{# NO HEADING OF ITS OWN, and no close: this panel is the BODY of the card core builds for a loaded tool, and that card's header already carries the name, the key that opens it, an eye and an X. See views/toolLoader.js. The CSV pair is NOT in the header: it used to be lifted there as two unlabelled arrows whose only account of themselves was a tooltip -- the same mistake the base image's channel-rename button made, and fixed the same way. They are labelled actions on a line of their own now, at the top of the panel, exactly as Opacity and "Upload channel names" sit at the top of the image card's body (see index.html). Loading and saving gates act on the whole tool rather than on any one marker, so the line comes before the marker picker and everything below it. The one thing the header DOES carry is the mode cog: Thresholding or Single Cell Classifier. It changes what the whole card is, so it sits with the card's own controls (lifted there by `data-tool-extras`), before the `?`. #}

{# An automatic-gating session mirrored into this tab says so here, with Take over (gatingAgentBridge.js). Pause, Resume and Stop are in core's agent panel over the viewer, not here: one place to pause one session. Hidden unless a session announces itself. #}

{# Whole-tool actions used rarely enough to fold away: Clear all gates. Behind one glyph, at the end of the line the other whole-tool actions sit on, rather than a third labelled button that would make a destructive action as easy to hit as Download. #}

{# SINGLE CELL CLASSIFIER: the same whole-tool line, for its files. Load Annotations reads a training-examples JSON (checked first, then Merge or Replace); Download Cells offers the calls, the scores and the examples. The overflow holds the two that forget things. #}

{# ONE LINE: `MARKER [ CD3 v ] *`. The caption stood on a line of its own above the picker, which in a 300px sidebar spent a whole row on six characters -- and the panel below it is all one-line controls, so the stacked pair read as a different kind of thing. `.control-row` is core's label-beside-control shape (viewer.css), the same one the Point size and Opacity rows use. Auto Threshold ends THIS line, not the slider's: it answers "gate this marker", so it sits beside the marker it gates, and the slider's line is left to the two numbers and the track they name. Still `.slider-auto-button` for its revert and busy states; `.gate-marker-auto` only keeps the row from stretching it (gating.css). #}

Marker

{# Clear: this marker back to never gated -- its full range, and its provenance gone -- the undo of every way a gate gets set, Auto's included (gatingSidebarController.onClearClick). #} {# The classifier's pair, in the same places: the wand picks about 40 clear positives and 40 clear negatives across the image itself, then trains and calls every cell; the eraser takes the marker back to how it was before its first run and keeps the examples. #}

{# Which label a click on a cell gives, one at a time; pressing the active one again (or Escape) stops labelling, so the canvas pans as usual. The counts are this marker's examples. Train, at the end of the row, learns from exactly these examples -- the ones clicked, loaded or left by the wand -- without picking any of its own. #}

{# After a run: "Positive cells: 12,458 / 38,291", the uncertain and the not-classified counts beside it. And one status line under it: what is happening, what is missing, or why the calls are stale. #} {# A GATING SESSION'S LAYER. Automatic gating trains the classifier at each gate it writes and keeps the calls beside the threshold, which still decides the marker (and is what Thresholding exports) until the layer is adopted here. The block names the session and the gate, and counts where the two part ways in the two colours the canvas draws them in -- the legend and the numbers are one thing. Adopt makes the layer decide; Discard forgets it; the switch draws the classifier's own 0.5 call instead of the rule's. Hidden without a layer; for an adopted one only the head and the counts stay (gatingClassifier.paintSession). #} {# After a run with amber cells: a few of them, spread across the tissue, one at a time, each labelled from the keyboard; then Train again. On the user's own labelled cells, four such labels after a wand run lifted agreement from 72% to 76-77% (panel.review_cells). The bar takes the button's place while a review is on. #} {# A Z-STACK ONLY: what the image shows while gating -- the plane, or a slab of planes around it combined (mean, max or median; 5 um by default), for a stain too faint to judge on one optical section. The outlines stay the plane's own cells, and the gate is always applied to each cell's whole-cell value: the slab is for looking. Built by gatingPlanes.js; hidden for a 2-D image, a 2-D mask and the 3-D view. #} {# THE WHOLE GATE ON ONE LINE: `0.42 ---o=====o--- 9.10`, which is the image channel's contrast window exactly (viewerSidebar's createChannelSlot). The numbers are the slider's own `.plx-number` boxes, inline at the two ends of the track they name: drawn as plain text until they are clicked (as every slider's numbers are, in main.css), still typeable, which is what a gate copied off a paper or from another sample has always wanted. At rest they show two decimals; clicked, every decimal the gate holds. #}

{# THE DISTRIBUTION, UNDER THE SLIDER THAT CUTS IT. Its plotting area is measured off the slider's rail every time it is drawn (drawGateDistribution), so one value is one x in both: a handle at 65% of the track has its line at 65% of the plot, directly below it. The line is a second handle on the same gate -- drag either. In its top-left corner, ‹ and › move the LOWER threshold one step: the step Left/Right take on its focused handle, through the slider's own path (PlexoraSlider#nudge), so they are the arrow keys for a mouse. Core's muted icon button, as the Auto wand is. Only the SVG is redrawn, so these stay put. #}

{# A Z-STACK ONLY, while a plane is on screen: its cells -- the outlines drawn -- shaded under the line above and counted by the gate's calls: "z 12 . 41 of 312 positive". Painted by gatingPlanes.js. #} {# WHICH CELLS AUTO FITTED, when QC has been run on the image: "QC-passed cells only . 2,318 left out by QC", the counts in full in its tooltip. The cells QC failed (a fold, a blurred field) are left out of the fit; the gate still applies to every cell. Painted by paintQcNote; hidden otherwise. #} {# WHERE THIS GATE CAME FROM, when anybody but a hand on the slider set it: "Set automatically . high confidence", "Refined by an agent . needs review", "Locked" -- and the user's say over it (Approve, Lock). One muted line, drawn by paintProvenance; hidden for a gate with no provenance. #} {# WHERE THE THREE INPUTS DISAGREE, if they do. A table, a mask and an image come from three steps of a pipeline and nothing in any of them says they belong together, so pairing a table with the wrong image, or a mask exported at another resolution, produces a panel that works and is answering about a different sample. Under the distribution and the slider that cuts it, because the distribution is the thing being doubted: this is the marker's own numbers, and this is what may be wrong with the frame they are in. Quiet by construction -- muted text on the soft amber DESIGN.md keeps for a non-blocking warning -- because every one of these states is one a real project is allowed to be in. See core's models/consistency.py, which decides them; this panel only shows them. #} {# The panel's two keys, where the hand on the mouse finds them: the same key caps the canvas's own hint uses (core's `.plx-kbd`). Each is a button as well, for the hand that stayed on the mouse: a click steps the marker exactly as its key does (stepMarker). #}