PANDORICA

Analytical tools for electron microscopy.

Bundled tools

• pandorica.stitch — serial-section tomogram stitcher: image-driven coarse→fine alignment — the image fixes each section's global pose (rotation, shift, anisotropic stretch) and the microtubules drive only the fine residual warp — with a diffeomorphism-guarded TPS warp, global pose solve, and CPU/GPU volume export. Falls back to an MT-only pose solve when volumes are absent. Plain-language tour: HOW_IT_WORKS.md. Dense reference: pandorica/stitch/README.md.
• pandorica.napari — napari plugin: visually validate the stitcher on real datasets and record coarse-alignment ground truth by hand.

Install

pip install pandorica                # core stitcher + CLI
pip install "pandorica[napari]"      # add the napari validator widgets

Use

python -m pandorica.stitch.cli <input_dir>

from pandorica.stitch.cli import run_stitch
run_stitch("path/to/sections")       # writes <input_dir>/stitched_output/

If tardis_em is also installed, the same entry point is exposed as the tardis_stitch console script.

Citation

If pandorica contributes to a publication or presentation, please cite the software:

@software{kiewisz_pandorica_2026,
  author  = {Kiewisz, Robert},
  title   = {pandorica: analytical tools for electron microscopy},
  year    = {2026},
  version = {1.0.3},
  url     = {https://github.com/RRobert92/pandorica},
  license = {PolyForm-Noncommercial-1.0.0}
}

Related prior work (scholarly context; not required by pandorica's license)

Pandorica's stitcher is a from-scratch Python reimplementation in the serial-section EM lineage; it does not include code from these projects. Citing them is a scholarly courtesy when positioning your work, not a legal obligation imposed by pandorica:

• Lindow et al., Journal of Microscopy (2021), SerialSectionAligner — doi:10.1111/jmi.13039
• Weber et al., PLoS ONE (2014), microtubulestitching

See pandorica/stitch/README.md for full author lists and the wider related-work list (IMOD, msemalign, Okapi-EM, …).

License

PolyForm Noncommercial License 1.0.0 — free for research, study, and use by educational, public-research, charitable, public-health, environmental, and government institutions, regardless of funding source. Commercial use requires a separate license; see COMMERCIAL.md to request one. Full terms in LICENSE.

Contributions require a Developer Certificate of Origin sign-off — see CONTRIBUTING.md.

Contact

Robert Kiewisz — robert.kiewisz@gmail.com