USE CASE · LIGHT & CORRELATIVE
From live fluorescence to ultrastructure.
Explore and annotate large multichannel light microscopy data with your whole lab, and correlate it with EM or X-ray when your project needs it.
Data: Drawitsch et al., eLife 2018.
THE CHALLENGE
What large light data demands
Modern light microscopy produces data faster than labs can open it, share it, or combine it with other modalities.
Too big, too many channels
Light-sheet and tiled volumes reach hundreds of gigabytes, across many channels and timepoints. A single workstation struggles to open them.
One dataset, many people
Annotation and review involve the whole lab, sometimes several sites. Everyone needs the same data and the same view.
From signal to ultrastructure
Fluorescence shows where things are, not what they look like up close. Correlative light and electron microscopy (CLEM) adds the ultrastructure, but only if both datasets line up precisely.
THE WORKFLOW
From raw channels to shared results, in WEBKNOSSOS
Four steps, one platform. Stop at step 3 for light microscopy alone, or add EM and X-ray in step 4.
01
Open large volumes in the browser
Upload or stream light-sheet and tiled volumes, then move from the whole sample down to single cells at full resolution, with nothing to install.
02
Every channel, every timepoint
Color each channel, set its contrast, and toggle or blend them to see exactly the signal you need, then move through your time series.
Data: Payne et al., Science 2021.
03
Annotate and measure
Mark cells with skeletons, segment them by hand or with AI quick-select, and measure every segment. A maximum intensity projection in the 3D view keeps the overview while you work.
Data: Valuchova et al., eLife 2020.
04
Register with EM or X-ray
Compose one dataset from your light and EM or X-ray data for CLEM. Match landmarks placed with the skeleton tool, or imported from BigWarp, to register even deformed samples precisely.
Data: Drawitsch et al., eLife 2018.
GO FURTHER
More tools for light microscopy
Beyond the core workflow, WEBKNOSSOS has many smaller features that save time along the way.
Automatic contrast
Get readable contrast on float data in one click with automatic histogram clipping.
Live transform editor
Nudge a layer into place with the live transform editor: translate, rotate and scale it without leaving the viewer.
IN PRACTICE
Light and correlative data on WEBKNOSSOS
Published light microscopy and correlative datasets you can open and explore in your browser.
“WEBKNOSSOS is very useful for safely storing large datasets and managing access across multiple users.”
SERVICES
Want help with stitching or registration?
Our team stitches, aligns and registers your light, electron and X-ray data, delivered in WEBKNOSSOS.