Visualization Tab

The Visualization tab displays cell crops from crops.zarr in a grid, with traces plotted alongside. Workspace must be set and validated on the landing page first.

Prerequisites

  1. Set workspace on landing page: Select a folder that contains crops.zarr (typically your processing output directory).

  2. Click Load to validate. The workspace must pass validation before navigating to Visualization.

  3. Once validated, click Visualization to open the tab.

Workflow Overview

  1. Workspace – Set and validate on landing (folder with crops.zarr)

  2. Select position – Choose which position to view

  3. Select channel – Choose which channel’s crops to display

  4. Browse frames – Use the frame slider to step through time

  5. Inspect crops and traces – View the crop grid and trace plot

Step-by-Step Guide

1. Set Workspace (Landing Page)

  1. On the landing page, click Browse next to Workspace Folder.

  2. Select the output directory that contains crops.zarr (same as the Processing “Save Directory”).

  3. Click Load to validate. A “Workspace valid” message confirms the setup.

  4. Click the Visualization card to open the tab.

2. Select Position and Channel

The Visualization page shows:

  • Position – Dropdown of position IDs from crops.zarr.

  • Channel – Dropdown of channel names (e.g. pc_ch_0, fl_ch_1).

  • Frame – Slider or controls to move through time frames.

Use the dropdowns to pick the position and channel to inspect.

3. View Crops and Traces

  • Crops grid: A paginated grid of cell crops for the chosen position, channel, and frame. Use the page controls to browse cells.

  • Traces plot: Plots traces for the visible crops at the current frame. Traces are loaded from traces/position_{id}.csv.

Crop images are streamed via WebSocket from the backend. The trace plot updates when you change the page or frame.

Output Structure

The workspace folder should contain:

output_dir/
├── crops.zarr/          # Per-cell crops and metadata
├── raw.zarr/            # Raw frames and intermediate arrays
├── traces/              # Per-position trace CSVs
│   ├── position_0.csv
│   └── ...
└── processing_config.yaml

Tips

  • Ensure the workspace path includes crops.zarr and traces/ from a completed processing run.

  • If you see “Set workspace and source on the landing page”, return to the root and run Load after selecting the workspace folder.

  • Use the frame controls to move through time and inspect cell behavior.

Troubleshooting

“Set workspace and source on the landing page”

  • Go to the landing page, select the workspace folder, and click Load.

  • Confirm validation succeeds before reopening Visualization.

“crops.zarr not found”

  • Ensure the selected folder is the processing output directory (the one containing crops.zarr).

  • Run Processing first to create crops.zarr and traces/.

Crops or traces don’t load

  • Check that Processing completed successfully for the chosen position.

  • Verify the backend API is running (default http://localhost:8765).

Next Steps

  • Use the Analysis tab to compare samples and fit models to merged trace data.

  • See Merge Workflow for combining multiple samples before analysis.