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Getting Started

This guide is for users who want to run the viewer locally and open data as quickly as possible.

Build And Launch

From the repository root:

cargo run

This opens the app landing screen.

Common Launch Paths

Open a saved project:

cargo run -- --project "/path/to/project.json"

Open a single local dataset directly:

cargo run -- "/path/to/ROI1.ome.zarr"

Open a mosaic from a project:

cargo run -- --project "/path/to/project.json" --mosaic "TMA1v3,TMA2"

Open a mosaic from a samplesheet:

cargo run -- --mosaic-samplesheet "/path/to/samplesheet.csv"

Optionally fix the mosaic column count:

cargo run -- --project "/path/to/project.json" --mosaic "TMA1v3,TMA2" --mosaic-cols 10

First Session Checklist

  1. Launch the app.
  2. Open a local OME-Zarr dataset or a saved project.
  3. In the left panel, inspect the layer list and select the active layer.
  4. In the right panel, adjust channel contrast, color, and overlay settings.
  5. Use F to fit the current view.

Interface Layout

  • Left panel: layers, tools, and project actions
  • Right panel: properties for the active layer and analysis-oriented tabs
  • Center canvas: imagery and overlays
  • Top bar: quick controls, including compact contrast controls when side panels are hidden

For the smoothest first experience, start with:

  • a local OME-Zarr image pyramid
  • an optional GeoJSON segmentation or mask overlay
  • a project JSON if you already have a workspace prepared