sitelab 0.0.1

SITE microscopy ingestion, metadata, visualization, and analysis platform.

sitelab

Early refactor scaffold for the Serial Imaging of Tumor and microEnvironment platform.

This package is intentionally small at first. Its first job is to make raw microscopy data inspectable and to capture channel meaning in a human-readable manifest before downstream analysis starts.

First milestone

• Inspect an .nd2 file without loading the full image into memory.
• Extract axes, sizes, voxel/time metadata, and raw channel names when available.
• Create a project manifest that maps raw channels to biological roles.
• Launch a napari viewer from the same backend manifest.

Install in a scientific Python environment

The Codex runtime used for editing may not include microscopy/GUI libraries. Install this package in the environment where you run napari and analysis:

cd path\to\sitelab
python -m pip install -e ".[nd2,viewer]"

For backend-only schema work:

python -m pip install -e .

Inspect an ND2 file

python -m sitelab inspect-nd2 `
  "..\..\data_sample\T2_40X_sample20260513_crop.nd2" `
  --out "..\..\data_sample\T2_40X_sample20260513_crop.site.json"

The output manifest is deliberately editable JSON. The first generated channel labels are placeholders; users should define biological meanings such as tumor_reporter, macrophages, lymphoid, nuclear_label, or brightfield_context.

Launch napari

python -m sitelab view-nd2 `
  "..\..\data_sample\T2_40X_sample20260513_crop.nd2" `
  --manifest "..\..\data_sample\T2_40X_sample20260513_crop.site.json"

This is the beginning of the hybrid GUI/scripting platform: the GUI should call the same importable Python objects that scripts, notebooks, and batch workflows use.