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Getting Started

MorphoStack runs locally. The canonical command is morphostack; the short alias is mst (same entry point).

MorphoStack

Requirements

  • Python 3.11+
  • Optional for analysis: OpenCV, scikit-image, scipy, tifffile, czifile, … (pip install -e ".[analysis]" or ".[all]")
  • Optional for API/UI: FastAPI, uvicorn (".[api]"), Node.js for web build/dev

Install from source

git clone https://github.com/sudoax0n/MorphoStack.git
cd MorphoStack
python -m venv .venv

License: dual AGPL-3.0-only or PolyForm Noncommercial 1.0.0 — see LICENSE. Cite MorphoStack if you use it (CITATION.cff).

Windows (PowerShell):

.\.venv\Scripts\python -m pip install -e ".[all]"
.\.venv\Scripts\morphostack doctor
.\.venv\Scripts\morphostack init --web   # optional UI deps

macOS / Linux:

source .venv/bin/activate
python -m pip install -e ".[all]"
morphostack doctor
morphostack init --web

Confirm both commands:

morphostack --version   # MorphoStack 0.1.0
mst --version           # MorphoStack 0.1.0

First analysis (CLI)

# Inspect shape + voxel source
morphostack inspect path/to/stack.tif

# Suggest a threshold
morphostack threshold path/to/stack.tif --method auto

# Run analysis with calibration overrides
morphostack analyze path/to/stack.tif \
  --threshold 100 \
  --voxel-x 0.1 --voxel-y 0.1 --voxel-z 0.5 \
  --out metrics.csv --report --mesh

Outputs next to (or under) your chosen paths:

Artifact Contents
metrics.csv Per-frame shape metrics
metrics.csv.manifest.json Provenance (SHA-256, settings, warnings)
metrics.csv.report.md Human-readable summary (--report)
mesh file With --mesh-export mesh.obj (or STL/PLY/GLB)

Use --bundle-dir runs to write metrics.csv + manifest.json + report.md into one folder.

Crowded field (one object)

morphostack analyze path/to/crowded.czi \
  --threshold 190 \
  --seed-x 360 --seed-y 517 --seed-frame 105 \
  --mesh --mesh-export mesh.obj \
  --bundle-dir runs

Browser UI

Developer mode (API + Vite hot reload):

morphostack dev --check
morphostack dev
# open http://127.0.0.1:5173

Single-port app (built UI + API; after npm run build or a release wheel):

morphostack app
# open http://127.0.0.1:8000

Next steps