WEBKNOSSOS × panluminate
A connectomics pipeline for pan-expansion microscopy
panluminate images whole-brain tissue at 20 nm with light. In WEBKNOSSOS, your lab segments, proofreads and shares it.
Workflow news, sample datasets and workshops. A few emails a year. Available now on request: request access.
Why pan-expansion microscopy
Wiring and molecular identity, in the same sample.
Electron microscopy resolves synapses but loses the molecules. Fluorescence keeps the molecules but loses the context. Pan-expansion microscopy (pan-ExM) physically expands the tissue, then stains every compartment, so synapses, organelles and protein labels are imaged together, with light.
The pipeline
Six steps from tissue to connectome.
panluminate expands, stains and images the tissue. The dataset streams into WEBKNOSSOS, where your lab segments it with AI, proofreads, annotates and shares the result.
01
Expand
The tissue grows physically, several times its size.
02
Stain
pan-staining then marks every cell compartment.
03
Image
Light-sheet imaging at 20 nm, across whole volumes.
04
Segment
AI neuron segmentation, with a model optimized for pan-ExM data.
05
Proofread
Your lab fixes splits and merges, together, in the browser.
06
Analyze
Annotate, query and share the connectome.
Who does what
From the bench to the browser.
panluminate takes care of the tissue and the imaging. WEBKNOSSOS gives your lab what it needs to turn that data into a connectome.
Sample preparation and imaging
- Tissue expansion, then pan-staining chemistry
- Light-sheet imaging of expanded tissue at 20 nm
- Delivery of the imaged dataset straight into WEBKNOSSOS
- Imaging services
Segmentation, proofreading and analysis
- AI neuron segmentation, with a model optimized for pan-ExM data
- Browse gigabyte-to-petabyte 3D datasets in the browser, no local install
- Proofreading via supervoxel-graph editing: split and merge fixes
- Skeleton and volume annotation, near-real-time collaboration
- Zarr / OME-NGFF, N5, Neuroglancer Precomputed; Python library and APIs
See it on real data
Open a dataset made with the pipeline.
One volume, taken through every step: expanded, stained and imaged by panluminate, then segmented and proofread in WEBKNOSSOS. It opens in your browser, no install needed.
Newsletter
Follow the pipeline as it develops.
Workflow news, sample datasets and workshop invitations. A few emails a year.
A connectomics pipeline for pan-expansion microscopy.