope, LaVision Biotech
🥼: Hongcheng Mai, Jie Luo, Helmholtz Munich
📝: pmc.ncbi.nlm.nih.gov/articles/PMC...
🎬: syGlass.io
#3DThursday #LSFM2025
