The StrataQuest Workspace

Open StrataQuest and you see three things: a panel for the image or whole slide on the left, a panel listing your layers in the middle, and the Operations Editor on the right. The middle panel is where you spend most of your time — every layer in your analysis lives there as a row, expanding into its four slots when you click it open.

Each slot is a vertical strip, sometimes empty, sometimes holding one engine, sometimes holding several engines chained together. The Pre-Processing slot is at the top because StrataQuest fires it first. Detection is next, because measurement waits for objects to measure. Measurements third. Post-Processing — refinement of the detected event list — is last.

Above all of this, the WBS (Work Breakdown Structure) column shows a flattened, numbered view of every engine your active layer will run, in order. It's the sentence StrataQuest will read when you click Run.

Pre-Processing. Where the image is prepared — flattened, sharpened, decomposed by channel — so the structures of interest are surfaced for the slot that follows. Background removalLoading..., illumination correction, channel extraction, color separation, smoothing filters. Most BOM engines that act on raw pixel data live here: Gauss filterLoading..., Median filterLoading..., Bilateral filterLoading..., and so on.

Detection. Where the image becomes a coded imageLoading... — a labeled map of detected events. Engines like LabelLoading..., the Classifier, Membrane detector, Nuclei detection, and Dots live here. Detection is the gate: nothing in Measurements or Post-Processing can run until this slot has produced labeled events.

Measurements. Per-event quantification — area, intensity, shape, location. The Measurements slot is where Standard MeasurementsLoading... and the various derived measurements operate. Output is one row of numbers per event.

Post-Processing. Refinement. Engines that select from the detected event list using the measurements just computed — Remove ObjectsLoading..., Remove labels by criterionLoading..., hole-filling. The slot exists because the right way to keep only the events that matter is to wait until you have the measurements in hand, and then select.

A slot can hold more than one engine. When you drop a second engine into the same slot, the Operations Editor connects them in series — the output of the first becomes the input of the second. This is how the BOM engines compose: a Gauss filter followed by an Otsu threshold followed by a Fill-holes operation is three engines in three slots (or the same slot, chained), and the WBS will show all three.

The composition is intentional. A single engine rarely produces what you want; chains are the common case. The Operations Editor exists because writing chains is what you do, and it should be visible — not buried in dialog boxes.

The Work Breakdown Structure column is StrataQuest's way of telling you what it's actually going to do. It's a flat, numbered list of every engine, in order, with the slot it lives in shown by indentation. When you read it top-to-bottom, you're reading exactly the sequence StrataQuest will run when you click execute.

The WBS is also where you trace. When a measurement comes back unexpected, the WBS shows you the chain that produced it — and points to the engine to look at first.