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	Navigate with J/K, previews, and a filmstrip; deep-zoom raw inputs and prepare a persistent revision-correct cache.
File Explorer	Navigate the sandbox sidebar and read capability badges.
Build a Pipeline	Compose a pipeline.json.pht-pipe 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.
Scatter plots	Bind plotting roles, page through section groups, click a point to open its colony, and export every section as a PDF.
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.
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.

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.