Constellation-based point-set registration for microscopy in 2D and 3D Align calibrated partial views to whole-slide images or thick tissue volumes using landmark geometry.
Microscopy alignment gets messy when images are rotated, scaled, or captured on completely different platforms. NucleiSky solves this by treating your nuclei like stars in a constellation.
Instead of relying on pixel intensity similarity, NucleiSky matches the geometry of the cells. Whether your data is a 2D field of view or a 3D tissue stack, NucleiSky finds the calibrated similarity transform that best overlaps two landmark constellations.
Imagine looking through a small telescope at a random patch of the night sky. Even without seeing the whole galaxy, you can figure out exactly where you are by matching your small star pattern against a full sky map. NucleiSky does the same for your tissue: it anchors high-magnification ROIs into whole-slide scans by estimating rotation, scale, and shift.
NucleiSky is a robust point-set registration pipeline built for real-world microscopy noise. It provides modular feature extraction, dynamically scaled RANSAC, geometric hashing, and tetrahedral pyramid matchers — ready to slot into automated spatial analysis pipelines.
Choose your setup and align your images in minutes:
No installation required. Run our interactive apps directly in Google Colab:
Prefer a local app? Use our standalone desktop installer.
To install the package for your own scripts:
pip install nucleiskyUse pip install "nucleisky[all]" when you also need optional segmentation, OME-Zarr, SimpleITK, and notebook dependencies. Core matching runs on CPU; GPU support only affects optional deep-learning segmentation backends such as Cellpose and InstanSeg.
2D Pipeline (ROI → Whole Slide)
3D Pipeline (Subvolume → Thick Tissue)
(Need a leaner installation? See our Installation Guide for modular backend options).
- 2D & 3D registration: Shared constellation logic for flat slides and volumetric stacks. 3D workflows should be reviewed with manual QC before downstream use.
- Scale-aware: Matches images captured at different pixel/voxel sizes when calibration metadata is correct.
- Rotation-aware: Supports unrestricted rotations unless you configure an angle bound.
- Modality-Agnostic: If you can segment the nuclei (or spots/cells), NucleiSky can match them.
- Export-Ready: Saves transforms, warped hyperstacks, and QC overlays for downstream analysis.
- Pixel and Voxel size matter immensely. NucleiSky measures physical distances in micrometres. If your scale metadata (µm/px) is missing or wrong, the search bounds break, and alignment fails. Always verify your metadata! See Data Preparation.
- Segmentation quality drives match quality. NucleiSky registers point sets. Missing, massively merged, or noisy nuclei obscure the constellation and make matching much harder. See Segmentation.
Start Here
Quality Control & Troubleshooting
Developer Deep Dives
We welcome PRs, feature ideas, and bug reports! For the fastest triage, please use our GitHub issue forms.
If you’re using NucleiSky in a new workflow, drop an issue and tell us:
- What you’re aligning (restains, multi-round, ROI-to-reference, etc.)
- What success looks like in your pipeline
- What would make adoption easier for your lab
Need troubleshooting help? Please include a QC overlay from your save_dir/original/ folder when you open a bug report!
If you find this tool useful in your research, please cite:
NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations.
Iván Hidalgo Cenalmor, Adán Olguín-Olguín, Carolina Prieto, Johannes Kumra Ahnlide, Pontus Nordenfelt, Ricardo Henriques, Mario Del Rosario, Guillaume Jacquemet bioRxiv 2026.06.29.735028;
doi: https://doi.org/10.64898/2026.06.29.735028
@article {Cenalmor2026,
author = {Cenalmor, Iv{\'a}n Hidalgo and Olgu{\'\i}n-Olgu{\'\i}n, Ad{\'a}n and Prieto, Carolina and Ahnlide, Johannes Kumra and Nordenfelt, Pontus and Henriques, Ricardo and Del Rosario, Mario and Jacquemet, Guillaume},
title = {NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations},
elocation-id = {2026.06.29.735028},
year = {2026},
doi = {10.64898/2026.06.29.735028},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2026/06/29/2026.06.29.735028},
eprint = {https://www.biorxiv.org/content/early/2026/06/29/2026.06.29.735028.full.pdf},
journal = {bioRxiv}
}