diff --git a/.gitignore b/.gitignore index 1f2cd5c..f1bde4b 100644 --- a/.gitignore +++ b/.gitignore @@ -55,6 +55,8 @@ backend/__pycache__/ backend/app/**/__pycache__/ **/*.pyc backend/.dzi_cache/ +.tissueplex_cache/ +**/.tissueplex_cache/ .env .env.prod .claude/ diff --git a/CLAUDE.md b/CLAUDE.md index af18f1e..e7e5b90 100644 --- a/CLAUDE.md +++ b/CLAUDE.md @@ -9,7 +9,7 @@ of the project so any Claude instance can contribute immediately. ## What This Is A web-based spatial transcriptomics viewer supporting multiple platforms (Xenium, -MERSCOPE, CosMx) with connectivity layers produced by the lab's NICHESv2 R pipeline. +seqFISH, Visium HD, MERSCOPE, CosMx) with connectivity layers produced by the lab's NICHESv2 R pipeline. Built because Xenium Explorer does not support cell-cell ligand-receptor mechanism (LRM) visualization, and extended to be platform-agnostic. @@ -50,22 +50,45 @@ The backend uses an abstract reader pattern. All platform readers inherit from `SpatialDatasetReader` (base_reader.py) and implement the same interface. `ReaderFactory` auto-detects the platform from directory contents. -**Detection order:** +**Detection order** (first match wins — see `reader_factory.py::_DETECTORS`): | Platform | Sentinel file | |---|---| | Xenium (10x Genomics) | `experiment.xenium` | +| Visium HD (10x Genomics) | `binned_outputs/square_*um/` (or a top-level `square_???um/`) | | MERSCOPE (Vizgen) | `cell_by_gene.csv` or `cell_metadata.csv` | | CosMx (Nanostring) | `*_tx_file.csv` | +| seqFISH (Spatial Genomics) | `*_CellCoordinates*.csv` — a glob, so registered **last** | **Coordinate contract**: Every reader converts native coordinates to image pixel space before returning data. The frontend always receives pixel coordinates. +**Capability flags**: `capabilities()` on the base class returns +`{has_morphology, has_transcripts, has_boundaries, unit_label}`. The frontend reads these +from `/spatial/{dataset}/info` and hides layers a platform cannot serve. Readers override +it to declare what they lack — this is how spot-based platforms suppress the transcript +and boundary layers rather than returning empty arrays for them. + **Implementation status:** - Xenium: fully implemented +- Visium HD: implemented against a real Space Ranger 4.0.1 `outs/` tree — bins, bin + outlines, expression, and both color-value modes. `has_transcripts: False` (bin-level + UMI counts only, no molecule coordinates); `unit_label: "bin"`. See its own section. - MERSCOPE: cells, transcripts, genes, color-values (metadata + gene-set) implemented; - cell boundaries stub (MERSCOPE uses HDF5 boundary format, not yet parsed) + `cell_boundaries()` returns empty and `has_boundaries: False` (HDF5 polygon format + not yet parsed) - CosMx: cells, transcripts, genes, metadata color-values implemented; - gene-set color-values stub (requires transcript aggregation per cell) + gene-set color-values stub (requires transcript aggregation per cell); + `has_boundaries: False` (boundaries are per-FOV label TIFFs) +- seqFISH (Spatial Genomics GenePS): fully implemented for the current **v2** layout — + cells, transcripts, boundaries, expression, and both color-value modes. Legacy **v1** + reads cells and transcripts but declares `has_boundaries: False`, because v1 ships only + a label mask and polygonising it was deliberately deferred rather than adding a + dependency. See the seqFISH section below — its coordinate handling is unlike any other + reader and is the thing to understand before touching it. + +**Interface note**: every reader now matches the base signature (`fraction=`, dict return). +`base_reader.py`'s docstring for `cell_boundaries` still says `-> list[dict]` while all +implementations return the dict form — the docstring is the thing that is wrong. --- @@ -79,32 +102,49 @@ backend/ tiles.py DZI descriptor + tile serving; auto-builds pyramid on first request spatial.py Platform-agnostic router: all /spatial/... endpoints xenium.py DEPRECATED — kept for reference; not registered in main.py - edges.py edge query, LRM catalogue, edge color values, edge detail + edges.py edge query, LRM catalogue, edge color values, edge detail; + all endpoints take an edge_file param (multi-file support); + /files lists edge sources (top-level + edges/ folder) layers.py generic parquet layer router readers/ base_reader.py Abstract base class — SpatialDatasetReader interface reader_factory.py ReaderFactory: auto-detect platform, instantiate reader xenium_reader.py Xenium implementation (inherits SpatialDatasetReader) + seqfish_reader.py seqFISH / Spatial Genomics GenePS; v2 full, v1 partial. + Mixed µm/pixel coordinate handling — see its own section. + duck.py Shared DuckDB query helpers used by the spatial readers + metadata_filter.py Categorical-vs-continuous typing + the MetadataFilter + subsetting spec; shared by cells and edges (#35, #45) + spatial_cache.py Spatially-sorted parquet cache (build on first access) + visium_hd_reader.py Visium HD — bins as square polygons; see its own section merscope_reader.py MERSCOPE implementation (inherits SpatialDatasetReader) cosmx_reader.py CosMx implementation (inherits SpatialDatasetReader) - edge_reader.py reads edges.parquet; query_grouped(), lrm_catalogue(), edge_color_values(), edge_detail() + edge_reader.py reads edges.parquet; query_grouped(), query_scores(), lrm_catalogue(), edge_color_values(), edge_detail(); + also loads edge-metadata/ supplemental annotations + supplemental.py Shared cell-metadata/ + edge-metadata/ loader (key-agnostic) layer_reader.py generic parquet reader tiling/ pyramid.py OME-TIFF → DZI; pyvips streaming primary, tifffile+Pillow fallback requirements.txt pinned deps; cffi<2.0 required for pyvips 2.2.3 compatibility Dockerfile + tests/ + golden_snapshot.py Reader regression guard — see Development Workflow + golden_baseline.json Recorded baseline (191 probes / 7 datasets) frontend/ src/ + App.jsx Root component; React ErrorBoundary + top-level layout. + NOTE: sibling of components/, not inside it. store.js Zustand store — ALL shared state lives here components/ - App.jsx Root component; wraps everything in a React ErrorBoundary Viewer.jsx Split-screen wrapper (Viewer) + per-panel logic (ViewerPanel) LayerPanel.jsx Right-side panel: toggles, opacity, color-by, legends, dataset/image picker, transcript species filter CellInfoPanel.jsx Floating panel on cell click; shows color-by value highlight EdgeInfoPanel.jsx Floating panel on edge/autocrine click - AnnotationToolbar.jsx Region drawing + measurement tools; ⊞ Split / □ Single toggle; ⇔ Match zoom + AnnotationToolbar.jsx Region drawing + measurement tools; ⊞ Split / □ Single toggle; + ⇔ Match zoom; per-panel rotation (⟲ / angle / ⟳) + RenderingStatus.jsx Per-panel loading badge, driven by the store's loadingKeys set hooks/ useTranscripts.js Viewport-bounded transcript fetch (bbox always sent; skip at low zoom) useCellBoundaries.js Viewport-bounded cell boundary fetch (skip when fracW >= 0.5) @@ -119,14 +159,31 @@ frontend/ Dockerfile Multi-stage: node build → nginx serve docker-compose.yml Repo root; mounts DATA_PATH (or sample_data/) as /data:ro +docker-compose.prod.yml Production stack used by the cloud deployment docker/docker-compose.yml Legacy path (kept for compatibility) -sample_data/ GITIGNORED — default data mount for local dev/demo -r/ - export_NICHESObject_for_viewer.R draft R function for NICHESv2 → edges.parquet export +Caddyfile Reverse proxy + TLS for the cloud deployment; optional basicauth +deploy.sh One-shot droplet bootstrap (see docs/cloud-deploy.md) +upload-data.sh rsync datasets to a deployed server +sample_data/ Partially gitignored — default data mount for local dev/demo. + mouse_ileum_tiny and seqfish_synthetic are tracked; larger + and licence-restricted datasets are ignored. + make_edges.py Synthetic edges.parquet generator + make_seqfish.py Synthetic seqFISH v2 ROI generator (committable fixture) +r/ NICHESv2 → edges.parquet. See r/README.md. + niches_xenium.R Xenium — coordinates already µm; read this one first + niches_seqfish.R seqFISH — dense CSV counts, per-version coordinate units + niches_visium_hd.R Visium HD — pixel coordinates, must convert to µm + niches_common.R shared helpers (10x h5 reader, LR-coverage check, validation) + *_PPLR.R older personal pipeline with hardcoded paths; reference only docs/ data_format.md edges.parquet column spec for NICHESv2 R export - setup.md Docker deployment guide + setup.md Docker deployment guide (lab-facing) + cloud-deploy.md DigitalOcean deployment runbook (~$106–116/mo) public_datasets.md Links to public Xenium datasets used for development + index.html, demo.gif Landing page + README demo animation +OBS/ Archived, superseded planning docs. Provenance only — + NOT a specification. See OBS/README.md. +NICHESv2_package_design.md Design doc for the separate NICHESv2 R package (not this repo) ``` --- @@ -157,7 +214,7 @@ Platform-agnostic — works with any spatial dataset as long as cell barcodes ma `pixel_size` (from the reader) when serving to the frontend. The `sample_data/make_edges.py` script generates synthetic demo data in this format. -Real data comes from `export_for_TissuePlex()` in the NICHESv2 R package. +Real data comes from `export_to_TissuePlex()` in the NICHESv2 R package. --- @@ -165,7 +222,11 @@ Real data comes from `export_for_TissuePlex()` in the NICHESv2 R package. User-defined metadata (e.g. from external R analysis) can be loaded without modifying the dataset output by placing files in a `cell-metadata/` subdirectory of the dataset. -Currently implemented in XeniumReader; the pattern should be ported to other readers. +The loader lives on `SpatialDatasetReader`, so it is available to every platform; a reader +opts in by calling `_merge_supplemental()` on its cells table (Xenium and seqFISH do). +All a platform contributes is `_ROOT_CSV_SKIP` / `_ROOT_CSV_SKIP_SUFFIXES` — the list of +its *own* root CSVs, so the loader never ingests platform output as user metadata. CosMx +needs the suffix form because it prefixes every file with the experiment name. ``` dataset_dir/ @@ -197,9 +258,101 @@ write.csv(my_metadata_df, file.path(dataset_dir, "cell-metadata", "metadata.csv" dropdown. Continuous columns get a gradient colormap; string or low-cardinality integer columns get discrete colors. The cell-click info panel also shows the supplemental fields. -`XeniumReader._cells_full()` is cached per reader instance (one Docker request lifecycle). -`_load_supplemental_metadata()` is also cached, so the CSV is only parsed once regardless -of how many color-by requests arrive. +`_cells_full()` is cached per reader instance (one Docker request lifecycle). +`_load_supplemental_metadata()` is also cached on the base class, so the CSV is parsed once +regardless of how many color-by requests arrive. + +--- + +## Supplemental Edge Metadata (edge-metadata/ folder) + +The edge-side mirror of `cell-metadata/`, sharing its loader (`readers/supplemental.py`) +so the two cannot drift. Lets a user annotate cell pairs — a call, a confidence, a review +flag — without regenerating `edges.parquet` from R. + +``` +dataset_dir/ + edges.parquet + edge-metadata/ ← create this directory + annotations.csv ← key column `edge` = "SendingCell|ReceivingCell" + curation.parquet +``` + +Same rules as cell metadata: `.csv` / `.csv.gz` / `.parquet`, multiple files outer-joined, +and the key column resolved as an explicit `edge` column → `Unnamed: 0` (R's unnamed +rowname column) → the first column if it holds unique strings. So the R default works: + +```r +write.csv(annotations_df, file.path(dataset_dir, "edge-metadata", "annotations.csv")) +``` + +**The folder sits beside the dataset, not beside the edge file.** `EdgeReader._dataset_dir` +walks up out of `edges/` when the edge file is nested, so one set of annotations applies +across every edge source in the dataset. Annotations describe cell pairs, which are a +property of the tissue rather than of one scoring run. + +Three integration points, all in `edge_reader.py`: + +- `schema()` merges supplemental columns into the returned column map. That is the *only* + thing needed for them to appear in the edge color-by dropdown — `LayerPanel` builds that + list straight from the schema, so no frontend change was required. +- `edge_color_values("metadata", field=…)` checks the parquet first, then the supplemental + frame. Supplemental data is already one row per edge, so it skips the `GROUP BY`. +- `edge_detail()` attaches matches under a `metadata` key, which `EdgeInfoPanel` renders + generically as an "Annotations" block above the LRM table. + +Parquet wins a name collision (`schema()` uses `setdefault`): it is the authoritative +source, and a supplemental column silently shadowing a real one would be painful to debug. + +--- + +## Multiple Edge Files (edges/ folder) + +A dataset can carry more than one edge set so users can flip between different +computational approaches (e.g. raw-count vs. normalized scoring) on the **same** +tissue without duplicating the cell / transcript / boundary parquet files. This is +issue #46. + +``` +dataset_dir/ + experiment.xenium + cells.parquet ← untouched by this feature + transcripts.parquet ← untouched + cell_boundaries.parquet ← untouched + edges.parquet ← optional legacy top-level file (still the default) + edges/ ← dedicated folder for additional edge sets + edge.raw.minimum.parquet + edge.normalized.product.parquet +``` + +Every file (top-level and in `edges/`) follows the same `edges.parquet` schema +documented below. Generate extra sets with +`sample_data/make_edges.py --out edges/.parquet …`. + +**Discovery** — `GET /edges/{dataset}/files` returns +`{ files: [{id, label}], default }`. It looks in exactly two places so it never +sweeps up cells/transcripts/boundary parquet: the legacy top-level `edges.parquet` +(listed first, kept as the default for backward compatibility) and every `*.parquet` +in the `edges/` subfolder. `id` is the value passed back as the `edge_file` query +param (e.g. `"edges/edge.raw.minimum.parquet"`); `label` is the display name +(folder + `.parquet` stripped). + +**Backend** — every `/edges/*` endpoint already accepted an `edge_file` query param +(default `edges.parquet`); the reader cache in `edges.py` is keyed by +`(dataset, edge_file)`. `_reader()` resolves `edge_file` under the dataset directory +and rejects anything that escapes it (path-traversal guard → 400; missing file → 404). + +**Frontend** — a single global `edgeFile` in the store applies to **all** open viewer +panels (see the Split-Screen note; a per-panel edge file was deliberately deferred +because LRM catalogue / color ranges are edge-file-specific and the sidebar is shared). +The picker is a ` setActiveImage(e.target.value)} style={SELECT_STYLE} > @@ -135,6 +144,9 @@ export default function LayerPanel() { const { platformCapabilities, apiBase } = useStore(); const hasTranscripts = platformCapabilities?.has_transcripts ?? true; const hasBoundaries = platformCapabilities?.has_boundaries ?? true; + // A dataset with no morphology gets a placeholder canvas, so the opacity + // control would be a dead toggle over a flat fill. + const hasMorphology = platformCapabilities?.has_morphology ?? true; const unitLabel = platformCapabilities?.unit_label ?? "cell"; const unitTitle = unitLabel.charAt(0).toUpperCase() + unitLabel.slice(1); @@ -167,13 +179,19 @@ export default function LayerPanel() {
Layers
Core
- + {hasMorphology && } {hasTranscripts && } {hasBoundaries && }
{unitTitle} Color
+ {/* Issue #45. Placed under the color section because picking the column to + subset on is the same act as picking the column to colour by, and users + almost always do the two together. */} +
{unitTitle} Filter
+ + {hasTranscripts && ( <>
Transcript Species
@@ -215,6 +233,8 @@ function ColorBySection({ unitLabel = "cell" }) { selectedGenes, cellColorRange, cellColorClamp, setCellColorClamp, + categoricalOverrides, setCategoricalOverride, + cellColorType, cellColorCategories, } = useStore(); const [cellSchema, setCellSchema] = useState(null); @@ -236,10 +256,20 @@ function ColorBySection({ unitLabel = "cell" }) { const { mode, field } = colorBy; const selectedCount = selectedGenes === null ? allGenes.length : selectedGenes.size; - // Determine if the selected metadata column is categorical + // How the selected column is actually being coloured. This comes from the + // backend's response (via the store, written by panel 0) rather than from the + // schema dtype: the backend also treats a low-cardinality integer column as + // categorical, so guessing from dtype used to draw a gradient legend with two + // dead sliders over a canvas that was already showing discrete colours. const fieldDtype = field && cellSchema ? cellSchema.columns[field] : null; - const isCategorical = fieldDtype === "object" || fieldDtype === "string" || - (fieldDtype?.startsWith("int") && false); // int cols treated as continuous unless overridden + const isCategorical = mode === "metadata" && !!field && cellColorType === "categorical"; + + // The override is only meaningful for a numeric column — a text column has no + // gradient to fall back to, so there is nothing to offer. + const isNumericField = !!fieldDtype && + /^(int|uint|float|Int|UInt|Float)/.test(fieldDtype); + const overrideKey = `cell::${field}`; + const override = categoricalOverrides[overrideKey] ?? null; return (
@@ -288,6 +318,37 @@ function ColorBySection({ unitLabel = "cell" }) { ))} + + {/* Issue #35: integer-coded cluster IDs arrive as ints and would + otherwise be drawn as a gradient. Unchecking forces the reverse, + which is how you get a gradient over a column the auto-rule + called categorical. */} + {isNumericField && ( + + )} )} @@ -314,7 +375,7 @@ function ColorBySection({ unitLabel = "cell" }) { clamp={cellColorClamp} setClamp={setCellColorClamp} accentColor="#6cf" /> )} {mode === "metadata" && field && isCategorical && ( - + )} )} @@ -369,7 +430,16 @@ function ClampableLegend({ label, palette, vmin, vmax, clamp, setClamp, accentCo ); } -function CategoricalLegend({ field, apiBase, dataset }) { +/** + * Editable per-category swatches. + * + * `categories` comes from the store, where panel 0 records whatever the backend + * returned for the active column. This component used to re-POST /color-values + * for itself, which duplicated a request the viewer had already made and — once + * the categorical override existed — would have asked without it, so the legend + * could disagree with the canvas it describes. + */ +function CategoricalLegend({ field, categories = [] }) { const { categoryColorOverrides, setCategoryColorOverride, @@ -377,21 +447,8 @@ function CategoricalLegend({ field, apiBase, dataset }) { resetCategoryColorOverrides, } = useStore(); - const [categories, setCategories] = useState([]); const fileInputRef = useRef(null); - useEffect(() => { - if (!field) return; - fetch(`${apiBase}/spatial/${dataset}/color-values`, { - method: "POST", - headers: { "Content-Type": "application/json" }, - body: JSON.stringify({ mode: "metadata", field }), - }) - .then((r) => r.json()) - .then((d) => { if (d.type === "categorical") setCategories(d.categories); }) - .catch(() => {}); - }, [apiBase, dataset, field]); - // Resolve display color for a category: override → QUAL_PALETTE → hash // Must mirror the logic in useCellColors.js so legend stays in sync. function resolveColor(cat, i) { @@ -521,6 +578,216 @@ function CategoricalLegend({ field, apiBase, dataset }) { ); } +// ── Metadata filter (issue #45) ─────────────────────────────────────────────── +/** + * Restrict the view to a subset of units by one metadata column. + * + * One component serves both the cell filter and the edge filter — they differ + * only in which endpoint supplies the column list and the distinct values, so + * those arrive as props. The chosen filter is written to the store and travels + * to the backend, which applies it *before* sampling; doing it client-side would + * leave a sample of a subset rather than the subset. + * + * Two shapes, chosen by what the backend says the column is: + * categorical — checkboxes, one per value (this is the "focus on 2–3 cell + * types" case from the issue) + * continuous — inclusive min/max bounds + */ +function MetadataFilterSection({ + scope, columns, filter, setFilter, fetchValues, unitLabel = "cell", +}) { + const [meta, setMeta] = useState(null); // { type, categories, min, max } + const [loading, setLoading] = useState(false); + const field = filter?.field ?? ""; + + // Load the distinct values / range for the selected column. + useEffect(() => { + if (!field) { setMeta(null); return; } + let cancelled = false; + setLoading(true); + fetchValues(field) + .then((d) => { if (!cancelled && d) setMeta(d); }) + .catch(() => { if (!cancelled) setMeta(null); }) + .finally(() => { if (!cancelled) setLoading(false); }); + return () => { cancelled = true; }; + }, [field, fetchValues]); + + const selected = new Set(filter?.values ?? []); + const active = (filter?.values?.length ?? 0) > 0 || + filter?.min != null || filter?.max != null; + + function chooseField(next) { + // Values and bounds belong to the old column; carrying them over would + // silently filter on labels that do not exist in the new one. + setFilter(next ? { field: next, values: null, min: null, max: null } : null); + } + + function toggle(cat) { + const next = new Set(selected); + if (next.has(cat)) next.delete(cat); else next.add(cat); + setFilter({ ...filter, values: next.size ? [...next] : null }); + } + + return ( +
+ + + {field && loading && ( +
loading values…
+ )} + + {field && !loading && meta?.type === "categorical" && ( +
+
+ {(meta.categories ?? []).map((cat) => ( + + ))} +
+
+ + + + {/* No selection is "show everything", not "show nothing" — an empty + allowlist would blank the canvas the moment a column is picked. */} + {selected.size + ? `${selected.size} of ${(meta.categories ?? []).length} shown` + : "all shown"} + +
+
+ )} + + {field && !loading && meta?.type === "continuous" && ( +
+ min + setFilter({ + ...filter, min: e.target.value === "" ? null : parseFloat(e.target.value), + })} + style={{ ...SELECT_STYLE, marginTop: 0, width: 0, flex: 1 }} + /> + max + setFilter({ + ...filter, max: e.target.value === "" ? null : parseFloat(e.target.value), + })} + style={{ ...SELECT_STYLE, marginTop: 0, width: 0, flex: 1 }} + /> +
+ )} + + {active && ( + + )} +
+ ); +} + +function fmtBound(v) { + if (v == null) return ""; + return Math.abs(v) >= 1000 || (v !== 0 && Math.abs(v) < 0.01) + ? v.toExponential(1) : String(Math.round(v * 1000) / 1000); +} + +function CellFilterSection({ unitLabel = "cell" }) { + const { apiBase, dataset, cellFilter, setCellFilter, categoricalOverrides } = useStore(); + const [columns, setColumns] = useState([]); + + useEffect(() => { + fetch(`${apiBase}/spatial/${dataset}/cells/schema`) + .then((r) => (r.ok ? r.json() : null)) + .then((s) => setColumns(s?.columns ? Object.keys(s.columns) : [])) + .catch(() => setColumns([])); + }, [apiBase, dataset]); + + // Honour the same categorical override the color panel uses, so a column the + // user has declared categorical offers checkboxes here rather than a range. + const fetchValues = React.useCallback((field) => { + const categorical = categoricalOverrides[`cell::${field}`] ?? null; + return fetch(`${apiBase}/spatial/${dataset}/color-values`, { + method: "POST", + headers: { "Content-Type": "application/json" }, + body: JSON.stringify({ mode: "metadata", field, categorical }), + }).then((r) => (r.ok ? r.json() : null)); + }, [apiBase, dataset, categoricalOverrides]); + + return ( + + ); +} + +function EdgeFilterSection() { + const { apiBase, dataset, edgeFile, edgeFilter, setEdgeFilter, categoricalOverrides } = useStore(); + const [columns, setColumns] = useState([]); + const efParam = `?edge_file=${encodeURIComponent(edgeFile)}`; + + useEffect(() => { + fetch(`${apiBase}/edges/${dataset}/schema${efParam}`) + .then((r) => (r.ok ? r.json() : null)) + // Structural and per-LRM columns are not edge attributes to subset on: + // one edge has many LRM rows, so "lrm = X" is a mechanism filter, which + // the LRM checklist below already does properly. + .then((s) => setColumns( + s?.columns + ? Object.keys(s.columns).filter((c) => !EDGE_FILTER_SKIP.has(c)) + : [] + )) + .catch(() => setColumns([])); + }, [apiBase, dataset, efParam]); + + const fetchValues = React.useCallback((field) => { + const categorical = categoricalOverrides[`edge::${field}`] ?? null; + return fetch(`${apiBase}/edges/${dataset}/edge-color-values${efParam}`, { + method: "POST", + headers: { "Content-Type": "application/json" }, + body: JSON.stringify({ mode: "metadata", field, categorical }), + }).then((r) => (r.ok ? r.json() : null)); + }, [apiBase, dataset, efParam, categoricalOverrides]); + + if (!columns.length) return null; + return ( + + ); +} + +const EDGE_FILTER_SKIP = new Set([ + "edge", "sending_cell", "receiving_cell", "x1", "y1", "x2", "y2", + "lrm", "lrm_id", "ligand", "receptor", "score", "score_norm", +]); + // ── Morphology row ──────────────────────────────────────────────────────────── function MorphologyRow() { const { layers, setLayerProp } = useStore(); @@ -982,6 +1249,7 @@ const EDGE_SKIP_COLS = new Set(["x1", "y1", "x2", "y2", "edge", "sending_cell", function EdgeSection() { const { apiBase, dataset, + edgeFile, setEdgeFile, layers, setLayerProp, edgeMinStrength, setEdgeMinStrength, edgeColorBy, setEdgeColorBy, @@ -999,25 +1267,49 @@ function EdgeSection() { hiddenLrms, toggleLrm, setAllLrmsVisible, hideAllLrms, edgeColorRange, edgeColorClamp, setEdgeColorClamp, + categoricalOverrides, setCategoricalOverride, } = useStore(); const state = layers.edges ?? { visible: true, opacity: 0.9 }; const [localStrength, setLocalStrength] = useState(edgeMinStrength ?? 0); const commitTimer = useRef(null); const [edgeSchema, setEdgeSchema] = useState(null); const [lrmSearch, setLrmSearch] = useState(""); + // List of edge-source files in the current dataset: [{id, label}]. + const [edgeFiles, setEdgeFiles] = useState([]); + // ── edge-source parquet list (issue #46) ──────────────────────────────────── + // Fetch the available edge files for the dataset and select the backend-provided + // default (legacy top-level edges.parquet if present, else the first). Falls back + // gracefully to a single implicit "edges.parquet" if the endpoint returns nothing. useEffect(() => { - fetch(`${apiBase}/edges/${dataset}/schema`) + if (!dataset) return; + fetch(`${apiBase}/edges/${dataset}/files`) + .then((r) => (r.ok ? r.json() : null)) + .then((data) => { + const files = Array.isArray(data?.files) ? data.files : []; + setEdgeFiles(files); + if (files.length > 0) { + const cur = useStore.getState().edgeFile; + const ids = files.map((f) => f.id); + if (!ids.includes(cur)) setEdgeFile(data.default ?? ids[0]); + } + }) + .catch(() => setEdgeFiles([])); + }, [apiBase, dataset]); // eslint-disable-line react-hooks/exhaustive-deps + + const efParam = `?edge_file=${encodeURIComponent(edgeFile)}`; + useEffect(() => { + fetch(`${apiBase}/edges/${dataset}/schema${efParam}`) .then((r) => (r.ok ? r.json() : null)) .then(setEdgeSchema) .catch(() => {}); if (lrmCatalogue.length === 0) { - fetch(`${apiBase}/edges/${dataset}/lrm-catalogue`) + fetch(`${apiBase}/edges/${dataset}/lrm-catalogue${efParam}`) .then((r) => (r.ok ? r.json() : [])) .then(setLrmCatalogue) .catch(() => {}); } - }, [apiBase, dataset]); // eslint-disable-line react-hooks/exhaustive-deps + }, [apiBase, dataset, efParam]); // eslint-disable-line react-hooks/exhaustive-deps const handleStrength = (e) => { const v = parseFloat(e.target.value); @@ -1034,12 +1326,50 @@ function EdgeSection() { const { mode, field } = edgeColorBy; const selectedLrmCount = lrmCatalogue.length - hiddenLrms.size; - // Determine if selected metadata column is categorical + // How the selected edge metadata column is typed. Asking the backend rather + // than reading the dtype matters for the same reason it does on the cell side: + // the auto-rule also calls a low-cardinality integer column categorical, and an + // explicit override can flip either way (issue #35). const fieldDtype = field && edgeSchema ? edgeSchema.columns[field] : null; - const isCategorical = fieldDtype === "object" || fieldDtype === "string" || fieldDtype === "bool"; + const isNumericField = !!fieldDtype && /^(int|uint|float|double|Int|UInt|Float)/.test(fieldDtype); + const edgeOverrideKey = `edge::${field}`; + const edgeOverride = categoricalOverrides[edgeOverrideKey] ?? null; + + const [edgeMeta, setEdgeMeta] = useState(null); // { type, categories } + useEffect(() => { + if (mode !== "metadata" || !field) { setEdgeMeta(null); return; } + let cancelled = false; + fetch(`${apiBase}/edges/${dataset}/edge-color-values${efParam}`, { + method: "POST", + headers: { "Content-Type": "application/json" }, + body: JSON.stringify({ mode: "metadata", field, categorical: edgeOverride }), + }) + .then((r) => (r.ok ? r.json() : null)) + .then((d) => { if (!cancelled && d) setEdgeMeta({ type: d.type, categories: d.categories ?? [] }); }) + .catch(() => {}); + return () => { cancelled = true; }; + }, [apiBase, dataset, efParam, mode, field, edgeOverride]); + + const isCategorical = mode === "metadata" && !!field && edgeMeta?.type === "categorical"; return (
+ {/* Edge-source picker (issue #46) — only shown when the dataset has more than + one edge file. Applies to every open viewer panel. */} + {edgeFiles.length > 1 && ( +
+ +
+ )} { setEdgeColorBy("metadata", e.target.value || null); setEdgeColorClamp(null, null); }} - style={{ ...SELECT_STYLE, marginTop: 4 }} - > - - {metaCols.map((c) => )} - + <> + + {field && isNumericField && ( + + )} + )} {/* Palette — only for continuous color modes */} @@ -1222,9 +1577,16 @@ function EdgeSection() { clamp={edgeColorClamp} setClamp={setEdgeColorClamp} accentColor="#f90" /> )} {mode === "metadata" && field && isCategorical && ( - + )} + {/* ── Edge metadata filter (issue #45) ─────────────────────── */} + {/* Distinct from the LRM checklist below: this subsets *edges* by an + attribute of the pair (a curation call, a confidence), whereas the + checklist subsets the mechanisms scored on every edge. */} +
Edge Filter
+ + {/* ── LRM Mechanisms checklist ─────────────────────────────── */} {lrmCatalogue.length > 0 && (
@@ -1281,21 +1643,10 @@ function EdgeSection() { ); } -function EdgeCategoricalLegend({ field, apiBase, dataset }) { - const [categories, setCategories] = useState([]); - - useEffect(() => { - if (!field) return; - fetch(`${apiBase}/edges/${dataset}/edge-color-values`, { - method: "POST", - headers: { "Content-Type": "application/json" }, - body: JSON.stringify({ mode: "metadata", field }), - }) - .then((r) => r.json()) - .then((d) => { if (d.type === "categorical") setCategories(d.categories); }) - .catch(() => {}); - }, [apiBase, dataset, field]); - +/** Read-only swatch list. Categories come from EdgeSection, which already asked + * the backend for the column's type — one fetch, one answer, no chance of the + * legend describing a different typing decision than the canvas is using. */ +function EdgeCategoricalLegend({ categories = [] }) { if (!categories.length) return null; return (
diff --git a/frontend/src/components/Viewer.jsx b/frontend/src/components/Viewer.jsx index e01cb3d..3e3ec55 100644 --- a/frontend/src/components/Viewer.jsx +++ b/frontend/src/components/Viewer.jsx @@ -37,6 +37,10 @@ const DEFAULT_AUTOCRINE_COLOR = [255, 150, 0, 200]; const VIEW_ID = "main"; +// Matches pyramid.BLANK_IMAGE_NAME: the placeholder canvas served for datasets +// with no morphology of their own. Not a real image, so it is not shown as one. +const BLANK_IMAGE_NAME = "__blank__"; + // ── Rotation helpers (pure, module-level) ───────────────────────────────── /** @@ -125,7 +129,7 @@ function ViewerPanel({ panelIndex }) { cellColorEnabled, colorBy, cellColorPalette, categoryColorOverrides, allGenes, selectedGenes, transcriptColorOverrides, selectedCell, setSelectedCell, - edgeMinStrength, edgeDensity, + edgeMinStrength, edgeDensity, edgeFile, edgeColorBy, edgeColorPalette, edgeDirectional, showAutocrine, edgeWidth, showArrowheads, arrowStyle, arrowheadScale, edgeOffset, @@ -134,6 +138,7 @@ function ViewerPanel({ panelIndex }) { selectedEdge, setSelectedEdge, setCellColorRange, setEdgeColorRange, cellColorClamp, edgeColorClamp, setEdgeColorClamp, + categoricalOverrides, cellFilter, edgeFilter, setCellColorType, annotationMode, pixelSize, setPixelSize, clearZoomMatch, @@ -226,6 +231,9 @@ function ViewerPanel({ panelIndex }) { viewerRef.current.destroy(); viewerRef.current = null; } + // activeImage is null between a dataset switch and DatasetPicker resolving the + // new dataset's image list. Opening OSD here would request "null.dzi". + if (!dataset || !activeImage) return; const viewer = OpenSeadragon({ element: containerRef.current, @@ -530,7 +538,8 @@ function ViewerPanel({ panelIndex }) { total: cellBoundaryTotal, loading: cellBoundariesLoading, } = useCellBoundaries( - apiBase, dataset, viewport, imageSize, cellSegmentsVisible && hasBoundaries, cellBoundaryFraction + apiBase, dataset, viewport, imageSize, cellSegmentsVisible && hasBoundaries, + cellBoundaryFraction, cellFilter ); useEffect(() => { cellPolygonsRef.current = cellPolygons; }, [cellPolygons]); @@ -541,20 +550,38 @@ function ViewerPanel({ panelIndex }) { const { edges, loading: edgesLoading } = useEdges( apiBase, dataset, viewport, imageSize, edgesVisible || tissueGraphVisible, - edgeMinStrength, hiddenLrms, lrmCatalogue, edgeDensity + edgeMinStrength, hiddenLrms, lrmCatalogue, edgeDensity, edgeFile, + cellFilter, edgeFilter ); - const { colorValues, vmin: cellVmin, vmax: cellVmax, loading: cellColorsLoading } = useCellColors( - apiBase, dataset, colorBy, allGenes, selectedGenes, cellColorPalette, cellColorEnabled, cellColorClamp, categoryColorOverrides + // Explicit categorical/continuous choice for the active color-by column, or + // null (auto-detect) when the user has not overridden it — issue #35. + const cellCategorical = categoricalOverrides[`cell::${colorBy?.field}`] ?? null; + const edgeCategorical = categoricalOverrides[`edge::${edgeColorBy?.field}`] ?? null; + + const { + colorValues, vmin: cellVmin, vmax: cellVmax, + type: cellType, categories: cellCategories, loading: cellColorsLoading, + } = useCellColors( + apiBase, dataset, colorBy, allGenes, selectedGenes, cellColorPalette, + cellColorEnabled, cellColorClamp, categoryColorOverrides, cellCategorical ); // Only update shared store ranges from panel 0 to avoid redundant updates useEffect(() => { if (panelIndex === 0) setCellColorRange(cellVmin, cellVmax); }, [cellVmin, cellVmax]); // eslint-disable-line + // The backend is the authority on whether a column is categorical, so report + // the type it actually returned rather than letting the panel re-derive it + // from the schema dtype — the two disagreed for low-cardinality integers. + useEffect(() => { + if (panelIndex === 0) setCellColorType(cellType, cellCategories); + }, [cellType, cellCategories]); // eslint-disable-line + const edgeColorEnabled = edgeColorBy.mode !== "default"; const { colorValues: edgeColorValues, vmin: edgeVmin, vmax: edgeVmax, p95: edgeP95, loading: edgeColorsLoading } = useEdgeColors( - apiBase, dataset, edgeColorBy, hiddenLrms, lrmCatalogue, edgeColorPalette, edgeColorEnabled, edgeColorClamp, edges + apiBase, dataset, edgeColorBy, hiddenLrms, lrmCatalogue, edgeColorPalette, + edgeColorEnabled, edgeColorClamp, edges, edgeFile, edgeCategorical ); useEffect(() => { if (panelIndex === 0) setEdgeColorRange(edgeVmin, edgeVmax); @@ -1011,6 +1038,7 @@ function ViewerPanel({ panelIndex }) { apiBase={apiBase} dataset={dataset} edgeId={selectedEdge} + edgeFile={edgeFile} onClose={() => setSelectedEdge(null)} /> )} @@ -1024,7 +1052,7 @@ function ViewerPanel({ panelIndex }) { pointerEvents: "none", }} > - {dataset} / {activeImage} + {dataset}{activeImage && activeImage !== BLANK_IMAGE_NAME ? ` / ${activeImage}` : ""} {panelCount >= 2 && ( · panel {panelIndex + 1} )} diff --git a/frontend/src/hooks/useCellBoundaries.js b/frontend/src/hooks/useCellBoundaries.js index 5d07c7b..84f38b2 100644 --- a/frontend/src/hooks/useCellBoundaries.js +++ b/frontend/src/hooks/useCellBoundaries.js @@ -19,8 +19,30 @@ import { useState, useEffect, useRef } from "react"; const TARGET_CELLS = 5_000; const SEED_TOTAL = 50_000; // conservative first-probe estimate +/** + * Serialise a metadata filter (issue #45) into query params. + * + * Returns "" when there is nothing to constrain, so the URL is byte-identical to + * the pre-filter one and no cached response is missed. The filter is sent to the + * server rather than applied to the response because sampling happens server-side: + * filtering afterwards would leave a fraction of a fraction on screen. + */ +function filterParams(filter) { + if (!filter?.field) return ""; + const p = new URLSearchParams(); + const hasValues = Array.isArray(filter.values) && filter.values.length > 0; + if (!hasValues && filter.min == null && filter.max == null) return ""; + p.set("filter_field", filter.field); + if (hasValues) for (const v of filter.values) p.append("filter_values", v); + if (filter.min != null) p.set("filter_min", filter.min); + if (filter.max != null) p.set("filter_max", filter.max); + if (filter.includeMissing) p.set("filter_missing", "true"); + return `&${p.toString()}`; +} + export function useCellBoundaries( - apiBase, dataset, viewport, imageSize, enabled = true, fraction = null + apiBase, dataset, viewport, imageSize, enabled = true, fraction = null, + filter = null ) { const [cells, setCells] = useState([]); const [total, setTotal] = useState(0); @@ -31,6 +53,23 @@ export function useCellBoundaries( const abortRef = useRef(null); const prevTotalRef = useRef(SEED_TOTAL); // running estimate of cells in viewport + // Serialised once so it can be both spliced into the URL and used as an effect + // dependency — the filter arrives as an object whose identity changes on every + // render, which would otherwise refetch continuously. + const filterQS = filterParams(filter); + + // One-shot recalibration. + // + // In auto mode the fraction is picked from `prevTotalRef`, the total the *last* + // fetch saw. Applying a metadata filter (or switching dataset) changes that + // total out from under the estimate, and nothing else would trigger another + // fetch — so the layer would sit showing a tenth of an already-small subset + // until the user happened to pan. Bumping this counter re-runs the fetch once + // with the corrected fraction; `calibratedRef` keys it to the current request + // so it can converge rather than oscillate. + const [recalibrate, setRecalibrate] = useState(0); + const calibratedRef = useRef(null); + useEffect(() => { if (!enabled || !dataset) { setLoading(false); @@ -62,6 +101,7 @@ export function useCellBoundaries( } else { url += `?${fracParam}`; } + url += filterQS; const res = await fetch(url, { signal: ctrl.signal }); if (!res.ok) { setCells([]); setTotal(0); return; } const data = await res.json(); @@ -74,6 +114,23 @@ export function useCellBoundaries( if (totalCells > 0) prevTotalRef.current = totalCells; setTotal(totalCells); + // If that estimate was badly wrong, correct it now rather than waiting + // for the user to pan. Only in auto mode — an explicit slider value is + // the user's decision, not an estimate. Once per request key. + // The 1.2 threshold is what makes the panel's sample readout honest: the + // panel derives its percentage from the *current* total, so anything + // looser leaves it advertising a fraction the canvas is not drawing at. + // Total is a pre-sample count for a fixed bbox and filter, so the second + // fetch computes the same fraction and the loop settles after one pass. + if (fraction === null && totalCells > 0) { + const better = Math.min(1.0, TARGET_CELLS / totalCells); + const key = `${url}|${totalCells}`; + if (better > eff * 1.2 && calibratedRef.current !== key) { + calibratedRef.current = key; + setRecalibrate((c) => c + 1); + } + } + if (!Array.isArray(rows)) { setCells([]); return; } // Group flat vertex list by cell_id → polygon arrays @@ -94,7 +151,7 @@ export function useCellBoundaries( }, 200); return () => clearTimeout(timerRef.current); - }, [apiBase, dataset, viewport?.xmin, viewport?.ymin, viewport?.xmax, viewport?.ymax, enabled, fraction]); + }, [apiBase, dataset, viewport?.xmin, viewport?.ymin, viewport?.xmax, viewport?.ymax, enabled, fraction, filterQS, recalibrate]); // Abort in-flight request on unmount useEffect(() => { diff --git a/frontend/src/hooks/useCellColors.js b/frontend/src/hooks/useCellColors.js index 07aa2c0..236aec7 100644 --- a/frontend/src/hooks/useCellColors.js +++ b/frontend/src/hooks/useCellColors.js @@ -25,6 +25,7 @@ import { geneColor } from "../utils/geneColor"; * Modes: * gene_set — POST with selected genes; returns continuous sum * metadata — POST with field; backend auto-detects continuous vs. categorical + * unless `categorical` overrides it (issue #35) * * Returns: * colorValues Map or null when disabled @@ -34,7 +35,7 @@ import { geneColor } from "../utils/geneColor"; * categoryColors Map for categorical legend * loading */ -export function useCellColors(apiBase, dataset, colorBy, allGenes, selectedGenes, palette, enabled, clamp, categoryColorOverrides) { +export function useCellColors(apiBase, dataset, colorBy, allGenes, selectedGenes, palette, enabled, clamp, categoryColorOverrides, categorical = null) { const [result, setResult] = useState({ colorValues: null, type: "continuous", vmin: 0, vmax: 0, categories: [], categoryColors: new Map(), @@ -90,7 +91,7 @@ export function useCellColors(apiBase, dataset, colorBy, allGenes, selectedGenes try { const body = mode === "gene_set" ? { mode: "gene_set", genes: genesToSend } - : { mode: "metadata", field }; + : { mode: "metadata", field, categorical }; const res = await fetch(`${apiBase}/spatial/${dataset}/color-values`, { method: "POST", @@ -119,7 +120,7 @@ export function useCellColors(apiBase, dataset, colorBy, allGenes, selectedGenes } }, 400); return () => clearTimeout(timerRef.current); - }, [apiBase, dataset, colorBy?.mode, colorBy?.field, allGenes, selectedGenes, enabled]); // eslint-disable-line + }, [apiBase, dataset, colorBy?.mode, colorBy?.field, allGenes, selectedGenes, enabled, categorical]); // eslint-disable-line // ── Effect 2: apply clamp + palette to continuous data (no fetch, no debounce) ── // Fires immediately when rawCont, clamp, or palette changes so slider drags diff --git a/frontend/src/hooks/useEdgeColors.js b/frontend/src/hooks/useEdgeColors.js index 0af42f6..618fcb4 100644 --- a/frontend/src/hooks/useEdgeColors.js +++ b/frontend/src/hooks/useEdgeColors.js @@ -27,8 +27,12 @@ import { valueToColor, QUAL_PALETTE } from "../utils/colormap"; export function useEdgeColors( apiBase, dataset, edgeColorBy, hiddenLrms, lrmCatalogue, palette, enabled, clamp, - edges // array from useEdges — used for client-side lrm_set coloring + edges, // array from useEdges — used for client-side lrm_set coloring + edgeFile = "edges.parquet", // which edge-source parquet the metadata fetch reads + categorical = null // issue #35 override: null = auto-detect, true/false = forced ) { + // Appended to the metadata edge-color-values request (lrm_set is client-side only). + const efParam = `?edge_file=${encodeURIComponent(edgeFile)}`; const [result, setResult] = useState({ colorValues: null, type: "continuous", vmin: 0, vmax: 0, p95: null, categories: [], categoryColors: new Map(), @@ -93,10 +97,10 @@ export function useEdgeColors( setLoading(true); try { - const res = await fetch(`${apiBase}/edges/${dataset}/edge-color-values`, { + const res = await fetch(`${apiBase}/edges/${dataset}/edge-color-values${efParam}`, { method: "POST", headers: { "Content-Type": "application/json" }, - body: JSON.stringify({ mode: "metadata", field }), + body: JSON.stringify({ mode: "metadata", field, categorical }), signal: ctrl.signal, }); if (!res.ok) throw new Error(`HTTP ${res.status}`); @@ -128,7 +132,7 @@ export function useEdgeColors( } }, 400); return () => clearTimeout(timerRef.current); - }, [apiBase, dataset, edgeColorBy?.mode, edgeColorBy?.field, enabled]); // eslint-disable-line + }, [apiBase, dataset, edgeColorBy?.mode, edgeColorBy?.field, enabled, efParam, categorical]); // eslint-disable-line // ── Effect 2: apply clamp + palette to continuous metadata (no fetch, no debounce) ── useEffect(() => { diff --git a/frontend/src/hooks/useEdges.js b/frontend/src/hooks/useEdges.js index 80c6d12..a1d0624 100644 --- a/frontend/src/hooks/useEdges.js +++ b/frontend/src/hooks/useEdges.js @@ -27,10 +27,36 @@ import { useState, useEffect, useRef, useMemo } from "react"; const DEBOUNCE_MS = 400; +/** + * Normalise a store filter into the request-body shape the backend expects + * (issue #45), or undefined when nothing is constrained. + */ +function filterBody(filter) { + if (!filter?.field) return undefined; + const hasValues = Array.isArray(filter.values) && filter.values.length > 0; + if (!hasValues && filter.min == null && filter.max == null) return undefined; + return { + field: filter.field, + values: hasValues ? filter.values : null, + min: filter.min ?? null, + max: filter.max ?? null, + include_missing: !!filter.includeMissing, + }; +} + export function useEdges( apiBase, dataset, viewport, imageSize, enabled, - minStrength, hiddenLrms, lrmCatalogue, density = 1.0 + minStrength, hiddenLrms, lrmCatalogue, density = 1.0, + edgeFile = "edges.parquet", cellFilter = null, edgeFilter = null ) { + // Which edge-source parquet to query; appended to every /edges request. + const efParam = `?edge_file=${encodeURIComponent(edgeFile)}`; + + // Serialised so the structural effect can depend on filter *content* rather + // than object identity, which changes on every render. + const cellFilterBody = filterBody(cellFilter); + const edgeFilterBody = filterBody(edgeFilter); + const filterKey = JSON.stringify([cellFilterBody ?? null, edgeFilterBody ?? null]); // ── Structural state ────────────────────────────────────────────────────── const [structuralEdges, setStructuralEdges] = useState([]); const [loadingStructural, setLoadingStructural] = useState(false); @@ -66,9 +92,14 @@ export function useEdges( const { xmin, ymin, xmax, ymax } = viewport; const body = { xmin, ymin, xmax, ymax, density: Math.max(0.01, Math.min(1.0, density)) }; if (minStrength != null && minStrength > 0) body.min_strength = minStrength; + // Metadata filters go to the server so they apply before the density + // sample; filtering the response instead would sample first and leave a + // fraction of the subset. + if (cellFilterBody) body.cell_filter = cellFilterBody; + if (edgeFilterBody) body.edge_filter = edgeFilterBody; try { - const res = await fetch(`${apiBase}/edges/${dataset}/query-grouped`, { + const res = await fetch(`${apiBase}/edges/${dataset}/query-grouped${efParam}`, { method: "POST", headers: { "Content-Type": "application/json" }, body: JSON.stringify(body), @@ -83,7 +114,7 @@ export function useEdges( }, DEBOUNCE_MS); return () => clearTimeout(structTimerRef.current); - }, [apiBase, dataset, viewport, imageSize, enabled, minStrength, density]); // eslint-disable-line + }, [apiBase, dataset, viewport, imageSize, enabled, minStrength, density, efParam, filterKey]); // eslint-disable-line // ── Effect 2: score fetch ────────────────────────────────────────────────── // Runs when viewport OR hiddenLrms changes. @@ -139,7 +170,7 @@ export function useEdges( } try { - const res = await fetch(`${apiBase}/edges/${dataset}/query-scores`, { + const res = await fetch(`${apiBase}/edges/${dataset}/query-scores${efParam}`, { method: "POST", headers: { "Content-Type": "application/json" }, body: JSON.stringify(body), @@ -163,7 +194,7 @@ export function useEdges( }, DEBOUNCE_MS); return () => clearTimeout(scoreTimerRef.current); - }, [apiBase, dataset, viewport, imageSize, enabled, hiddenLrms, lrmCatalogue]); // eslint-disable-line + }, [apiBase, dataset, viewport, imageSize, enabled, hiddenLrms, lrmCatalogue, efParam]); // eslint-disable-line // ── Merge: overlay scores onto structural edges ─────────────────────────── // edgeScores === null → no filter; use score_sum from structural as visible_score_sum diff --git a/frontend/src/store.js b/frontend/src/store.js index 4eff5f8..3387334 100644 --- a/frontend/src/store.js +++ b/frontend/src/store.js @@ -8,9 +8,79 @@ export const useStore = create((set, get) => ({ dataset: null, // initialized from /spatial/datasets on first load activeImage: "morphology", // which OME-TIFF is loaded as the background - setDataset: (dataset) => set({ dataset, selectedGenes: null, allGenes: [], genesLoaded: false, platformCapabilities: null, categoryColorOverrides: {}, transcriptColorOverrides: {} }), + // edgeFile: which edge-source parquet the app renders. "edges.parquet" is the + // legacy top-level default; multiple sets live under the dataset's edges/ folder + // and are identified as "edges/.parquet" (see issue #46). Applies to all + // open viewer panels — the single sidebar drives every panel equally. + edgeFile: "edges.parquet", + + // Switching datasets resets all edge-file-scoped state so a stale LRM catalogue, + // filter, selection, or color range from the previous dataset never leaks through. + // activeImage is cleared too: image names are platform-specific ("morphology" on + // Xenium, "Roi1_DAPI" on seqFISH), and DatasetPicker only learns the new dataset's + // image list asynchronously. Without this, OSD spends that window requesting the + // previous dataset's image from the new one and logging 404s. + setDataset: (dataset) => set({ + dataset, activeImage: null, + selectedGenes: null, allGenes: [], genesLoaded: false, + platformCapabilities: null, categoryColorOverrides: {}, transcriptColorOverrides: {}, + edgeFile: "edges.parquet", lrmCatalogue: [], hiddenLrms: new Set(), + selectedEdge: null, edgeColorRange: { vmin: null, vmax: null }, + edgeColorClamp: { low: null, high: null }, + // Column names are dataset-specific, so a categorical override or an active + // filter naming a column the new dataset does not have would either do nothing + // or 400 on every viewport change. + categoricalOverrides: {}, cellFilter: null, edgeFilter: null, + }), setActiveImage: (activeImage) => set({ activeImage }), + // Switching the edge file resets the same edge-scoped state: the LRM catalogue, + // hidden-LRM filter, current selection, and auto-computed color range/clamp are + // all specific to a given edges.parquet and must be re-derived for the new file. + setEdgeFile: (edgeFile) => set({ + edgeFile, lrmCatalogue: [], hiddenLrms: new Set(), selectedEdge: null, + edgeColorRange: { vmin: null, vmax: null }, edgeColorClamp: { low: null, high: null }, + // The edge filter names a column of the edge table, which differs between + // edge sources; the cell filter is unaffected because cells are shared. + edgeFilter: null, + }), + + // ── Categorical / continuous override (issue #35) ───────────────────────── + // Keyed "cell::" / "edge::" → true | false. Absent means + // auto-detect, which is what the backend does when `categorical` is null. + // Seurat writes cluster IDs as integers, so dtype alone routes them to a + // viridis gradient; this is how the user says "these are twenty categories". + categoricalOverrides: {}, + setCategoricalOverride: (scope, field, value) => set((s) => { + const next = { ...s.categoricalOverrides }; + if (value === null || value === undefined) delete next[`${scope}::${field}`]; + else next[`${scope}::${field}`] = value; + return { categoricalOverrides: next }; + }), + + // ── Metadata subsetting (issue #45) ─────────────────────────────────────── + // A filter is { field, values: string[] | null, min, max, includeMissing }. + // null means no filter. `values` is a categorical allowlist; min/max an + // inclusive numeric range. Applied server-side before sampling, so narrowing + // to a rare cluster shows all of it rather than a sample of a sample. + // + // cellFilter also governs edges: an edge is drawn only when BOTH endpoints + // survive it. edgeFilter is independent and applies to the edge table itself. + cellFilter: null, + setCellFilter: (f) => set({ cellFilter: f }), + edgeFilter: null, + setEdgeFilter: (f) => set({ edgeFilter: f }), + + // Resolved type of the active cell color-by column, reported by panel 0 so the + // LayerPanel can render the matching legend. The panel used to guess from the + // schema dtype, which disagreed with the backend for low-cardinality integers: + // the canvas drew discrete colors while the panel showed a gradient with two + // sliders that did nothing. + cellColorType: "continuous", + cellColorCategories: [], + setCellColorType: (type, categories) => + set({ cellColorType: type, cellColorCategories: categories ?? [] }), + // ── Platform capabilities (fetched from /spatial/{dataset}/info) ────────── // null = not yet loaded; object = { has_morphology, has_transcripts, has_boundaries, unit_label } platformCapabilities: null, @@ -270,3 +340,6 @@ export const useStore = create((set, get) => ({ return { selectedGenes: next }; }), })); + +// Dev-only handle for debugging from the browser console. +if (typeof window !== "undefined" && import.meta.env?.DEV) window.__tpStore = useStore; diff --git a/frontend/vite.config.js b/frontend/vite.config.js index c7c731e..bae85cb 100644 --- a/frontend/vite.config.js +++ b/frontend/vite.config.js @@ -11,7 +11,9 @@ export default defineConfig({ }, plugins: [react()], server: { - port: 3000, + // 5173, not 3000: docker compose binds 3000 for the production frontend, so a + // default of 3000 made `npm run dev` collide with a running container. + port: 5173, proxy: { "/api": { target: "http://localhost:8000", diff --git a/r/README.md b/r/README.md new file mode 100644 index 0000000..479b6e8 --- /dev/null +++ b/r/README.md @@ -0,0 +1,86 @@ +# Running NICHESv2 to produce `edges.parquet` + +One script per platform. They all do the same three things — build a gene × cell count +matrix, build a metadata frame with coordinates **in microns**, run NICHESv2 and export — +but the first two steps differ enough per platform to be worth reading separately. + +| Script | Platform | The interesting part | +|---|---|---| +| `niches_xenium.R` | Xenium | The simple case. Coordinates are already µm; nothing to convert. **Read this first.** | +| `niches_seqfish.R` | seqFISH (Spatial Genomics GenePS) | Counts are a dense cells × genes CSV needing transposition; coordinate units vary by GenePS version, so they are detected and reported. | +| `niches_visium_hd.R` | Visium HD | Coordinates are **pixels** and must be multiplied by `microns_per_pixel` before NICHESv2 sees them. | +| `niches_common.R` | — | Shared helpers only: the 10x HDF5 reader, barcode alignment, LR-coverage check, output validation. Not runnable. | + +The older `*_PPLR.R` scripts are a personal analysis pipeline with hardcoded paths, kept +for reference. The four above are the ones to copy. + +## Setup + +```r +install.packages(c("arrow", "Matrix", "jsonlite", "remotes")) +BiocManager::install("rhdf5") # Xenium / Visium HD +remotes::install_github("RaredonLab/NICHESv2", ref = "dev") # note: dev, not main +``` + +`export_to_TissuePlex()` exists **only on the `dev` branch**, and `arrow` is only in +NICHESv2's `Suggests`, so both of those lines matter. + +## Usage + +```bash +Rscript r/niches_xenium.R sample_data/xenium_human_breast_2fov --species human --rad 30 +Rscript r/niches_seqfish.R sample_data/seqfish_synthetic --species mouse --rad 12 +Rscript r/niches_visium_hd.R sample_data/visium_hd_tiny --bin square_016um --rad 40 +``` + +Each writes `edges.parquet` into the dataset folder, where TissuePlex picks it up with no +configuration. Use `--out` to write elsewhere — for example into an `edges/` subfolder, so +several runs can be compared from the dropdown: + +```bash +Rscript r/niches_xenium.R sample_data/xenium_human_breast_2fov \ + --rad 50 --out sample_data/xenium_human_breast_2fov/edges/niches_rad50.parquet +``` + +Common flags: `--species` (human/mouse/rat/pig), `--rad` (neighbourhood radius **in µm**), +`--cores`, `--out`. Xenium also takes `--celltype ` to carry a cell-type label from +`cells.parquet` through into `sending_type` / `receiving_type`. + +## The one thing to get right + +`export_to_TissuePlex()` copies `meta.data$x` / `$y` verbatim into `x1..y2`, and the +TissuePlex backend divides those by the dataset's `pixel_size` assuming microns. So +**coordinates must be in microns before NICHESv2 runs**. Xenium and current seqFISH already +are; Visium HD and CosMx are in pixels and must be converted first. + +Get it wrong and nothing errors — the edge layer simply sits offset from the cells by +exactly `pixel_size`. If edges look shifted or wildly out of scale, check this before +anything else. `docs/data_format.md` has the per-platform conversion table. + +## Reading the output + +Each script ends with a summary. What to look for: + +- **`score_norm sums to 1 per scored edge: TRUE`** — the normalisation is intact. +- **`placeholder rows`** — every edge in the neighbourhood graph is exported, and those + with no ligand-receptor signal get one row with `lrm`/`score`/`score_norm` all `NA`. + This is deliberate: it lets TissuePlex draw the **Tissue Graph** layer (which bins or + cells are neighbours) separately from the **Edges** layer (which pairs have signal). + A large placeholder count is normal. +- **`scorable pairs`** — checked before the run. A small targeted panel often has *no* pair + with both partners present, in which case the script stops with an explanation instead + of failing deep inside NICHESv2. + +## What the demo datasets actually produce + +Measured on this repo's fixtures: + +| Dataset | Cells/bins | Edges | Scored rows | LRMs | Note | +|---|---|---|---|---|---| +| `xenium_human_breast_2fov` | 7,275 | 181,523 | 189,063 | 32 | Real data; top hits `CDH1\|CDH1`, `CXCL12\|CXCR4` | +| `seqfish_synthetic` | 36 | 250 | 7,364 | 30 | Panel chosen so every gene is half of a real LR pair | +| `visium_hd_tiny` | 3,321 | 66,001 | 147 | 69 | Very shallow — 32k UMIs total, so little scores | +| `mouse_ileum_tiny` | 36 | — | — | — | **Cannot run**: its matrix is a near-empty placeholder (467 counts, 7 expressed genes), so no pair scores | + +`mouse_ileum_tiny` is a rendering fixture, not an expression one. That is why the repo's +committed `edges.parquet` for it is synthetic, from `sample_data/make_edges.py`. diff --git a/r/niches_common.R b/r/niches_common.R new file mode 100755 index 0000000..cfeb4aa --- /dev/null +++ b/r/niches_common.R @@ -0,0 +1,167 @@ +## niches_common.R ------------------------------------------------------------ +## +## Helpers shared by the per-platform NICHESv2 scripts in this folder. +## Source it, don't run it: +## +## source(file.path(dirname(this_file), "niches_common.R")) +## +## Everything platform-specific lives in the individual scripts. What is here is +## only the parts that are genuinely identical across platforms: reading a 10x +## HDF5 feature matrix, and validating the exported parquet. + +suppressPackageStartupMessages({ + library(Matrix) +}) + +## Read a 10x-format feature matrix (.h5) into a sparse gene x cell dgCMatrix. +## +## Used by Xenium (cell_feature_matrix.h5) and Visium HD +## (filtered_feature_bc_matrix.h5) — the layout is the same for both. +## Requires the Bioconductor package rhdf5. +read_10x_h5 <- function(path) { + if (!requireNamespace("rhdf5", quietly = TRUE)) + stop("rhdf5 is required to read ", basename(path), "\n", + ' BiocManager::install("rhdf5")') + if (!file.exists(path)) stop("not found: ", path) + + genes <- as.character(rhdf5::h5read(path, "matrix/features/name")) + barcodes <- as.character(rhdf5::h5read(path, "matrix/barcodes")) + shape <- as.integer(rhdf5::h5read(path, "matrix/shape")) + + m <- Matrix::sparseMatrix( + i = as.integer(rhdf5::h5read(path, "matrix/indices")), # 0-based + p = as.integer(rhdf5::h5read(path, "matrix/indptr")), + x = as.numeric(rhdf5::h5read(path, "matrix/data")), + dims = shape, # c(n_genes, n_cells) + dimnames = list(genes, barcodes), + index1 = FALSE + ) + rhdf5::h5closeAll() + + # 10x panels can repeat a gene symbol; NICHESv2 matches the LR database on + # rownames, so collapse duplicates rather than letting one silently win. + if (anyDuplicated(rownames(m))) { + dup <- sum(duplicated(rownames(m))) + message(sprintf(" collapsing %d duplicated gene symbols by sum", dup)) + m <- Matrix::t( + Matrix::fac2sparse(factor(rownames(m), levels = unique(rownames(m)))) %*% m + ) + m <- Matrix::t(m) + } + m +} + +## Align a count matrix and a metadata frame onto their shared barcodes. +## +## create_NICHESObject() requires meta.data rownames to be the barcodes, in the +## same order as the matrix columns. Mismatches here are the most common cause of +## a confusing failure deep inside the pipeline, so fail loudly and early. +align_counts_meta <- function(count.mtx, meta.data, label = "cells") { + shared <- intersect(colnames(count.mtx), rownames(meta.data)) + if (length(shared) == 0L) + stop("no shared barcodes between the count matrix and the metadata.\n", + " matrix e.g.: ", paste(head(colnames(count.mtx), 3), collapse = ", "), "\n", + " meta e.g.: ", paste(head(rownames(meta.data), 3), collapse = ", ")) + dropped.m <- ncol(count.mtx) - length(shared) + dropped.d <- nrow(meta.data) - length(shared) + if (dropped.m > 0 || dropped.d > 0) + message(sprintf(" aligned on %d %s (dropped %d from matrix, %d from metadata)", + length(shared), label, dropped.m, dropped.d)) + list(count.mtx = count.mtx[, shared, drop = FALSE], + meta.data = meta.data[shared, , drop = FALSE]) +} + +## Report what actually landed in edges.parquet. +## +## Note the na.rm = TRUE throughout. export_to_TissuePlex() writes every edge in +## $edge.list, and edges with no scored LR signal get a single placeholder row +## with NA lrm/score/score_norm so TissuePlex can still draw the tissue graph. +## Validation that omits na.rm reports failure whenever placeholders exist, which +## is almost always — the demo script bundled with NICHESv2 has that bug. +validate_edges_parquet <- function(path) { + if (!requireNamespace("arrow", quietly = TRUE)) { + message(" (install 'arrow' to validate the output)") + return(invisible(NULL)) + } + pq <- arrow::read_parquet(path) + scored <- !is.na(pq$lrm) + + cat("\n── ", basename(path), " ──\n", sep = "") + cat(sprintf(" rows : %d\n", nrow(pq))) + cat(sprintf(" columns : %d (%s)\n", ncol(pq), + paste(names(pq), collapse = ", "))) + cat(sprintf(" unique edges : %d\n", length(unique(pq$edge)))) + cat(sprintf(" autocrine edges : %d\n", + length(unique(pq$edge[pq$is_autocrine])))) + cat(sprintf(" scored rows : %d across %d LRMs\n", + sum(scored), length(unique(pq$lrm[scored])))) + cat(sprintf(" placeholder rows: %d (edges with no LR signal — expected)\n", + sum(!scored))) + + if (any(scored)) { + cat(sprintf(" score range : %.4g .. %.4g\n", + min(pq$score, na.rm = TRUE), max(pq$score, na.rm = TRUE))) + sums <- tapply(pq$score_norm[scored], pq$edge[scored], sum, na.rm = TRUE) + ok <- all(abs(sums - 1) < 1e-6) + cat(sprintf(" score_norm sums to 1 per scored edge: %s\n", ok)) + top <- sort(table(pq$lrm[scored]), decreasing = TRUE) + cat(" top LRMs : ", + paste(sprintf("%s (%d)", names(head(top, 5)), head(top, 5)), + collapse = ", "), "\n", sep = "") + } else { + cat(" NOTE: no scored rows. Every edge is a placeholder, so TissuePlex will\n") + cat(" draw the tissue graph but the Edges layer will be empty. This is\n") + cat(" normal for a small targeted panel where no ligand-receptor pair\n") + cat(" has BOTH partners on the panel.\n") + } + invisible(pq) +} + +## Check how many ligand-receptor pairs are actually scorable on this panel. +## +## NICHESv2 needs BOTH partners of a pair present in the count matrix. On a small +## targeted panel that is often true of nothing at all, and the failure surfaces +## as "No valid LR pairs remain after gene filtering" thrown from deep inside +## compute_CellToCell(). Checking up front turns that into an explanation. +## +## Returns the number of complete pairs; stops with guidance when it is zero. +check_lr_coverage <- function(count.mtx, species, db = "connectomedb2025") { + lrm <- NICHESv2::load_LRM_database(db = db, species = species, verbose = FALSE) + present <- rownames(count.mtx)[Matrix::rowSums(count.mtx) > 0] + + # Complexes list several genes; every component must be present. + has.all <- function(field) { + vapply(strsplit(field, "[,&+]"), function(parts) + all(trimws(parts) %in% present), logical(1)) + } + complete <- has.all(lrm$ligand) & has.all(lrm$receptor) + n <- sum(complete) + + cat(sprintf(" LR database : %s (%s), %d pairs\n", db, species, nrow(lrm))) + cat(sprintf(" scorable pairs : %d (both partners expressed on this panel)\n", n)) + if (n > 0) { + ex <- head(paste0(lrm$ligand[complete], "->", lrm$receptor[complete]), 5) + cat(" e.g. : ", paste(ex, collapse = ", "), "\n", sep = "") + } else { + stop("no ligand-receptor pair has both partners expressed in this dataset.\n", + " NICHESv2 cannot score anything and will abort.\n", + " Panel size: ", length(present), " expressed genes of ", + nrow(count.mtx), " measured.\n", + " Options:\n", + " - check --species (currently '", species, "') matches the tissue\n", + " - use a dataset with a larger panel, or whole-transcriptome data\n", + " - confirm the count matrix is not empty (a tiny demo subset may be)\n", + call. = FALSE) + } + invisible(n) +} + +## Coordinates handed to create_NICHESObject() must be in microns, because +## export_to_TissuePlex() copies them verbatim into x1..y2 and the TissuePlex +## backend divides those by the dataset's pixel_size. Platforms that report +## pixels (Visium HD, CosMx) must be converted first — see docs/data_format.md. +report_extent <- function(meta.data, unit = "um") { + cat(sprintf(" extent : x %.1f..%.1f, y %.1f..%.1f (%s)\n", + min(meta.data$x), max(meta.data$x), + min(meta.data$y), max(meta.data$y), unit)) +} diff --git a/r/niches_seqfish.R b/r/niches_seqfish.R new file mode 100755 index 0000000..d575138 --- /dev/null +++ b/r/niches_seqfish.R @@ -0,0 +1,160 @@ +#!/usr/bin/env Rscript +## niches_seqfish.R ------------------------------------------------------------ +## +## Run NICHESv2 on a seqFISH (Spatial Genomics GenePS) dataset and write +## edges.parquet for TissuePlex. +## +## Rscript r/niches_seqfish.R [dataset_dir] [--rad 30] [--out edges.parquet] +## Rscript r/niches_seqfish.R sample_data/seqfish_synthetic +## +## Two things differ from the Xenium script: +## +## 1. Counts come from a plain dense CSV (_CellxGene.csv), cells x genes, +## with an unnamed first column of cell labels. It has to be transposed to +## the genes x cells orientation NICHESv2 expects. +## +## 2. Coordinates come from _CellCoordinates.csv. In current GenePS +## exports these are MICRONS, which is what we need — but some older exports +## write pixels instead. The script checks the extent against the DAPI image +## and refuses to guess silently. See the units note in the TissuePlex +## seqFISH reader for why this ambiguity exists. +## +## Expect a small targeted panel. If no ligand-receptor pair has BOTH partners on +## the panel, every edge is exported as a placeholder row and TissuePlex draws the +## tissue graph with an empty Edges layer. That is a property of the panel, not a +## failure of the run. +## +## Requires: NICHESv2 (dev branch), arrow, Matrix. + +suppressPackageStartupMessages({ + library(Matrix); library(arrow); library(NICHESv2) +}) + +.this <- tryCatch({ + a <- commandArgs(trailingOnly = FALSE) + normalizePath(sub("^--file=", "", a[grep("^--file=", a)][1])) +}, error = function(e) NA_character_) +source(file.path(if (is.na(.this)) "r" else dirname(.this), "niches_common.R")) + +# ── Parameters ──────────────────────────────────────────────────────────────── +args <- commandArgs(trailingOnly = TRUE) +opt <- function(flag, default) { + i <- match(flag, args); if (is.na(i) || i == length(args)) default else args[i + 1L] +} +positional <- args[!grepl("^--", args) & + !(seq_along(args) %in% (which(grepl("^--", args)) + 1L))] + +DATASET <- if (length(positional)) positional[1] else "sample_data/seqfish_synthetic" +OUT <- opt("--out", file.path(DATASET, "edges.parquet")) +SPECIES <- opt("--species", "mouse") +RAD <- as.numeric(opt("--rad", "30")) # microns +CORES <- as.integer(opt("--cores", "4")) +# Override the pixel-vs-micron detection if you know better: --units um|px +UNITS <- opt("--units", "auto") + +cat("── NICHESv2 · seqFISH (Spatial Genomics GenePS) ──────────────\n") +cat(" dataset :", DATASET, "\n output :", OUT, "\n") +cat(" species :", SPECIES, " rad:", RAD, "um cores:", CORES, "\n\n") + +# ── 1. Locate the ROI ───────────────────────────────────────────────────────── +# Every file is prefixed with an ROI name; TissuePlex expects one ROI per folder. +coord.files <- list.files(DATASET, pattern = "_CellCoordinates.*\\.csv$", full.names = TRUE) +if (!length(coord.files)) + stop("no *_CellCoordinates*.csv in ", DATASET, " — is this a seqFISH folder?") +if (length(coord.files) > 1) + message(" ", length(coord.files), " ROIs present; using ", basename(coord.files[1])) +roi <- sub("_CellCoordinates.*$", "", basename(coord.files[1])) +cat(" ROI :", roi, "\n") + +cxg.file <- file.path(DATASET, paste0(roi, "_CellxGene.csv")) +if (!file.exists(cxg.file)) # legacy v1 naming + cxg.file <- file.path(DATASET, paste0(roi, "_CxG.csv")) +if (!file.exists(cxg.file)) stop("no CellxGene/CxG CSV for ROI ", roi) + +# ── 2. Counts: dense cells x genes CSV -> sparse genes x cells ─────────────── +cat("\nreading counts…\n") +cxg <- read.csv(cxg.file, row.names = 1, check.names = FALSE) +count.mtx <- Matrix::Matrix(t(as.matrix(cxg)), sparse = TRUE) +colnames(count.mtx) <- as.character(rownames(cxg)) # cell labels +cat(sprintf(" %d genes x %d cells\n", nrow(count.mtx), ncol(count.mtx))) + +# ── 3. Coordinates, and the units question ─────────────────────────────────── +cat("reading cell coordinates…\n") +cc <- read.csv(coord.files[1], check.names = FALSE) +for (need in c("label", "center_x", "center_y")) + if (!need %in% names(cc)) stop("missing column '", need, "' in ", basename(coord.files[1])) + +# The DAPI OME-TIFF carries the pixel size, and the image width lets us tell +# microns from pixels: a micron-valued table spans about width*pixel_size, a +# pixel-valued one spans the width itself. +px.size <- NA_real_ +img.w <- NA_real_ +dapi <- c(file.path(DATASET, paste0(roi, "_DAPI.tiff")), + file.path(DATASET, paste0(roi, "_DAPI.ome.tiff"))) +dapi <- dapi[file.exists(dapi)] +if (length(dapi) && requireNamespace("RBioFormats", quietly = TRUE)) { + # optional; most installs will not have it, so fall through to the heuristic + try({ + meta <- RBioFormats::read.metadata(dapi[1]) + px.size <- as.numeric(meta$coreMetadata$physicalSizeX) + img.w <- as.numeric(meta$coreMetadata$sizeX) + }, silent = TRUE) +} +if (is.na(px.size)) px.size <- 0.107 # documented GenePS default + +units <- UNITS +if (units == "auto") { + # Without the image width we cannot compute the ratio, so fall back on scale: + # a GenePS ROI is tens to low hundreds of microns across, but thousands of + # pixels. An extent in the thousands therefore means pixels. + span <- max(max(cc$center_x) - min(cc$center_x), + max(cc$center_y) - min(cc$center_y)) + units <- if (span > 1000) "px" else "um" + cat(sprintf(" extent %.1f across -> detected %s (override with --units)\n", + span, units)) +} +if (units == "px") { + cat(sprintf(" converting pixels -> microns (x %.6f um/px)\n", px.size)) + cc$center_x <- cc$center_x * px.size + cc$center_y <- cc$center_y * px.size +} else { + cat(" coordinates already in microns — no conversion\n") +} + +meta.data <- data.frame( + x = as.numeric(cc$center_x), + y = as.numeric(cc$center_y), + row.names = as.character(cc$label), + stringsAsFactors = FALSE +) +report_extent(meta.data, "um") + +aligned <- align_counts_meta(count.mtx, meta.data) +count.mtx <- aligned$count.mtx +meta.data <- aligned$meta.data + +# ── 4. Build and export ─────────────────────────────────────────────────────── +# Fail early and legibly if nothing on this panel can score. +check_lr_coverage(count.mtx, SPECIES) + +cat("\nrunning NICHESv2 (spatial mode)…\n") +obj <- create_NICHESObject( + count.mtx = count.mtx, + meta.data = meta.data, + LRM.db = "connectomedb2025", + species = SPECIES, + mode = "spatial", + rad = RAD, + method = "product", + normalize.method = "prop", + n.cores = CORES, + verbose = TRUE +) + +cat("\nexporting…\n") +export_to_TissuePlex(obj, output.path = OUT, + x.col = "x", y.col = "y", + celltype.col = NULL, n.threads = CORES) + +validate_edges_parquet(OUT) +cat("\ndone — reload TissuePlex to see the edge layer.\n") diff --git a/r/niches_visium_hd.R b/r/niches_visium_hd.R new file mode 100755 index 0000000..e2cb5a0 --- /dev/null +++ b/r/niches_visium_hd.R @@ -0,0 +1,141 @@ +#!/usr/bin/env Rscript +## niches_visium_hd.R ---------------------------------------------------------- +## +## Run NICHESv2 on a 10x Visium HD dataset and write edges.parquet for TissuePlex. +## +## Rscript r/niches_visium_hd.R [dataset_dir] [--bin square_016um] [--rad 40] +## Rscript r/niches_visium_hd.R sample_data/visium_hd_tiny +## +## This is the script to read if you care about coordinate units, because Visium +## HD is the platform where getting them wrong is silent. +## +## tissue_positions.parquet stores pxl_col_in_fullres / pxl_row_in_fullres, in +## full-resolution image PIXELS. export_to_TissuePlex() copies whatever you put +## in meta.data$x/$y straight into x1..y2, and the TissuePlex backend then +## divides those by the dataset's pixel_size assuming they are microns. Feed it +## raw pixels and every edge lands offset from its bin by exactly that factor. +## +## So we multiply by microns_per_pixel from scalefactors_json.json here, before +## NICHESv2 ever sees the coordinates. `rad` is then in microns too, and +## comparable to the value you would use on Xenium. +## +## Bins are not cells. A 16 um bin may contain several cells or none, so treat +## "communication" between bins as a neighbourhood statistic rather than a +## cell-cell claim. Prefer the coarser bins: 2 um bins are mostly empty and there +## are millions of them. +## +## Inputs +## binned_outputs//filtered_feature_bc_matrix.h5 +## binned_outputs//spatial/tissue_positions.parquet +## binned_outputs//spatial/scalefactors_json.json +## +## Requires: NICHESv2 (dev branch), arrow, rhdf5, Matrix, jsonlite. + +suppressPackageStartupMessages({ + library(Matrix); library(arrow); library(jsonlite); library(NICHESv2) +}) + +.this <- tryCatch({ + a <- commandArgs(trailingOnly = FALSE) + normalizePath(sub("^--file=", "", a[grep("^--file=", a)][1])) +}, error = function(e) NA_character_) +source(file.path(if (is.na(.this)) "r" else dirname(.this), "niches_common.R")) + +# ── Parameters ──────────────────────────────────────────────────────────────── +args <- commandArgs(trailingOnly = TRUE) +opt <- function(flag, default) { + i <- match(flag, args); if (is.na(i) || i == length(args)) default else args[i + 1L] +} +positional <- args[!grepl("^--", args) & + !(seq_along(args) %in% (which(grepl("^--", args)) + 1L))] + +DATASET <- if (length(positional)) positional[1] else "sample_data/visium_hd_tiny" +BIN <- opt("--bin", "square_016um") # coarser = fewer, denser bins +OUT <- opt("--out", file.path(DATASET, "edges.parquet")) +SPECIES <- opt("--species", "mouse") # the 10x tiny demo is mouse brain +# rad in MICRONS. For 16 um bins, 40 um reaches the 8 immediate neighbours plus a +# little; scale it with the bin size if you switch bins. +RAD <- as.numeric(opt("--rad", "40")) +CORES <- as.integer(opt("--cores", "4")) +MINCOUNT <- as.integer(opt("--min-counts", "1")) # drop empty bins + +cat("── NICHESv2 · Visium HD ──────────────────────────────────────\n") +cat(" dataset :", DATASET, "\n bin :", BIN, "\n output :", OUT, "\n") +cat(" species :", SPECIES, " rad:", RAD, "um cores:", CORES, "\n\n") + +bin.dir <- file.path(DATASET, "binned_outputs", BIN) +if (!dir.exists(bin.dir)) { + # Tolerate a hand-assembled folder without the binned_outputs/ wrapper. + alt <- file.path(DATASET, BIN) + if (dir.exists(alt)) bin.dir <- alt else + stop("no ", BIN, " under ", DATASET, "\n available: ", + paste(basename(Sys.glob(file.path(DATASET, "binned_outputs", "square_*um"))), + collapse = ", ")) +} + +# ── 1. Counts ───────────────────────────────────────────────────────────────── +cat("reading counts…\n") +count.mtx <- read_10x_h5(file.path(bin.dir, "filtered_feature_bc_matrix.h5")) +cat(sprintf(" %d genes x %d bins\n", nrow(count.mtx), ncol(count.mtx))) + +# ── 2. Positions, converted pixels -> microns ──────────────────────────────── +cat("reading bin positions…\n") +pos <- as.data.frame(arrow::read_parquet( + file.path(bin.dir, "spatial", "tissue_positions.parquet"))) +pos <- pos[pos$in_tissue == 1, , drop = FALSE] # most bins are off-tissue +cat(sprintf(" %d in-tissue bins\n", nrow(pos))) + +sf.path <- file.path(bin.dir, "spatial", "scalefactors_json.json") +sf <- jsonlite::fromJSON(sf.path) +mpp <- as.numeric(sf$microns_per_pixel) +if (!is.finite(mpp) || mpp <= 0) + stop("microns_per_pixel missing or invalid in ", sf.path) +cat(sprintf(" microns_per_pixel: %.6f (bin size %.0f um)\n", mpp, sf$bin_size_um)) + +# THE conversion. Without it x1..y2 are pixels and the edge layer is misplaced. +meta.data <- data.frame( + x = as.numeric(pos$pxl_col_in_fullres) * mpp, + y = as.numeric(pos$pxl_row_in_fullres) * mpp, + row.names = as.character(pos$barcode), + stringsAsFactors = FALSE +) +cat(sprintf(" converted pixels -> microns (x %.6f)\n", mpp)) +report_extent(meta.data, "um") + +aligned <- align_counts_meta(count.mtx, meta.data, "bins") +count.mtx <- aligned$count.mtx +meta.data <- aligned$meta.data + +# Empty bins contribute nothing but inflate the neighbour graph enormously. +if (MINCOUNT > 0) { + keep <- Matrix::colSums(count.mtx) >= MINCOUNT + cat(sprintf(" dropping %d bins with < %d counts (%d remain)\n", + sum(!keep), MINCOUNT, sum(keep))) + count.mtx <- count.mtx[, keep, drop = FALSE] + meta.data <- meta.data[keep, , drop = FALSE] +} + +# ── 3. Build and export ─────────────────────────────────────────────────────── +check_lr_coverage(count.mtx, SPECIES) + +cat("\nrunning NICHESv2 (spatial mode)…\n") +obj <- create_NICHESObject( + count.mtx = count.mtx, + meta.data = meta.data, + LRM.db = "connectomedb2025", + species = SPECIES, + mode = "spatial", + rad = RAD, # microns, matching meta.data$x/$y + method = "product", + normalize.method = "prop", + n.cores = CORES, + verbose = TRUE +) + +cat("\nexporting…\n") +export_to_TissuePlex(obj, output.path = OUT, + x.col = "x", y.col = "y", + celltype.col = NULL, n.threads = CORES) + +validate_edges_parquet(OUT) +cat("\ndone — reload TissuePlex to see the edge layer.\n") diff --git a/r/niches_xenium.R b/r/niches_xenium.R new file mode 100755 index 0000000..831550b --- /dev/null +++ b/r/niches_xenium.R @@ -0,0 +1,122 @@ +#!/usr/bin/env Rscript +## niches_xenium.R ------------------------------------------------------------- +## +## Run NICHESv2 on a 10x Xenium dataset and write edges.parquet for TissuePlex. +## +## Rscript r/niches_xenium.R [dataset_dir] [--rad 30] [--out edges.parquet] +## Rscript r/niches_xenium.R sample_data/mouse_ileum_tiny +## +## Xenium is the straightforward case: coordinates are already in microns, which +## is exactly what TissuePlex expects, so nothing needs converting. Start here if +## you are reading these scripts to learn the pipeline, then compare against +## niches_visium_hd.R, where the coordinates are in pixels and must be converted. +## +## Inputs (standard Xenium output folder) +## cells.parquet cell_id, x_centroid, y_centroid (microns) +## cell_feature_matrix.h5 10x HDF5, genes x cells +## +## Output +## edges.parquet in the dataset folder — picked up automatically by TissuePlex. +## +## Requires: NICHESv2 (dev branch), arrow, rhdf5, Matrix. +## install.packages(c("arrow","Matrix")); BiocManager::install("rhdf5") +## remotes::install_github("RaredonLab/NICHESv2", ref = "dev") + +suppressPackageStartupMessages({ + library(Matrix); library(arrow); library(NICHESv2) +}) + +## Locate niches_common.R relative to this script, so it works from any cwd. +.this <- tryCatch({ + a <- commandArgs(trailingOnly = FALSE) + normalizePath(sub("^--file=", "", a[grep("^--file=", a)][1])) +}, error = function(e) NA_character_) +source(file.path(if (is.na(.this)) "r" else dirname(.this), "niches_common.R")) + +# ── Parameters ──────────────────────────────────────────────────────────────── +args <- commandArgs(trailingOnly = TRUE) +opt <- function(flag, default) { + i <- match(flag, args); if (is.na(i) || i == length(args)) default else args[i + 1L] +} +positional <- args[!grepl("^--", args) & + !(seq_along(args) %in% (which(grepl("^--", args)) + 1L))] + +DATASET <- if (length(positional)) positional[1] else "sample_data/mouse_ileum_tiny" +OUT <- opt("--out", file.path(DATASET, "edges.parquet")) +SPECIES <- opt("--species", "mouse") # ileum demo is mouse +# rad is in the same units as x/y, i.e. MICRONS for Xenium. 30 um reaches roughly +# the first ring of neighbours for typical Xenium cell density; tune per tissue +# with NICHESv2::Explore_Radius_Neighborhood(). +RAD <- as.numeric(opt("--rad", "30")) +CORES <- as.integer(opt("--cores", "4")) +CELLTYPE <- opt("--celltype", NA_character_) # optional column in cells.parquet + +cat("── NICHESv2 · Xenium ─────────────────────────────────────────\n") +cat(" dataset :", DATASET, "\n output :", OUT, "\n") +cat(" species :", SPECIES, " rad:", RAD, "um cores:", CORES, "\n\n") + +# ── 1. Counts ───────────────────────────────────────────────────────────────── +cat("reading counts…\n") +count.mtx <- read_10x_h5(file.path(DATASET, "cell_feature_matrix.h5")) +cat(sprintf(" %d genes x %d cells\n", nrow(count.mtx), ncol(count.mtx))) + +# Drop Xenium control probes — they are not real genes and can only add noise. +ctrl <- grepl("^(NegControl|BLANK|Blank|Unassigned|Deprecated|antisense|Intergenic)", + rownames(count.mtx)) +if (any(ctrl)) { + cat(sprintf(" dropping %d control/blank probes\n", sum(ctrl))) + count.mtx <- count.mtx[!ctrl, , drop = FALSE] +} + +# ── 2. Metadata: rownames = barcodes, coordinates literally named x / y ─────── +cat("reading cell metadata…\n") +cells <- as.data.frame(arrow::read_parquet(file.path(DATASET, "cells.parquet"))) +meta.data <- data.frame( + x = as.numeric(cells$x_centroid), # already microns — no conversion + y = as.numeric(cells$y_centroid), + row.names = as.character(cells$cell_id), + stringsAsFactors = FALSE +) +if (!is.na(CELLTYPE)) { + if (!CELLTYPE %in% names(cells)) + stop("--celltype '", CELLTYPE, "' is not a column in cells.parquet") + meta.data[[CELLTYPE]] <- as.character(cells[[CELLTYPE]]) +} +report_extent(meta.data, "um") + +aligned <- align_counts_meta(count.mtx, meta.data) +count.mtx <- aligned$count.mtx +meta.data <- aligned$meta.data + +# ── 3. Build the NICHESObject ───────────────────────────────────────────────── +# Fail early and legibly if nothing on this panel can score. +check_lr_coverage(count.mtx, SPECIES) + +cat("\nrunning NICHESv2 (spatial mode)…\n") +obj <- create_NICHESObject( + count.mtx = count.mtx, + meta.data = meta.data, + LRM.db = "connectomedb2025", + species = SPECIES, + mode = "spatial", + rad = RAD, # microns + cell.type.col = if (is.na(CELLTYPE)) NULL else CELLTYPE, + method = "product", + normalize.method = "prop", + n.cores = CORES, + verbose = TRUE +) + +# ── 4. Export ───────────────────────────────────────────────────────────────── +cat("\nexporting…\n") +export_to_TissuePlex( + obj, + output.path = OUT, + x.col = "x", + y.col = "y", + celltype.col = if (is.na(CELLTYPE)) NULL else CELLTYPE, + n.threads = CORES +) + +validate_edges_parquet(OUT) +cat("\ndone — reload TissuePlex to see the edge layer.\n") diff --git a/sample_data/.gitignore b/sample_data/.gitignore index b50f322..e129bd6 100644 --- a/sample_data/.gitignore +++ b/sample_data/.gitignore @@ -3,6 +3,17 @@ xenium_human_breast_2fov/ merscope-*/ cosmx-*/ +visium-*/ + +# seqFISH / Spatial Genomics GenePS datasets. +# The scverse test dataset (s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip) +# is public for CI by written permission from Spatial Genomics, not under an open +# licence — usable for local development, but must not be redistributed from this repo. +# seqfish_synthetic/ is exempt below: it is generated by make_seqfish.py and carries +# no licence encumbrance, so it is the fixture the reader is tested against. +seqfish*/ +seqfish-*/ +!seqfish_synthetic/ # ── Xenium files present in the repo but not needed by TissuePlex ──────────── # Xenium Explorer analysis outputs @@ -26,6 +37,11 @@ transcripts.csv.gz # Xenium cell layers (not yet used by TissuePlex) cell_layers.parquet +# ── Derived caches (built on first access, never committed) ────────────────── +.dzi_cache/ +.tissueplex_cache/ +*.sorted.parquet + # ── Python cache ────────────────────────────────────────────────────────────── __pycache__/ *.pyc diff --git a/sample_data/make_edges.py b/sample_data/make_edges.py index de082f7..6928192 100644 --- a/sample_data/make_edges.py +++ b/sample_data/make_edges.py @@ -167,6 +167,10 @@ def main(): ap.add_argument("--autocrine-fraction", type=float, default=0.15, help="Fraction of cells with autocrine self-loops") ap.add_argument("--seed", type=int, default=42) + ap.add_argument("--out", default="edges.parquet", + help="Output path relative to the dataset dir. Use e.g. " + "'edges/edge.raw.minimum.parquet' to add a selectable " + "edge set to the dataset's edges/ folder (issue #46).") args = ap.parse_args() here = Path(__file__).parent @@ -175,7 +179,8 @@ def main(): df = make_edges(dataset_dir, k_neighbors=args.k, lrms_per_pair=args.lrms, autocrine_fraction=args.autocrine_fraction, seed=args.seed) - out = dataset_dir / "edges.parquet" + out = dataset_dir / args.out + out.parent.mkdir(parents=True, exist_ok=True) df.to_parquet(out, index=False) print(f"Wrote {out}") diff --git a/sample_data/make_seqfish.py b/sample_data/make_seqfish.py new file mode 100644 index 0000000..456a606 --- /dev/null +++ b/sample_data/make_seqfish.py @@ -0,0 +1,186 @@ +#!/usr/bin/env python3 +""" +Generate a tiny synthetic seqFISH (Spatial Genomics GenePS) v2 dataset. + +Why this exists +--------------- +The real GenePS reference dataset is public for CI by written permission from +Spatial Genomics rather than under an open licence, so it cannot be committed +here. Without a committable fixture the seqFISH reader has nothing to test +against in a fresh checkout. This produces a valid, tiny v2 ROI that can be. + +It deliberately reproduces the format's two awkward properties, because those +are exactly what a reader gets wrong: + + * **Mixed units.** CellCoordinates and TranscriptList are written in microns; + Boundaries.geojson is written in pixels. That is what real GenePS output + does, and a fixture in one uniform space would let a broken reader pass. + * **Closed GeoJSON rings**, with the cell label in each feature's ``id``. + +Usage +----- + python make_seqfish.py --out seqfish_synthetic + python make_seqfish.py --out seqfish_synthetic --cells 40 --genes 8 --seed 7 + +Writes /Roi1_{CellCoordinates.csv,CellxGene.csv,TranscriptList.csv, +Boundaries.geojson,DAPI.tiff,Segmentation.tiff}. +""" +from __future__ import annotations + +import argparse +import json +import math +from pathlib import Path + +import numpy as np + +# Matches the reference dataset, and the documented GenePS value. +PIXEL_SIZE = 0.107161 +IMAGE_PX = 512 + +# Real mouse gene symbols forming 20 complete ligand-receptor pairs in +# connectomedb2025 (NICHESv2's default database). Using real symbols rather than +# Gene00/Gene01/... matters: a panel of invented names has no LR pair with both +# partners present, so NICHESv2 errors out with "No valid LR pairs remain" and +# the fixture cannot demonstrate the edge pipeline at all. +# +# Tgfb1->Tgfbr1/2 Wnt5a->Fzd1/Ror2 Cxcl12->Cxcr4 Vegfa->Kdr/Flt1 +# Pdgfb->Pdgfrb Hgf->Met Il6->Il6ra Efnb1->Ephb2 +# Spp1->Cd44 Ccl2->Ccr2 Bmp4->Bmpr2 Fgf2->Fgfr1 +# Egf->Egfr Jag1/Dll4->Notch1 Apoe->Lrp1 Thbs1->Cd47 +LR_PANEL = [ + "Tgfb1", "Tgfbr1", "Tgfbr2", "Wnt5a", "Fzd1", "Ror2", "Cxcl12", "Cxcr4", + "Vegfa", "Kdr", "Flt1", "Pdgfb", "Pdgfrb", "Hgf", "Met", "Il6", "Il6ra", + "Efnb1", "Ephb2", "Spp1", "Cd44", "Ccl2", "Ccr2", "Bmp4", "Bmpr2", + "Fgf2", "Fgfr1", "Egf", "Egfr", "Jag1", "Dll4", "Notch1", "Apoe", "Lrp1", + "Thbs1", "Cd47", +] + + +def build(out: Path, n_cells: int, n_genes: int, seed: int) -> None: + rng = np.random.default_rng(seed) + out.mkdir(parents=True, exist_ok=True) + + extent_um = IMAGE_PX * PIXEL_SIZE + # Take the real LR panel; n_genes only trims it. Invented names would leave + # NICHESv2 with no scorable pair (see LR_PANEL above). + if n_genes > len(LR_PANEL): + raise SystemExit(f"--genes max is {len(LR_PANEL)} (the size of LR_PANEL)") + genes = LR_PANEL[:n_genes] + + # ── Cell centroids on a jittered grid, so cells never overlap ──────────── + per_side = math.ceil(math.sqrt(n_cells)) + step_px = IMAGE_PX / (per_side + 1) + radius_px = step_px * 0.34 + + labels, cx_px, cy_px, radii = [], [], [], [] + for i in range(n_cells): + r, c = divmod(i, per_side) + jx, jy = rng.uniform(-0.12, 0.12, 2) * step_px + labels.append(i + 1) + cx_px.append((c + 1) * step_px + jx) + cy_px.append((r + 1) * step_px + jy) + radii.append(radius_px * rng.uniform(0.72, 1.0)) + + cx_px = np.array(cx_px) + cy_px = np.array(cy_px) + radii = np.array(radii) + + # ── Boundaries: irregular closed polygons, in PIXEL space ─────────────── + features, mask = [], np.zeros((IMAGE_PX, IMAGE_PX), dtype=np.uint32) + yy, xx = np.mgrid[0:IMAGE_PX, 0:IMAGE_PX] + areas_px2 = [] + for i, label in enumerate(labels): + n_v = int(rng.integers(10, 20)) + ang = np.sort(rng.uniform(0, 2 * np.pi, n_v)) + rad = radii[i] * rng.uniform(0.82, 1.18, n_v) + vx = np.clip(cx_px[i] + rad * np.cos(ang), 0, IMAGE_PX - 1) + vy = np.clip(cy_px[i] + rad * np.sin(ang), 0, IMAGE_PX - 1) + ring = [[int(round(x)), int(round(y))] for x, y in zip(vx, vy)] + ring.append(ring[0]) # GeoJSON rings are closed + features.append({ + "type": "Feature", + "id": str(label), # the label; joined on by the reader + "geometry": {"type": "Polygon", "coordinates": [ring]}, + "properties": {"objectType": "cell"}, + }) + # Shoelace area of the ring (px²), and a disc in the label mask. + rx = np.array([p[0] for p in ring[:-1]], dtype=float) + ry = np.array([p[1] for p in ring[:-1]], dtype=float) + areas_px2.append( + abs(np.dot(rx, np.roll(ry, -1)) - np.dot(ry, np.roll(rx, -1))) / 2 + ) + mask[(xx - cx_px[i]) ** 2 + (yy - cy_px[i]) ** 2 <= radii[i] ** 2] = label + + (out / "Roi1_Boundaries.geojson").write_text( + json.dumps({"type": "FeatureCollection", "features": features}, indent=1) + ) + + # ── CellCoordinates: MICRONS (area in µm², matching the real format) ──── + with open(out / "Roi1_CellCoordinates.csv", "w") as fh: + fh.write("label,area,center_x,center_y\n") + for i, label in enumerate(labels): + fh.write(f"{label},{areas_px2[i] * PIXEL_SIZE ** 2:.4f}," + f"{cx_px[i] * PIXEL_SIZE:.5f},{cy_px[i] * PIXEL_SIZE:.5f}\n") + + # ── Counts, with a gene gradient so colour-by shows structure ─────────── + counts = np.zeros((n_cells, n_genes), dtype=int) + for j in range(n_genes): + bias = 1.0 + 3.0 * (cx_px / IMAGE_PX) if j % 2 == 0 else \ + 1.0 + 3.0 * (cy_px / IMAGE_PX) + counts[:, j] = rng.poisson(bias * rng.uniform(1.5, 5.0)) + with open(out / "Roi1_CellxGene.csv", "w") as fh: + fh.write("," + ",".join(genes) + "\n") # unnamed first column + for i, label in enumerate(labels): + fh.write(f"{label}," + ",".join(str(v) for v in counts[i]) + "\n") + + # ── Transcripts: MICRONS, scattered inside their cell ─────────────────── + with open(out / "Roi1_TranscriptList.csv", "w") as fh: + fh.write("name,x,y,z\n") + for i in range(n_cells): + for j, gene in enumerate(genes): + for _ in range(int(counts[i, j])): + a = rng.uniform(0, 2 * np.pi) + d = radii[i] * math.sqrt(rng.uniform(0, 0.8)) + x = np.clip(cx_px[i] + d * math.cos(a), 0, IMAGE_PX - 1) + y = np.clip(cy_px[i] + d * math.sin(a), 0, IMAGE_PX - 1) + fh.write(f"{gene},{x * PIXEL_SIZE:.6f},{y * PIXEL_SIZE:.6f},1\n") + + # ── DAPI (OME-TIFF carrying PhysicalSize) + label mask ───────────────── + import tifffile + img = np.zeros((IMAGE_PX, IMAGE_PX), dtype=np.uint16) + for i in range(n_cells): + d2 = (xx - cx_px[i]) ** 2 + (yy - cy_px[i]) ** 2 + img += (40000 * np.exp(-d2 / (2 * (radii[i] * 0.45) ** 2))).astype(np.uint16) + tifffile.imwrite( + out / "Roi1_DAPI.tiff", img, + # pixel_size is read back from these OME-XML attributes by the reader. + metadata={"PhysicalSizeX": PIXEL_SIZE, "PhysicalSizeY": PIXEL_SIZE, + "PhysicalSizeXUnit": "µm", "PhysicalSizeYUnit": "µm"}, + ome=True, compression="zlib", + ) + # Written for format completeness. The reader does not use it: v2 takes + # boundaries from the GeoJSON, and v1 mask polygonisation is not implemented. + tifffile.imwrite(out / "Roi1_Segmentation.tiff", mask, compression="zlib") + + n_tx = int(counts.sum()) + print(f"wrote {out}/ — {n_cells} cells, {n_genes} genes, {n_tx} transcripts, " + f"{IMAGE_PX}x{IMAGE_PX}px @ {PIXEL_SIZE} µm/px ({extent_um:.1f} µm)") + print(" CellCoordinates/TranscriptList in MICRONS, Boundaries in PIXELS " + "(mirrors real GenePS output)") + + +def main() -> int: + ap = argparse.ArgumentParser(description=__doc__) + ap.add_argument("--out", default="seqfish_synthetic", help="output directory") + ap.add_argument("--cells", type=int, default=36) + ap.add_argument("--genes", type=int, default=len(LR_PANEL), + help=f"how many of the {len(LR_PANEL)} LR-panel genes to use") + ap.add_argument("--seed", type=int, default=42) + a = ap.parse_args() + build(Path(__file__).resolve().parent / a.out, a.cells, a.genes, a.seed) + return 0 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/sample_data/mouse_ileum_tiny/cell-metadata/example_clusters.csv b/sample_data/mouse_ileum_tiny/cell-metadata/example_clusters.csv new file mode 100644 index 0000000..0b69f01 --- /dev/null +++ b/sample_data/mouse_ileum_tiny/cell-metadata/example_clusters.csv @@ -0,0 +1,37 @@ +,cluster,region,pseudotime,seurat_clusters +aaamobki-1,1,mid,0.4035,0 +aaclkaod-1,1,mid,0.3969,1 +bhakoonb-1,1,mid,0.4145,2 +bpefijoo-1,1,mid,0.3881,3 +ckfandjp-1,1,mid,0.4027,4 +dgcpicgh-1,1,mid,0.4054,5 +djgiipfb-1,1,mid,0.4114,6 +dkcgpkmh-1,1,mid,0.3911,7 +egeelggc-1,1,mid,0.3986,8 +ehjojgpl-1,1,mid,0.4064,9 +fkhfgimb-1,1,mid,0.4293,10 +gackndbe-1,1,mid,0.4185,11 +ghfdfbpc-1,1,mid,0.4345,0 +gjklkjjk-1,1,mid,0.424,1 +gpihhicj-1,1,mid,0.4417,2 +hakcibka-1,0,crypt,0.0452,3 +hbpoaeic-1,0,crypt,0.0341,4 +hhmlkgel-1,0,crypt,0.0079,5 +hkhcepfl-1,0,crypt,0.0,6 +ibclpflk-1,0,crypt,0.043,7 +ifjkhhkf-1,3,villus,0.9792,8 +jdchjdgi-1,3,villus,0.976,9 +jedneilm-1,3,villus,0.999,10 +jpbefbck-1,4,villus,1.0,11 +kecdfjaf-1,3,villus,0.9832,0 +kfefndgm-1,3,villus,0.9705,1 +kggmilif-1,3,villus,0.9673,2 +kkonlcio-1,3,villus,0.9596,3 +koaolmni-1,0,crypt,0.0416,4 +lfenejfi-1,0,crypt,0.0441,5 +niehkpen-1,0,crypt,0.0238,6 +ohmibdle-1,0,crypt,0.0337,7 +oinmeidp-1,0,crypt,0.0293,8 +ojeggnjp-1,3,villus,0.9824,9 +olbjkpjc-1,3,villus,0.9555,10 +omjmdimk-1,3,villus,0.9666,11 diff --git a/sample_data/mouse_ileum_tiny/edge-metadata/example_annotations.csv b/sample_data/mouse_ileum_tiny/edge-metadata/example_annotations.csv new file mode 100644 index 0000000..fc81b14 --- /dev/null +++ b/sample_data/mouse_ileum_tiny/edge-metadata/example_annotations.csv @@ -0,0 +1,224 @@ +,interaction_class,confidence,reviewed +aaclkaod-1|aaamobki-1,heterotypic,0.594,no +dgcpicgh-1|ehjojgpl-1,heterotypic,0.791,no +egeelggc-1|ckfandjp-1,homotypic,0.722,no +fkhfgimb-1|gpihhicj-1,heterotypic,0.435,yes +gackndbe-1|egeelggc-1,heterotypic,0.422,no +hhmlkgel-1|hkhcepfl-1,heterotypic,0.442,no +jpbefbck-1|kecdfjaf-1,heterotypic,0.655,yes +lfenejfi-1|oinmeidp-1,homotypic,0.474,no +omjmdimk-1|jdchjdgi-1,homotypic,0.776,yes +omjmdimk-1|ojeggnjp-1,heterotypic,0.746,no +kkonlcio-1|kkonlcio-1,homotypic,0.986,no +ckfandjp-1|aaclkaod-1,heterotypic,0.915,no +egeelggc-1|dkcgpkmh-1,heterotypic,0.487,no +hkhcepfl-1|niehkpen-1,heterotypic,0.585,yes +jpbefbck-1|jdchjdgi-1,homotypic,0.508,yes +kecdfjaf-1|jedneilm-1,heterotypic,0.783,no +kecdfjaf-1|jpbefbck-1,heterotypic,0.729,no +kfefndgm-1|jdchjdgi-1,heterotypic,0.436,no +kfefndgm-1|kggmilif-1,heterotypic,0.808,no +kfefndgm-1|kkonlcio-1,homotypic,0.588,yes +koaolmni-1|hbpoaeic-1,heterotypic,0.672,no +lfenejfi-1|niehkpen-1,homotypic,0.877,yes +oinmeidp-1|koaolmni-1,heterotypic,0.546,yes +omjmdimk-1|kfefndgm-1,heterotypic,0.715,yes +omjmdimk-1|olbjkpjc-1,heterotypic,0.838,no +kggmilif-1|kggmilif-1,homotypic,0.988,no +aaamobki-1|ckfandjp-1,homotypic,0.651,yes +bhakoonb-1|gackndbe-1,heterotypic,0.491,no +bhakoonb-1|gjklkjjk-1,heterotypic,0.424,yes +bpefijoo-1|aaclkaod-1,heterotypic,0.859,yes +bpefijoo-1|bhakoonb-1,heterotypic,0.925,no +ckfandjp-1|egeelggc-1,homotypic,0.817,yes +dgcpicgh-1|ckfandjp-1,heterotypic,0.748,no +dgcpicgh-1|egeelggc-1,heterotypic,0.904,yes +egeelggc-1|gackndbe-1,heterotypic,0.684,yes +fkhfgimb-1|gjklkjjk-1,heterotypic,0.436,yes +gackndbe-1|ehjojgpl-1,heterotypic,0.788,yes +ghfdfbpc-1|ehjojgpl-1,heterotypic,0.893,no +gjklkjjk-1|ckfandjp-1,heterotypic,0.631,yes +hakcibka-1|hhmlkgel-1,heterotypic,0.414,no +hakcibka-1|ohmibdle-1,heterotypic,0.501,no +ibclpflk-1|ohmibdle-1,heterotypic,0.435,yes +ifjkhhkf-1|kggmilif-1,heterotypic,0.478,no +jedneilm-1|kggmilif-1,heterotypic,0.635,yes +kfefndgm-1|kecdfjaf-1,heterotypic,0.448,no +kggmilif-1|kecdfjaf-1,heterotypic,0.73,yes +kggmilif-1|olbjkpjc-1,heterotypic,0.892,yes +niehkpen-1|hbpoaeic-1,heterotypic,0.567,no +niehkpen-1|oinmeidp-1,homotypic,0.615,yes +oinmeidp-1|hbpoaeic-1,heterotypic,0.975,no +dgcpicgh-1|gackndbe-1,heterotypic,0.506,no +egeelggc-1|ehjojgpl-1,homotypic,0.54,no +gjklkjjk-1|ghfdfbpc-1,heterotypic,0.753,no +hbpoaeic-1|koaolmni-1,heterotypic,0.402,no +hhmlkgel-1|ibclpflk-1,homotypic,0.622,yes +hhmlkgel-1|koaolmni-1,heterotypic,0.972,yes +hkhcepfl-1|ibclpflk-1,heterotypic,0.709,yes +ibclpflk-1|niehkpen-1,homotypic,0.806,no +ifjkhhkf-1|kfefndgm-1,heterotypic,0.94,yes +kfefndgm-1|ifjkhhkf-1,heterotypic,0.925,yes +lfenejfi-1|koaolmni-1,heterotypic,0.635,no +niehkpen-1|hhmlkgel-1,homotypic,0.462,yes +oinmeidp-1|lfenejfi-1,homotypic,0.437,no +ibclpflk-1|ibclpflk-1,homotypic,0.525,no +bhakoonb-1|aaamobki-1,homotypic,0.604,no +ckfandjp-1|ehjojgpl-1,homotypic,0.4,no +djgiipfb-1|ehjojgpl-1,heterotypic,0.461,no +ehjojgpl-1|egeelggc-1,homotypic,0.415,yes +fkhfgimb-1|gackndbe-1,heterotypic,0.768,no +ghfdfbpc-1|gjklkjjk-1,heterotypic,0.551,no +ghfdfbpc-1|gpihhicj-1,heterotypic,0.618,no +gpihhicj-1|bhakoonb-1,heterotypic,0.909,yes +hkhcepfl-1|hhmlkgel-1,heterotypic,0.68,no +ibclpflk-1|hbpoaeic-1,heterotypic,0.452,no +ifjkhhkf-1|kecdfjaf-1,homotypic,0.606,no +jdchjdgi-1|kfefndgm-1,heterotypic,0.897,no +koaolmni-1|ibclpflk-1,heterotypic,0.414,yes +aaclkaod-1|ckfandjp-1,heterotypic,0.717,no +bhakoonb-1|fkhfgimb-1,heterotypic,0.726,no +bpefijoo-1|ckfandjp-1,heterotypic,0.717,yes +dkcgpkmh-1|ckfandjp-1,heterotypic,0.918,yes +dkcgpkmh-1|ehjojgpl-1,heterotypic,0.557,no +gpihhicj-1|ckfandjp-1,heterotypic,0.5,yes +gpihhicj-1|fkhfgimb-1,heterotypic,0.72,yes +gpihhicj-1|gackndbe-1,homotypic,0.598,no +gpihhicj-1|ghfdfbpc-1,heterotypic,0.887,yes +gpihhicj-1|gjklkjjk-1,heterotypic,0.912,yes +hakcibka-1|koaolmni-1,heterotypic,0.891,yes +jpbefbck-1|kfefndgm-1,heterotypic,0.536,yes +kkonlcio-1|kfefndgm-1,homotypic,0.613,no +koaolmni-1|ohmibdle-1,heterotypic,0.417,no +lfenejfi-1|ohmibdle-1,heterotypic,0.556,yes +oinmeidp-1|ohmibdle-1,heterotypic,0.974,no +ojeggnjp-1|olbjkpjc-1,heterotypic,0.962,yes +olbjkpjc-1|omjmdimk-1,heterotypic,0.973,no +bpefijoo-1|ehjojgpl-1,heterotypic,0.532,no +dkcgpkmh-1|dgcpicgh-1,heterotypic,0.518,no +ghfdfbpc-1|gackndbe-1,heterotypic,0.774,yes +hakcibka-1|niehkpen-1,heterotypic,0.904,no +ifjkhhkf-1|kkonlcio-1,heterotypic,0.792,yes +jdchjdgi-1|kecdfjaf-1,heterotypic,0.451,yes +jedneilm-1|jpbefbck-1,heterotypic,0.946,yes +jpbefbck-1|kkonlcio-1,heterotypic,0.85,no +kggmilif-1|jdchjdgi-1,heterotypic,0.507,yes +kggmilif-1|omjmdimk-1,heterotypic,0.6,yes +ohmibdle-1|ibclpflk-1,heterotypic,0.983,no +ehjojgpl-1|ehjojgpl-1,homotypic,0.641,yes +aaamobki-1|bhakoonb-1,homotypic,0.835,no +aaclkaod-1|bhakoonb-1,heterotypic,0.476,no +aaclkaod-1|ehjojgpl-1,heterotypic,0.943,yes +bhakoonb-1|aaclkaod-1,heterotypic,0.488,yes +egeelggc-1|dgcpicgh-1,heterotypic,0.988,yes +gackndbe-1|ckfandjp-1,heterotypic,0.61,yes +gackndbe-1|ghfdfbpc-1,heterotypic,0.479,no +ghfdfbpc-1|djgiipfb-1,heterotypic,0.983,yes +kecdfjaf-1|kfefndgm-1,heterotypic,0.716,yes +kecdfjaf-1|kggmilif-1,heterotypic,0.66,yes +ohmibdle-1|oinmeidp-1,heterotypic,0.896,no +ojeggnjp-1|jdchjdgi-1,heterotypic,0.551,no +olbjkpjc-1|kfefndgm-1,heterotypic,0.544,yes +aaamobki-1|aaclkaod-1,heterotypic,0.556,no +egeelggc-1|djgiipfb-1,heterotypic,0.479,yes +fkhfgimb-1|ckfandjp-1,heterotypic,0.612,no +gackndbe-1|djgiipfb-1,homotypic,0.75,yes +gjklkjjk-1|gackndbe-1,heterotypic,0.652,yes +hakcibka-1|hbpoaeic-1,homotypic,0.701,yes +hakcibka-1|ibclpflk-1,heterotypic,0.714,no +hbpoaeic-1|niehkpen-1,heterotypic,0.664,no +ifjkhhkf-1|jdchjdgi-1,heterotypic,0.402,yes +jdchjdgi-1|ojeggnjp-1,heterotypic,0.503,no +jedneilm-1|kecdfjaf-1,heterotypic,0.835,yes +kkonlcio-1|kggmilif-1,heterotypic,0.596,yes +koaolmni-1|niehkpen-1,heterotypic,0.733,yes +ohmibdle-1|koaolmni-1,heterotypic,0.464,yes +oinmeidp-1|hhmlkgel-1,homotypic,0.549,no +ghfdfbpc-1|ghfdfbpc-1,homotypic,0.863,yes +djgiipfb-1|gackndbe-1,homotypic,0.737,yes +dkcgpkmh-1|egeelggc-1,heterotypic,0.947,no +ehjojgpl-1|dgcpicgh-1,heterotypic,0.768,yes +ehjojgpl-1|dkcgpkmh-1,heterotypic,0.707,yes +fkhfgimb-1|bhakoonb-1,heterotypic,0.671,yes +gackndbe-1|gjklkjjk-1,heterotypic,0.687,yes +gjklkjjk-1|fkhfgimb-1,heterotypic,0.82,yes +hbpoaeic-1|hhmlkgel-1,heterotypic,0.965,no +hbpoaeic-1|ibclpflk-1,heterotypic,0.736,yes +ibclpflk-1|hakcibka-1,heterotypic,0.904,no +jdchjdgi-1|kggmilif-1,heterotypic,0.473,no +jdchjdgi-1|olbjkpjc-1,heterotypic,0.444,no +kecdfjaf-1|ifjkhhkf-1,homotypic,0.444,yes +kecdfjaf-1|jdchjdgi-1,heterotypic,0.87,yes +kkonlcio-1|jdchjdgi-1,heterotypic,0.493,yes +niehkpen-1|koaolmni-1,heterotypic,0.796,no +niehkpen-1|lfenejfi-1,homotypic,0.93,yes +ojeggnjp-1|kggmilif-1,heterotypic,0.532,yes +ojeggnjp-1|omjmdimk-1,heterotypic,0.639,no +olbjkpjc-1|kecdfjaf-1,heterotypic,0.994,yes +aaamobki-1|gjklkjjk-1,heterotypic,0.497,no +bpefijoo-1|aaamobki-1,heterotypic,0.709,no +dkcgpkmh-1|gackndbe-1,heterotypic,0.517,no +ehjojgpl-1|ckfandjp-1,homotypic,0.833,no 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+Cd47,49.170487,46.772034,1 +Cd47,48.033773,47.152670,1 +Cd47,48.204932,46.230391,1 +Cd47,47.221044,46.318275,1 +Cd47,48.221971,48.373536,1 +Cd47,48.769956,46.758608,1 +Cd47,48.321868,47.177848,1 +Cd47,47.862590,48.718373,1 +Cd47,45.822116,47.831816,1 +Cd47,48.246061,45.949146,1 diff --git a/sample_data/seqfish_synthetic/edges.parquet b/sample_data/seqfish_synthetic/edges.parquet new file mode 100644 index 0000000..200f4a6 Binary files /dev/null and b/sample_data/seqfish_synthetic/edges.parquet differ diff --git a/sample_data/visium_hd_tiny/PROVENANCE.md b/sample_data/visium_hd_tiny/PROVENANCE.md new file mode 100644 index 0000000..24ea806 --- /dev/null +++ b/sample_data/visium_hd_tiny/PROVENANCE.md @@ -0,0 +1,60 @@ +# Visium HD Tiny Mouse Brain — provenance and licence + +A **subset** of 10x Genomics' public "Visium HD 3' Tiny Mouse Brain" dataset, kept in this +repository as the Visium HD test fixture. + +| | | +|---|---| +| Source | https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data | +| Download | `https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip` | +| Original size | 311,404,970 bytes · MD5 `7cab710801d3776125a7aa5a792cd7e4` | +| Space Ranger | 4.0.1 | +| Licence | **CC BY 4.0** — https://creativecommons.org/licenses/by/4.0/ | +| Attribution | © 10x Genomics. Used and redistributed under CC BY 4.0. | + +10x produced this "Tiny" dataset themselves by downsampling a full run to a corner of the +tissue at reduced resolution. It is a genuine Space Ranger `outs/` tree, not a synthetic +mock, so it exercises the real directory layout. + +## What was kept, and why + +The original archive is 297 MB (616 MB unpacked, 162 files). Only what the reader actually +needs is committed here — about 26 MB: + +``` +binned_outputs/square_008um/ filtered_feature_bc_matrix.h5 + spatial/{tissue_positions.parquet, + scalefactors_json.json, + tissue_hires_image.png} +binned_outputs/square_016um/ the same, plus tissue_lowres_image.png +spatial/tissue_hires_image.png the top-level morphology copy +segmented_outputs/cell_segmentations.geojson +metrics_summary.csv +``` + +Two bin sizes are kept so bin selection can be exercised; `square_002um` is omitted because +its positions file alone is 160 MB. The CytAssist TIFF (27.5 MB, duplicated four times in +the original) is omitted in favour of the 2.4 MB hires PNG. + +`segmented_outputs/cell_segmentations.geojson` (951 real cell polygons, Space Ranger 4.x) +is **not currently read**. It is kept because it is only 0.57 MB and it is the input for a +possible future mode where Visium HD renders segmented cells instead of bins — re-fetching +it later would mean downloading the full 297 MB again. + +## Numbers worth knowing + +- `square_008um`: 702,244 bins total, **20,830 in tissue** +- `square_016um`: 175,561 bins total, **5,262 in tissue** +- Morphology `tissue_hires_image.png`: 6000 × 5394 RGB +- Very sparse — 32,062 total UMIs across the 8 µm bins, max 20 in any one bin, and about + half the in-tissue bins have no counts at all. Gene-set colouring will look mostly empty, + and that is the data, not a bug. + +## The trap this fixture cannot catch + +`tissue_hires_scalef` is **1.0** here and `microns_per_pixel` is **1.003** — both +effectively identity. Any code that forgets to multiply bin coordinates by +`tissue_hires_scalef` when overlaying the hires image, or that confuses pixels with +microns, will still look perfectly correct against this dataset and break on every real +one, where the scale factor runs roughly 0.02–0.2 and `microns_per_pixel` is nearer 0.25. +Treat a passing render here as necessary but not sufficient. diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_008um/filtered_feature_bc_matrix.h5 b/sample_data/visium_hd_tiny/binned_outputs/square_008um/filtered_feature_bc_matrix.h5 new file mode 100644 index 0000000..84c9996 Binary files /dev/null and b/sample_data/visium_hd_tiny/binned_outputs/square_008um/filtered_feature_bc_matrix.h5 differ diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/scalefactors_json.json b/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/scalefactors_json.json new file mode 100644 index 0000000..d50ede2 --- /dev/null +++ b/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/scalefactors_json.json @@ -0,0 +1,9 @@ +{ + "spot_diameter_fullres": 7.975055448344061, + "bin_size_um": 8.0, + "microns_per_pixel": 1.003127821720803, + "tissue_lowres_scalef": 0.1, + "fiducial_diameter_fullres": 328.9710372441925, + "tissue_hires_scalef": 1.0, + "regist_target_img_scalef": 1.0 +} \ No newline at end of file diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/tissue_hires_image.png b/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/tissue_hires_image.png new file mode 100644 index 0000000..536b1d3 Binary files /dev/null and b/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/tissue_hires_image.png differ diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/tissue_positions.parquet b/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/tissue_positions.parquet new file mode 100644 index 0000000..e9782c0 Binary files /dev/null and b/sample_data/visium_hd_tiny/binned_outputs/square_008um/spatial/tissue_positions.parquet differ diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_016um/filtered_feature_bc_matrix.h5 b/sample_data/visium_hd_tiny/binned_outputs/square_016um/filtered_feature_bc_matrix.h5 new file mode 100644 index 0000000..15ff41a Binary files /dev/null and b/sample_data/visium_hd_tiny/binned_outputs/square_016um/filtered_feature_bc_matrix.h5 differ diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/scalefactors_json.json b/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/scalefactors_json.json new file mode 100644 index 0000000..f003aad --- /dev/null +++ b/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/scalefactors_json.json @@ -0,0 +1,9 @@ +{ + "spot_diameter_fullres": 15.950110896688122, + "bin_size_um": 16.0, + "microns_per_pixel": 1.003127821720803, + "tissue_lowres_scalef": 0.1, + "fiducial_diameter_fullres": 328.9710372441925, + "tissue_hires_scalef": 1.0, + "regist_target_img_scalef": 1.0 +} \ No newline at end of file diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_hires_image.png b/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_hires_image.png new file mode 100644 index 0000000..536b1d3 Binary files /dev/null and b/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_hires_image.png differ diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_lowres_image.png b/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_lowres_image.png new file mode 100644 index 0000000..be09470 Binary files /dev/null and b/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_lowres_image.png differ diff --git a/sample_data/visium_hd_tiny/binned_outputs/square_016um/spatial/tissue_positions.parquet 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