File Explorer

The sidebar on the left of every page is a sandbox-scoped file browser. It classifies each entry on the fly so you can see at a glance which folder is an image directory, which JSON files are PhenoTypic pipelines, and which output folders carry a finished CLI run.

Initial state

When the hub boots, the sidebar lists the immediate children of the --root you passed. Folders are collapsed by default — the file browser is lazy: clicking a folder fetches and renders one level of children at a time.

The sidebar header carries three controls:

Control	Effect
Hidden files toggle	Show entries whose names start with .. Off by default.
External symlinks toggle	Show symlinks whose targets fall outside the sandbox root. Off by default — symlinks-to-elsewhere are a security hazard for the GUI’s path-resolution.
Refresh button	Flush the classifier’s LRU cache. Use this after dropping new files into a directory or moving a CLI output around.

Capability badges

Every entry is run through a small classifier (phenotypic.gui.shell._classifier) that emits one or more capability tags:

Badge	Meaning
img	Directory contains image files. The number in parens is a count, capped at 1000 so very large directories don’t pay for a full scan.
cfg	File is a PhenoTypic pipeline JSON (detected by the "pipe_cfgs" or legacy "operations" marker in the first 4 KB).
out	Directory is a CLI output root: contains both deliverables/master_measurements.parquet and a results/ subdirectory.
?	Directory could not be listed due to a permission error.

Click the plates row to expand it. The three TIFFs from the previous step appear as children, and the parent folder swaps its closed-folder icon (📁) for the open one (📂). A second click collapses the folder again.

Hide the sidebar

The chevron button at the far left of the top bar (« when the sidebar is visible, » when hidden) collapses the file explorer so the active tool’s pane spans the full width. Useful when you’re focused on the builder canvas or the run console’s log tail and don’t need the tree.

The collapsed flag is persisted to your browser’s localStorage under shell-sidebar-collapse-store, so it survives a page reload and remains in effect as you tab between Builder, Viewer, and Run. Clear your site data (or click the chevron again) to bring the sidebar back.

Hand-off to the run console

Clicking a sidebar entry doesn’t just expand it — the path is also stamped into a shared selection store. The Run console reads that store and offers context-appropriate Set as pipeline / Set as input dir / Set as output dir buttons in its hand-off banner. You’ll use that flow on the Run Locally page.

Next: Build a Pipeline.