Pandorica Scientific is the home for the open-source work of Robert Kiewisz — tools for electron microscopy and practical software for everyday problems.
The projects share a simple idea: if a task can be automated, it should be. They turn difficult, repetitive work into plug-and-play tools that need little user interaction, install easily, and do not create a maintenance burden.
- Automate the routine. Let software handle the repeatable work reliably.
- Keep interaction minimal. Ask for input only when a person’s judgement is genuinely needed.
- Make hard problems approachable. Provide practical defaults instead of exposing unnecessary complexity.
- Make installation simple. Sensible defaults work out of the box; advanced controls stay available for experts who want to fine-tune.
- Avoid ongoing maintenance. Users should use the tool, not spend time managing it.
🔬 pandorica — analytical tools for electron microscopy
Stitches serial-section electron tomograms into one continuous volume, automatically. Image data fixes each section's global pose — rotation, shift, anisotropic stretch — and microtubule splines drive only the fine residual warp, guarded so the deformation stays an orientation-preserving diffeomorphism and cannot fold the volume back on itself. A global pose solve replaces pairwise accumulation, so alignment error does not drift down the stack. Ships with a napari plugin for validating results on real datasets and recording coarse-alignment ground truth by hand.
pip install pandorica
python -m pandorica.stitch.cli <input_dir>Python · PolyForm Noncommercial 1.0.0 · integrates with tardis_em
🏠 continuum — your household's whole financial picture, on hardware you own
Most personal-finance software starts by asking which bank you use. Continuum never does. It reads the export files your bank already gives you, works out their structure from the files themselves, and checks what it extracted against the statement's own balances before trusting a single row.
It also brings household paperwork into the same system. Scan a document; built-in OCR makes it searchable by what's inside.
It never connects to your bank, and it runs on a machine you control.
docker compose upTypeScript · SvelteKit · Docker (amd64 · arm64) · PolyForm Noncommercial 1.0.0
📟 ble-vitals-monitor — passive vitals monitor and logger
An unofficial, strictly receive-only monitor for a baby-vitals wristband. It listens to the Bluetooth Low Energy advertisements the wristband already broadcasts in the clear, decodes heart rate, blood-oxygen saturation and skin temperature, and logs every reading to a microSD card as timestamped CSV — all without ever connecting to, pairing with, or transmitting to the wristband or its base station, so the official system keeps working untouched. Runs on an inexpensive ESP32 "Cheap Yellow Display"; small Swift command-line tools cover the same job on a Mac.
Not a medical device and not a safety monitor. A hobby and educational project. Independent, and not affiliated with or endorsed by the manufacturer.
C++ · ESP32 · Swift · PolyForm Noncommercial 1.0.0
TARDIS — Transformer And Rapid Dimensionless Instance Segmentation — and its companion packages were developed at the Simons Machine Learning Center at the New York Structural Biology Center, and belong to that group. The copies in this organization are forks kept for continued maintenance and contribution upstream; they are not Pandorica Scientific projects, and the canonical repositories remain under SMLC-NYSBC.
| Fork | Upstream | Purpose |
|---|---|---|
| TARDIS | SMLC-NYSBC/TARDIS | Instance segmentation of microtubules, membranes and filaments in electron microscopy data · docs |
| napari-tardis_em | SMLC-NYSBC/napari-tardis_em | napari plugin front-end for TARDIS |
| tardis_em_analysis | SMLC-NYSBC/tardis_em_analysis | Shared analysis libraries used by both |
pandorica extends this line of work into serial-section reconstruction. When
tardis_em is installed alongside it, the stitcher is also exposed as the
tardis_stitch console script.
Archive — earlier microscopy scripts, kept for reference
Small, unmaintained helper scripts from earlier electron-tomography work. They still do what they say, but they are not developed further.
- Assit_Automatic_Tomogram_Flattening_IMOD — console interface for the IMOD automatic tomogram-flattening tool (2023, GPL-3.0)
- etomo_Batch_SetUp — eTomo batch settings for automatic reconstruction of roughly 300 nm plastic serial sections (2021, MIT)
The three active projects are released under the PolyForm Noncommercial License 1.0.0. They are free to use for research, study, and teaching — by educational, public-research, charitable, public-health, environmental and government institutions, whatever their funding source. Commercial use needs a separate licence; each repository explains how to ask for one.
The TARDIS forks stay under their upstream MIT licence. Archived scripts carry the licence stated in their own repository.
Contributions are welcome and require a Developer Certificate of Origin
sign-off — see the CONTRIBUTING.md in each repository.
Robert Kiewisz — robert.kiewisz@gmail.com · Poland
