GUI Walkthrough

A screenshot-driven tour through the PhenoTypic hub — from a fresh sandbox to a finished run with viewable results. Each page is short and focused on a single workflow so you can jump to whichever step you need.

The walkthrough uses a small synthetic yeast plate dataset (3 plates, 8 × 12 grid each, generated with phenotypic.data.make_synthetic_plate) so you can follow along without your own data. The accompanying capture script scripts/capture_gui_tutorial_screenshots.py regenerates the synthetic plates, runs the CLI to produce real output, and takes every screenshot in this guide — re-run it after a GUI change to keep the images aligned with the implementation.

What’s covered

Page	Goal
Setup	Generate the synthetic dataset and launch the hub.
Browse source images	Deep-zoom the raw input images under a source root with cascading dropdowns and a metadata panel.
Browse — find the ideal starting time	Flip Browse to Timeline mode and navigate a folder/EXIF matrix with arrow keys to find a starting time and deep-zoom any frame.
File Explorer	Navigate the sandbox sidebar and read capability badges.
Build a Pipeline	Compose a pipeline.json with the fixed linear port map, side loader, and zoom controls.
Run Locally	Submit a local subprocess run and tail the dashboard.
Run on SLURM	Fill in SLURM resources and ship a submission to a cluster.
View Results	Open the results viewer against a finished CLI output.
Pick points	Curate detected colonies manually with the in-builder point picker.
Analysis	Compose phenotypic.analysis filters + endpoint model and emit analysis.{csv,parquet}.
Aux ports	Fill operation-typed parameters (e.g. FilamentousFungiDetector.inoculum_detector) through side-loader port targets.
QC curation loop	Configure QualityCheck analyzers and curate flagged colonies in a tight feedback loop.
Heatmap exploration	Pick a measurement and walk through time on a plate to spot edge / contamination patterns.
Fill a scalar aux target	Select a gold side port, watch it turn green, and fill it with a compatible palette operation.
Open an embedded Pipeline aux	Fill a side value with + New Pipeline, build the nested chain, and use breadcrumbs to return.
Fix validation issues	Triage the toolbar issue badge, fix missing side values, and understand unsupported development DAG states.
QC review walkthrough	Switch the QC tab to Review; walk worst-first groups for a module, curate in the tile gallery, mark reviewed, and watch the metric recompute in place.
Tune co-pilot	Open the /tune/ read-only co-pilot over a tune output: monitor trials, curate A/B overlays, review the search space, and launch the next run.
Error analysis	Rank the measurements that separate an error category from the good baseline, read off a cutoff, and copy a filter spec.
Results — trait emergence over time	Open the results-viewer Timeline tab, pick a Y grouping + a monotonic X time column, scan one plate’s overlay time-course, and deep-zoom any plate.

Prerequisites

• PhenoTypic installed via uv sync --group dev (see Getting Started).

• Playwright with Chromium installed if you want to regenerate the screenshots yourself: uv run playwright install chromium.

For a comprehensive reference of every panel, store, and admonition in the hub, see the GUI hub guide. This walkthrough is the “happy path”; the reference is the manual.