Franzi ashlar and testing RGB camera issues in docker

.github/workflows/build-docker-server.yaml

@@ -45,6 +45,9 @@ jobs:
           # Don't download unnecessary data:
           fetch-depth: 0
           filter: 'blob:none'
+          # We fetch tags so that the staged pallet bundle has a record of ancestral tags, for
+          # pseudoversion string generation:
+          fetch-tags: true
 
       - name: Wait for frontend to build
         id: wait-build-frontend
@@ -92,6 +95,40 @@ jobs:
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
+      - name: Determine version string
+        id: version-string
+        run: |
+          # Get the SHA of the actual commit (not the fake merge commit) on PR-triggered runs
+          # (refer to https://stackoverflow.com/a/68068674/23202949):
+          if [ -n "${{ github.event.pull_request.head.sha }}" ]; then
+            ACTUAL_SHA="${{ github.event.pull_request.head.sha }}"
+          else
+            # Note: we want to have a SHA to check out even in merge queues, so we always fall back
+            # to a SHA even if it's a fictional SHA detached from any branches:
+            ACTUAL_SHA="${{ github.sha }}"
+          fi
+
+          TAG="$(git describe --tags --exact-match --match "v*" "$ACTUAL_SHA" 2>/dev/null || printf "")"
+          VERSION="$(git describe --tags --match "v*" --abbrev=7 "$ACTUAL_SHA")"
+          TIMESTAMP="$(TZ=UTC git show -s --format=%ad --date=format:'t%Y%m%d%H%M%S' "$ACTUAL_SHA")"
+
+          if [[ "$VERSION" != "$TAG" ]]; then
+            VERSION="$VERSION-$TIMESTAMP"
+            if [[ -n "${{ github.event.pull_request.head.sha }}" ]]; then
+              # We're in a pull request
+              VERSION="$VERSION-pr${{ github.event.pull_request.number }}"
+            fi
+          fi
+
+          echo "version: $VERSION"
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Record version
+        run: |
+          VERSION="${{ steps.version-string.outputs.version }}"
+          echo "version = \"$VERSION\"" > ./imswitch/version.py
+          cat ./imswitch/version.py
+
       - name: Build and push by digest
         id: build
         uses: docker/build-push-action@v6

.github/workflows/build-frontend.yaml

@@ -25,6 +25,9 @@ jobs:
           # This repo has tons of cruft in its history, so we try to only fetch files we actually need:
           fetch-depth: 0
           filter: 'blob:none'
+          # We fetch tags so that the staged pallet bundle has a record of ancestral tags, for
+          # pseudoversion string generation:
+          fetch-tags: true
 
       - name: Use cached ~/.npm
         uses: actions/cache@v4
@@ -37,6 +40,40 @@ jobs:
         working-directory: ./frontend
         run: npm install
 
+      - name: Determine version string
+        id: version-string
+        run: |
+          # Get the SHA of the actual commit (not the fake merge commit) on PR-triggered runs
+          # (refer to https://stackoverflow.com/a/68068674/23202949):
+          if [ -n "${{ github.event.pull_request.head.sha }}" ]; then
+            ACTUAL_SHA="${{ github.event.pull_request.head.sha }}"
+          else
+            # Note: we want to have a SHA to check out even in merge queues, so we always fall back
+            # to a SHA even if it's a fictional SHA detached from any branches:
+            ACTUAL_SHA="${{ github.sha }}"
+          fi
+
+          TAG="$(git describe --tags --exact-match --match "v*" "$ACTUAL_SHA" 2>/dev/null || printf "")"
+          VERSION="$(git describe --tags --match "v*" --abbrev=7 "$ACTUAL_SHA")"
+          TIMESTAMP="$(TZ=UTC git show -s --format=%ad --date=format:'t%Y%m%d%H%M%S' "$ACTUAL_SHA")"
+
+          if [[ "$VERSION" != "$TAG" ]]; then
+            VERSION="$VERSION-$TIMESTAMP"
+            if [[ -n "${{ github.event.pull_request.head.sha }}" ]]; then
+              # We're in a pull request
+              VERSION="$VERSION-pr${{ github.event.pull_request.number }}"
+            fi
+          fi
+
+          echo "version: $VERSION"
+          echo "version=$VERSION" >> $GITHUB_OUTPUT
+
+      - name: Record version
+        run: |
+          VERSION="${{ steps.version-string.outputs.version }}"
+          echo "export const APP_VERSION = \"$VERSION\";" > ./frontend/src/version.js
+          cat ./frontend/src/version.js
+
       - name: Build
         working-directory: ./frontend
         run: |

.vscode/launch.json

@@ -14,6 +14,16 @@
             "subProcess": true,
             "python": "${workspaceFolder}/.venv/bin/python"
         },
+        {
+            "name": "Python: Aktuelle Datei (WINDOWS)",
+            "type": "python",
+            "request": "launch",
+            "program": "${file}",
+            "console": "integratedTerminal",
+            "justMyCode": false, 
+            "subProcess": true,
+            "python": "${workspaceFolder}/.venv/Scripts/python.exe"
+        },
         {
             "name": "Python: Aktuelle Datei x86",
             "type": "python",

docker/build-imswitch-deps.sh

@@ -30,10 +30,6 @@ export PATH="/root/.local/bin:$PATH"
 # slow-changing dependencies without installing ImSwitch itself yet.
 # This creates a separately-cached Docker image layer from the rapidly-changing source.
 mkdir -p /opt/imswitch/imswitch
-cat >/opt/imswitch/imswitch/__init__.py <<EOF
-# temporary placeholder to be overwritten by build-imswitch.sh
-__version__ = "0.0.0"
-EOF
 cp /mnt/ImSwitch/pyproject.toml /opt/imswitch/pyproject.toml
 cp /mnt/ImSwitch/uv.lock /opt/imswitch/uv.lock
 cd /opt/imswitch

docs/labware_opentrons.md

@@ -0,0 +1,206 @@
+# Opentrons-style Labware in ImSwitch
+
+ImSwitch ships an Opentrons-compatible labware layer that replaces the older
+hard-coded `wellplate_layouts` module. Plates are described by JSON files
+that follow the [Opentrons labware schema v2](https://github.com/Opentrons/opentrons/blob/edge/shared-data/labware/schemas/2.json),
+loaded once at controller startup and exposed to the frontend through a small
+set of REST endpoints.
+
+This document covers:
+
+1. Where labware definitions live and how they are discovered
+2. The on-disk JSON schema (mm) and the in-memory model (µm)
+3. Adding a new plate — both built-in (Python generator) and via dropping in
+   an Opentrons community JSON
+4. The HTTP endpoints
+5. The frontend `LabwareSelectionPanel`
+6. The OME-NGFF `plate_metadata.json` sidecar emitted by experiments
+
+---
+
+## 1. Layout on disk
+
+```
+imswitch/imcontrol/model/labware/
+├── __init__.py                # public API: LabwareManager, load_labware_*
+├── models.py                  # Pydantic models (Opentrons mm + ImSwitch µm)
+├── loader.py                  # JSON → LabwareDefinition (mm → µm)
+├── manager.py                 # LabwareManager: discovery, caching, offsets
+├── selector.py                # WellSelectionPattern → resolved wells/points
+├── generators.py              # Built-in SBS plate generator (Python → JSON)
+├── schema_v2.json             # Vendored Opentrons schema (relaxed `format`)
+└── definitions/
+    ├── openuc2/
+    │   ├── corning_6_wellplate_16.8ml_flat/1.json
+    │   ├── corning_12_wellplate_6.9ml_flat/1.json
+    │   ├── corning_24_wellplate_3.4ml_flat/1.json
+    │   ├── corning_48_wellplate_1.6ml_flat/1.json
+    │   ├── corning_96_wellplate_360ul_flat/1.json
+    │   ├── corning_384_wellplate_112ul_flat/1.json
+    │   ├── greiner_96_wellplate_650ul_uclear/1.json
+    │   ├── ibidi_8well_chambered_coverslip/1.json
+    │   ├── slide_4x_histosample_heidstar/1.json
+    │   ├── ropod_2slides_uc2/1.json
+    │   └── dep_chip_8x6_uc2/1.json
+    └── <your-namespace>/<your_load_name>/<version>.json
+```
+
+`LabwareManager` recursively scans `definitions/` on first use. The directory
+layout follows Opentrons' convention: `<namespace>/<loadName>/<version>.json`.
+The `loadName` field inside the JSON is what the rest of ImSwitch (and the
+frontend) uses to refer to the plate.
+
+## 2. Units
+
+| Layer                    | Units | Purpose                                     |
+|--------------------------|-------|---------------------------------------------|
+| JSON on disk             | mm    | Opentrons-native, drag-drop community defs  |
+| `OpentronsLabwareV2`     | mm    | Loader-internal Pydantic mirror             |
+| `LabwareDefinition` (RAM)| µm    | What every other ImSwitch module sees       |
+
+Conversion happens in exactly one place: `loader.py` (`MM_TO_UM = 1000.0`).
+
+## 3. Adding a new plate
+
+### 3a. Drop in an Opentrons community JSON
+
+The fastest way: download a JSON from the
+[Opentrons labware library](https://labware.opentrons.com/) (or write your own),
+place it at:
+
+```
+imswitch/imcontrol/model/labware/definitions/<namespace>/<loadName>/<version>.json
+```
+
+then restart ImSwitch. The new plate appears in `getLabwareList` and in the
+frontend's labware dropdown automatically.
+
+The schema requirements are minimal:
+
+- `schemaVersion: 2`
+- `parameters.loadName` — must match the folder name
+- `parameters.format` — any string (`"96Standard"`, `"384Standard"`,
+  `"24Standard"`, `"irregular"`, …); ImSwitch does not gate behaviour on it
+- `ordering` — list of columns of well IDs (must agree with `wells` keys)
+- `wells` — dict keyed by well ID (`"A1"`, `"H12"`, …) with `x`, `y`, `z`,
+  `depth`, `totalLiquidVolume`, `shape` (`"circular"` or `"rectangular"`),
+  and `diameter` *or* `xDimension`/`yDimension`
+- `dimensions` — `xDimension`/`yDimension`/`zDimension` of the outer plate
+- `metadata.displayName`, `metadata.displayCategory`,
+  `metadata.displayVolumeUnits` (`"µL"` | `"mL"` | `"L"`)
+- `brand.brand`
+- `cornerOffsetFromSlot` — vector `{x, y, z}`
+
+Any additional Opentrons fields are tolerated (`extra="allow"`).
+
+A bad file is logged with a `LabwareValidationError` and skipped — it never
+blocks controller startup.
+
+### 3b. Add a built-in SBS plate via the generator
+
+Built-in plates live in `generators.py` (`_BUILTIN_SPECS`). Append a new entry
+and run:
+
+```bash
+python -m imswitch.imcontrol.model.labware.generators
+```
+
+This regenerates the JSONs under `definitions/openuc2/`. Example spec:
+
+```python
+dict(
+    rows=4, cols=6,
+    well_diameter_mm=16.26,
+    well_depth_mm=17.4,
+    total_volume_uL=3400.0,
+    well_spacing_x_mm=19.3,
+    well_spacing_y_mm=19.3,
+    a1_x_offset_mm=17.48,
+    a1_y_offset_mm=13.67,
+    load_name="corning_24_wellplate_3.4ml_flat",
+    display_name="Corning 24 Well Plate 3.4 mL Flat",
+    brand="Corning",
+    format_override="24Standard",
+    tags=["SBS", "wellPlate", "_generated"],
+),
+```
+
+The generator follows the SBS convention: A1 at the back-left of the plate.
+
+## 4. HTTP endpoints
+
+All endpoints hang off `ExperimentController`.
+
+### New (preferred)
+
+- `GET /ExperimentController/getLabwareList`
+  → `[{load_name, display_name, format, rows, cols, well_count, tags, ...}]`
+- `GET /ExperimentController/getLabwareDefinition?load_name=...&offset_x_um=...&offset_y_um=...`
+  → full `LabwareDefinition` (µm) with optional rigid offset baked in
+- `POST /ExperimentController/selectWellsByPattern`
+  body: `{ loadName, pattern: WellSelectionPattern, offsetXUm, offsetYUm }`
+  → resolved wells + their µm coordinates
+- `POST /ExperimentController/applyWellSelectionToExperiment`
+  body: `{ loadName, pattern, offsetXUm, offsetYUm, conditionLabels, pointNameTemplate }`
+  → `{ points: [...] }` ready to push into the experiment's `pointList`
+
+### `WellSelectionPattern` shape
+
+```json
+{
+  "wells":   ["A1", "B5"],          // explicit IDs (optional)
+  "ranges":  ["A1:C3", "H12"],      // Excel-style ranges (optional)
+  "rows":    ["A", "C"],            // entire rows (optional)
+  "columns": [1, 6, 12],            // entire columns (optional)
+  "all":     false                  // shorthand for the whole plate
+}
+```
+
+Pattern fields are unioned. `pointNameTemplate` understands `{well_id}`,
+`{row}`, `{column}`, `{label}`.
+
+### Compatibility wrappers (legacy clients)
+
+- `GET /ExperimentController/getAvailableWellplateLayouts`
+- `GET /ExperimentController/getWellplateLayout?layout_name=...`
+
+Both delegate to the labware manager and return the legacy dict shape the
+old frontend canvas understands (`{name, wells: [...], width, height,
+unit: "um", ...}`). The `generateCustomWellplateLayout` endpoint and the
+`wellplate_layouts` module have been removed — define plates as JSON instead.
+
+## 5. Frontend: `LabwareSelectionPanel`
+
+`frontend/src/components/LabwareSelectionPanel.jsx` mounts inside
+`WellSelectorComponent` and exposes:
+
+- **Labware picker** — populated from `getLabwareList`; switching it clears
+  the current well selection and (after confirmation) the experiment's
+  point list
+- **Well chip grid** — click chips to toggle, *or* type a pattern
+  (`A1:C3, B5`) and hit *Resolve* to expand it into chips
+- **Condition labels** — tag selected wells with a free-text label that
+  travels through to the OME-NGFF metadata
+- **Sub-position generator** — emit one point per well at the well centre,
+  *or* an `Nx × Ny` rectangular grid inside each well with user-set µm
+  spacing; a small SVG preview shows the dot pattern in the well outline
+- **Apply** — append or replace the experiment's `pointList`
+
+The panel uses the new endpoints exclusively. Layout switching (the legacy
+`Layout` dropdown in `WellSelectorComponent`) shows a confirmation dialog
+when the existing `pointList` is non-empty so users do not lose their
+selections by accident.
+
+## 6. OME-NGFF plate metadata sidecar
+
+When an experiment runs against a labware definition, ImSwitch writes a
+`plate_metadata.json` sidecar next to the OME-Zarr store. The file follows
+the [OME-NGFF 0.4 plate spec](https://ngff.openmicroscopy.org/0.4/#plate-md)
+plus an `imswitch_well` block per well that carries:
+
+- `labwareLoadName`, `wellRow`, `wellColumn`
+- `conditionLabel` (if set)
+- the resolved acquisition `points` for that well
+
+See `imswitch/imcontrol/model/io/ome_writers/plate_metadata.py` for the
+exact schema.

frontend/package.json

@@ -1,6 +1,5 @@
 {
-  "name": "microscope-app",
-  "version": "1.6.4",
+  "name": "imswitch-frontend",
   "private": true,
   "homepage": "/imswitch/ui",
   "dependencies": {