From bb96cdc41a6d504cd9b20b5c8798b5b6e5e37448 Mon Sep 17 00:00:00 2001
From: Tristan Simas <tristan.simas@mail.mcgill.ca>
Date: Thu, 24 Sep 2026 01:00:23 -0400
Subject: [PATCH 1/6] Expose lossless TIFF artifact compression in pipeline
 config

---
 external/PolyStore                            |  2 +-
 openhcs/core/config.py                        | 11 +++
 openhcs/core/context/processing_context.py    |  3 +
 openhcs/core/orchestrator/orchestrator.py     |  1 +
 .../function_artifact_materialization.py      | 25 +++++--
 openhcs/core/steps/function_io.py             | 13 +++-
 openhcs/processing/materialization/core.py    | 20 +++++-
 tests/unit/test_config_document.py            | 13 +++-
 .../test_function_artifact_materialization.py |  3 +-
 ...ion_artifact_materialization_io_hotpath.py | 21 ++++++
 tests/unit/test_tiff_output_compression.py    | 72 +++++++++++++++++++
 11 files changed, 171 insertions(+), 13 deletions(-)
 create mode 100644 tests/unit/test_tiff_output_compression.py

diff --git a/external/PolyStore b/external/PolyStore
index 6534b10e7a..9588e0c2cb 160000
--- a/external/PolyStore
+++ b/external/PolyStore
@@ -1 +1 @@
-Subproject commit 6534b10e7a4dc077fe4d0a710bb05b995ee1ba57
+Subproject commit 9588e0c2cb76548fc4865a5670015a591223f284
diff --git a/openhcs/core/config.py b/openhcs/core/config.py
index 8aec5091bc..8aaa01daba 100644
--- a/openhcs/core/config.py
+++ b/openhcs/core/config.py
@@ -69,6 +69,7 @@ class StreamingConfigMeta(EnableableMeta, AutoRegisterMeta):
 Lz4ZarrCompressorFactory = _polystore_config.Lz4ZarrCompressorFactory
 ZstdZarrCompressorFactory = _polystore_config.ZstdZarrCompressorFactory
 ZarrChunkStrategy = _polystore_config.ZarrChunkStrategy
+TiffCompression = _polystore_config.TiffCompression
 
 
 class MaterializationBackend(Enum):
@@ -616,6 +617,16 @@ class ZarrConfig(AnnotatedDataclassValidationMixin, _polystore_config.ZarrConfig
     """
 
 
+@abbreviation("tiff")
+@global_pipeline_config(
+    inherit_as_none=False,
+    field_abbreviations={"compression": "codec", "compression_level": "level"},
+)
+@dataclass(frozen=True)
+class TiffConfig(AnnotatedDataclassValidationMixin, _polystore_config.TiffConfig):
+    """Lossless TIFF output settings shared by image and artifact materialization."""
+
+
 @abbreviation("vfs")
 @global_pipeline_config(always_viewable_fields=["materialization_backend"])
 @dataclass(frozen=True)
diff --git a/openhcs/core/context/processing_context.py b/openhcs/core/context/processing_context.py
index ac44a2abab..e9a6f47172 100644
--- a/openhcs/core/context/processing_context.py
+++ b/openhcs/core/context/processing_context.py
@@ -19,6 +19,7 @@
     AnalysisConsolidationConfig,
     PlateMetadataConfig,
     StreamingConfig,
+    TiffConfig,
 )
 from openhcs.core.compiled_step_plan import CompiledStepPlan
 from openhcs.core.debug import (
@@ -97,6 +98,7 @@ def __init__(
         filemanager: FileManager | None = None,
         analysis_consolidation_config: AnalysisConsolidationConfig | None = None,
         plate_metadata_config: PlateMetadataConfig | None = None,
+        tiff_config: TiffConfig | None = None,
         auto_add_output_plate_to_plate_manager: bool = False,
         output_plate_root: str | None = None,
         transport_config: ZMQConfig = OPENHCS_ZMQ_CONFIG,
@@ -147,6 +149,7 @@ def __init__(
             if plate_metadata_config is not None
             else PlateMetadataConfig()
         )
+        self.tiff_config = tiff_config if tiff_config is not None else TiffConfig()
         self.auto_add_output_plate_to_plate_manager = (
             auto_add_output_plate_to_plate_manager
         )
diff --git a/openhcs/core/orchestrator/orchestrator.py b/openhcs/core/orchestrator/orchestrator.py
index 22ed3ea28a..09d3836fb2 100644
--- a/openhcs/core/orchestrator/orchestrator.py
+++ b/openhcs/core/orchestrator/orchestrator.py
@@ -574,6 +574,7 @@ def create_context(self, axis_id: str) -> ProcessingContext:
                 effective_config.analysis_consolidation_config
             ),
             plate_metadata_config=effective_config.plate_metadata_config,
+            tiff_config=effective_config.tiff_config,
             auto_add_output_plate_to_plate_manager=(
                 effective_config.auto_add_output_plate_to_plate_manager
             ),
diff --git a/openhcs/core/steps/function_artifact_materialization.py b/openhcs/core/steps/function_artifact_materialization.py
index d27788c823..e8923bb942 100644
--- a/openhcs/core/steps/function_artifact_materialization.py
+++ b/openhcs/core/steps/function_artifact_materialization.py
@@ -405,7 +405,14 @@ def backend_kwargs(
                     f"context values: {sorted(conflicts)!r}."
                 )
             values.update(contextual_values)
-            result[backend] = RawBackendKwargs(values)
+            result[backend] = RawBackendKwargs(
+                values,
+                tiff_config=(
+                    kwargs.tiff_config
+                    if isinstance(kwargs, RawBackendKwargs)
+                    else None
+                ),
+            )
 
         streamable_viewer_surfaces = self.streamable_viewer_surfaces(
             filemanager=filemanager,
@@ -496,7 +503,7 @@ def backend_plan(
             )
         )
         return ArtifactMaterializationBackendPlan(
-            persistent_backend_kwargs=self.persistent_backend_kwargs(),
+            persistent_backend_kwargs=self.persistent_backend_kwargs(context),
             streaming_viewer_surfaces=(
                 {
                     config.backend.value: config.streaming_viewer_surface(context)
@@ -514,7 +521,7 @@ def backend_plan(
         )
 
     @abstractmethod
-    def persistent_backend_kwargs(self) -> BackendKwargs:
+    def persistent_backend_kwargs(self, context: "ProcessingContext") -> BackendKwargs:
         """Return persistent materialization backends owned by this policy."""
 
 
@@ -525,8 +532,14 @@ class PersistentArtifactMaterializationTargetPlan(ArtifactMaterializationTargetP
     target_key = "persistent"
     backend: str
 
-    def persistent_backend_kwargs(self) -> BackendKwargs:
-        return {self.backend: RawBackendKwargs()}
+    def persistent_backend_kwargs(self, context: "ProcessingContext") -> BackendKwargs:
+        return {
+            self.backend: RawBackendKwargs(
+                tiff_config=(
+                    context.tiff_config if self.backend == Backend.DISK.value else None
+                ),
+            )
+        }
 
 
 class StreamingOnlyArtifactMaterializationTargetPlan(ArtifactMaterializationTargetPlan):
@@ -534,7 +547,7 @@ class StreamingOnlyArtifactMaterializationTargetPlan(ArtifactMaterializationTarg
 
     target_key = "streaming_only"
 
-    def persistent_backend_kwargs(self) -> BackendKwargs:
+    def persistent_backend_kwargs(self, context: "ProcessingContext") -> BackendKwargs:
         return {}
 
 
diff --git a/openhcs/core/steps/function_io.py b/openhcs/core/steps/function_io.py
index 64236b7bf6..d2e5e5e38b 100644
--- a/openhcs/core/steps/function_io.py
+++ b/openhcs/core/steps/function_io.py
@@ -10,6 +10,7 @@
 from typing import TYPE_CHECKING, Callable, ClassVar, Mapping, Sequence, TypeAlias
 
 from metaclass_registry import AutoRegisterMeta
+from polystore.config import tiff_write_batches
 from polystore.zarr_batch import ZarrBatchAxis, ZarrBatchAxisRole, ZarrBatchLayout
 
 from openhcs.constants.constants import (
@@ -380,9 +381,17 @@ def save_materialized_data(
         materialized_paths,
         materialized_backend,
     )
-    filemanager.save_batch(
-        payloads, list(materialized_paths), materialized_backend, **save_kwargs
+    tiff_config = (
+        context.tiff_config if materialized_backend == Backend.DISK.value else None
     )
+    for indices, batch_config in tiff_write_batches(materialized_paths, tiff_config):
+        filemanager.save_batch(
+            [payloads[index] for index in indices],
+            [materialized_paths[index] for index in indices],
+            materialized_backend,
+            **save_kwargs,
+            **({"tiff_config": batch_config} if batch_config is not None else {}),
+        )
 
 
 def get_all_image_paths(
diff --git a/openhcs/processing/materialization/core.py b/openhcs/processing/materialization/core.py
index c8733dc8d5..2dda9451a0 100644
--- a/openhcs/processing/materialization/core.py
+++ b/openhcs/processing/materialization/core.py
@@ -22,6 +22,7 @@
 import numpy as np
 import pandas as pd
 from metaclass_registry import AutoRegisterMeta
+from polystore.config import TiffConfig, tiff_write_batches
 from polystore.streaming.viewer_transport import (
     PathMappedViewerStreamSourceMetadata,
     ViewerStreamBackendKwargs,
@@ -158,6 +159,7 @@ class RawBackendKwargs(BackendCallKwargs, Mapping[str, MaterializationValue]):
 
     backend_kwargs_kind = "raw"
     values: Mapping[str, MaterializationValue] = field(default_factory=dict)
+    tiff_config: TiffConfig | None = None
 
     def __getitem__(self, key: str) -> MaterializationValue:
         return self.values[key]
@@ -172,13 +174,27 @@ def to_filemanager_kwargs(
         self,
         output: Output,
     ) -> dict:
-        return dict(self.values)
+        values = dict(self.values)
+        if self.tiff_config is not None and self.tiff_config.applies_to_path(output.path):
+            values["tiff_config"] = self.tiff_config
+        return values
 
     def filemanager_batches(
         self,
         outputs: Sequence[Output],
     ) -> tuple[tuple[tuple[Output, ...], dict], ...]:
-        return ((tuple(outputs), dict(self.values)),)
+        return tuple(
+            (
+                tuple(outputs[index] for index in indices),
+                {
+                    **self.values,
+                    **({"tiff_config": config} if config is not None else {}),
+                },
+            )
+            for indices, config in tiff_write_batches(
+                tuple(output.path for output in outputs), self.tiff_config
+            )
+        )
 
 
 class TabularRow(dict[str, MaterializationValue]):
diff --git a/tests/unit/test_config_document.py b/tests/unit/test_config_document.py
index 57621a2d92..157caefc62 100644
--- a/tests/unit/test_config_document.py
+++ b/tests/unit/test_config_document.py
@@ -7,7 +7,12 @@
 
 import pytest
 
-from openhcs.core.config import GlobalPipelineConfig, PipelineConfig
+from openhcs.core.config import (
+    GlobalPipelineConfig,
+    PipelineConfig,
+    TiffCompression,
+    TiffConfig,
+)
 from openhcs.core.config_document import (
     ConfigDocumentAuthority,
     ConfigDocumentField,
@@ -27,6 +32,12 @@ def test_config_document_field_owns_exact_public_name() -> None:
     "config",
     (
         GlobalPipelineConfig(num_workers=3),
+        GlobalPipelineConfig(
+            tiff_config=TiffConfig(
+                compression=TiffCompression.DEFLATE,
+                compression_level=3,
+            )
+        ),
         PipelineConfig(),
     ),
 )
diff --git a/tests/unit/test_function_artifact_materialization.py b/tests/unit/test_function_artifact_materialization.py
index dfdb539877..fce6077a7e 100644
--- a/tests/unit/test_function_artifact_materialization.py
+++ b/tests/unit/test_function_artifact_materialization.py
@@ -43,7 +43,7 @@
     RuntimeExecutionAxisScope,
 )
 from openhcs.core.components.parser_metaprogramming import FilenameParseResult
-from openhcs.core.config import AnalysisConsolidationConfig, WellFilterMode
+from openhcs.core.config import AnalysisConsolidationConfig, TiffConfig, WellFilterMode
 from openhcs.core.function_patterns import (
     DEFAULT_GROUP_KEY,
     CompiledFunctionGroup,
@@ -468,6 +468,7 @@ def _context(filemanager):
     context.axis_id = "A01"
     context.step_axis_filters = {}
     context.analysis_consolidation_config = AnalysisConsolidationConfig()
+    context.tiff_config = TiffConfig()
     return context
 
 
diff --git a/tests/unit/test_function_artifact_materialization_io_hotpath.py b/tests/unit/test_function_artifact_materialization_io_hotpath.py
index d8fe1aa816..3a046f5758 100644
--- a/tests/unit/test_function_artifact_materialization_io_hotpath.py
+++ b/tests/unit/test_function_artifact_materialization_io_hotpath.py
@@ -7,6 +7,7 @@
 import numpy as np
 import pytest
 from polystore.base import DataSink
+from polystore.config import TiffCompression, TiffConfig
 from polystore.streaming.identity import StreamProducerIdentity
 
 from openhcs.core.steps.function_artifact_materialization import (
@@ -15,6 +16,7 @@
 )
 from openhcs.processing.materialization.core import (
     MaterializationSpec,
+    Output,
     RawBackendKwargs,
 )
 from openhcs.processing.materialization.options import ImageFileOptions
@@ -38,6 +40,25 @@ def save_batch(self, data_list, identifiers, **kwargs):
         raise AssertionError("This projection test must not save")
 
 
+def test_persistent_tiff_kwargs_apply_only_to_tiff_outputs() -> None:
+    config = TiffConfig(compression=TiffCompression.DEFLATE)
+    kwargs = RawBackendKwargs(tiff_config=config)
+    outputs = (
+        Output(path="/results/summary.csv", content="well,count\nA01,1\n"),
+        Output(path="/results/labels.tif", content=np.zeros((8, 8), dtype=np.int32)),
+        Output(path="/results/labels2.tiff", content=np.zeros((8, 8), dtype=np.int32)),
+    )
+
+    batches = kwargs.filemanager_batches(outputs)
+
+    assert tuple(output.path for output in batches[0][0]) == ("/results/summary.csv",)
+    assert batches[0][1] == {}
+    assert tuple(output.path for output in batches[1][0]) == (
+        "/results/labels.tif", "/results/labels2.tiff"
+    )
+    assert batches[1][1] == {"tiff_config": config}
+
+
 class _FileManager:
     def __init__(self) -> None:
         self.backend = _PersistentBackend()
diff --git a/tests/unit/test_tiff_output_compression.py b/tests/unit/test_tiff_output_compression.py
new file mode 100644
index 0000000000..7ada403ad4
--- /dev/null
+++ b/tests/unit/test_tiff_output_compression.py
@@ -0,0 +1,72 @@
+"""Lossless TIFF compression crosses the declared OpenHCS output boundary."""
+
+from types import SimpleNamespace
+
+import numpy as np
+import tifffile
+from polystore.disk import DiskBackend
+from polystore.filemanager import FileManager
+
+from openhcs.constants.constants import Backend
+from openhcs.core.config import GlobalPipelineConfig, TiffCompression, TiffConfig
+from openhcs.core.steps.function_artifact_materialization import (
+    PersistentArtifactMaterializationTargetPlan,
+)
+from openhcs.core.steps.function_io import save_materialized_data
+from openhcs.processing.materialization import (
+    ImageFileOptions,
+    MaterializationSpec,
+    MaterializedFilenameIdentity,
+    materialize,
+)
+
+
+def test_configured_main_flow_tiff_output_is_lossless(tmp_path) -> None:
+    config = TiffConfig(compression=TiffCompression.DEFLATE, compression_level=3)
+    assert GlobalPipelineConfig().tiff_config == TiffConfig()
+    pixels = np.zeros((2, 256, 256), dtype=np.int32)
+    pixels[0, 40:60, 80:100] = 5
+    path = tmp_path / "labels.tif"
+    context = SimpleNamespace(
+        microscope_handler=SimpleNamespace(parser=object(), microscope_type="test"),
+        tiff_config=config,
+    )
+
+    save_materialized_data(
+        FileManager({Backend.DISK.value: DiskBackend()}),
+        [pixels],
+        [str(path)],
+        Backend.DISK.value,
+        None,
+        context,
+        "A01",
+    )
+
+    with tifffile.TiffFile(path) as output:
+        assert output.pages[0].compression.value != 1
+    np.testing.assert_array_equal(tifffile.imread(path), pixels)
+
+
+def test_configured_named_artifact_tiff_output_is_lossless(tmp_path) -> None:
+    config = TiffConfig(compression=TiffCompression.DEFLATE, compression_level=3)
+    pixels = np.zeros((2, 256, 256), dtype=np.int32)
+    pixels[1, 60:80, 90:110] = 11
+    path = materialize(
+        MaterializationSpec(
+            ImageFileOptions(
+                filename_suffix=".tif",
+                filename_identity=MaterializedFilenameIdentity.ARTIFACT_NAME,
+            )
+        ),
+        pixels,
+        str(tmp_path / "artifact"),
+        FileManager({Backend.DISK.value: DiskBackend()}),
+        backends=[Backend.DISK.value],
+        backend_kwargs=PersistentArtifactMaterializationTargetPlan(
+            backend=Backend.DISK.value
+        ).persistent_backend_kwargs(SimpleNamespace(tiff_config=config)),
+    )
+
+    with tifffile.TiffFile(path) as output:
+        assert output.pages[0].compression.value != 1
+    np.testing.assert_array_equal(tifffile.imread(path), pixels)

From 550cc85ccbbe4f66fb908378a09b57daf2ec0ccf Mon Sep 17 00:00:00 2001
From: Tristan Simas <tristan.simas@mail.mcgill.ca>
Date: Thu, 24 Sep 2026 01:15:52 -0400
Subject: [PATCH 2/6] Document TIFF output configuration and refresh reviewed
 authorities

---
 docs/audits/architecture_a_m.json             | 18 ++---
 docs/audits/architecture_n_z_development.json | 14 ++--
 .../pr129_tiff_compression_review_20260924.md | 30 ++++++++
 docs/audits/user_docs.json                    | 70 ++++++++++++-------
 docs/source/concepts/storage_system.rst       | 12 ++++
 .../configuration_reference.rst               |  7 ++
 external/PolyStore                            |  2 +-
 7 files changed, 111 insertions(+), 42 deletions(-)
 create mode 100644 docs/audits/pr129_tiff_compression_review_20260924.md

diff --git a/docs/audits/architecture_a_m.json b/docs/audits/architecture_a_m.json
index 2de6bf56fc..fc58681038 100644
--- a/docs/audits/architecture_a_m.json
+++ b/docs/audits/architecture_a_m.json
@@ -168,7 +168,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares AnalysisConsolidationConfig and its standalone consolidation policy."
       },
       {
@@ -178,7 +178,7 @@
       },
       {
         "path": "tests/unit/test_function_artifact_materialization.py",
-        "sha256": "4ae063cac0f93a03b5b4aab7304c8d7e6bcfc04ec74d107ea14c94f76be755ca",
+        "sha256": "ba4f8f5f165ab87c3000d6d371a6f25cf4ec6a5d39b5047abaa392c827fe9ae8",
         "role": "Proves consolidation consumes runtime CSV values, uses the compiled backend destination, ignores non-table artifacts, and propagates failures."
       },
       {
@@ -188,7 +188,7 @@
       },
       {
         "path": "openhcs/processing/materialization/core.py",
-        "sha256": "1372625f3d7dc04cf6822a1887871dfa9a149b2313df7d7acefd452a6ad0f932",
+        "sha256": "e79e734ce159f54eee10e7238b0b00a6a03e065af3c3c171e6934a3480a162fd",
         "role": "Owns writer runtime-path selection before rendering and the shared ROI target request."
       }
     ],
@@ -675,7 +675,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares OpenHCS domain configuration that consumes ObjectState mechanics."
       }
     ],
@@ -841,7 +841,7 @@
       },
       {
         "path": "openhcs/core/context/processing_context.py",
-        "sha256": "9384fcc4d5ed7ea8607257ec448958f85a88a5caa6ae06f22142cc51b58b479e",
+        "sha256": "c7b79f50661c528261ce8c577fd67c753c84a5e499aa87cd5e540b53417351a2",
         "role": "Owns the compiled multiprocessing-axis identity for one processing context."
       },
       {
@@ -912,7 +912,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the OpenHCS global, pipeline, step, and standalone configuration hierarchy."
       }
     ],
@@ -1142,7 +1142,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares standalone ExperimentalAnalysisConfig options and all directory-workflow filenames."
       },
       {
@@ -1805,7 +1805,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the WellFilterConfig family preview policy and WellFilterMode member operators."
       },
       {
@@ -1955,7 +1955,7 @@
       },
       {
         "path": "tests/unit/test_config_document.py",
-        "sha256": "c6b291080398669b8449cb6ddaa78350f6c5b09f4f0cc57ebe92ac5f32460915",
+        "sha256": "0ee12db4633ab39b34f630e4ee1b0c48b40d8226f91fddc504bb3311b9612cda",
         "role": "Proves explicit, defaulted, and invalid typed field projections from canonical configuration source."
       },
       {
diff --git a/docs/audits/architecture_n_z_development.json b/docs/audits/architecture_n_z_development.json
index 55003c0404..2110b5c60d 100644
--- a/docs/audits/architecture_n_z_development.json
+++ b/docs/audits/architecture_n_z_development.json
@@ -220,7 +220,7 @@
       },
       {
         "path": "openhcs/core/orchestrator/orchestrator.py",
-        "sha256": "ca733be328ed5f1f033ee521fbf9bf0b088791bd19542f0071ddb01b4f2d3d9c",
+        "sha256": "843e994d7b16592f43a15ce36c33a51ead534cf22df792838ce2b800621114b7",
         "role": "PipelineOrchestrator configuration ownership, resolution, compiler setup, and executor lifecycle."
       },
       {
@@ -250,7 +250,7 @@
       },
       {
         "path": "openhcs/core/context/processing_context.py",
-        "sha256": "9384fcc4d5ed7ea8607257ec448958f85a88a5caa6ae06f22142cc51b58b479e",
+        "sha256": "c7b79f50661c528261ce8c577fd67c753c84a5e499aa87cd5e540b53417351a2",
         "role": "Owns explicit release of the context-local image-stack cache without discarding observations."
       },
       {
@@ -290,7 +290,7 @@
     "authority": [
       {
         "path": "openhcs/core/orchestrator/orchestrator.py",
-        "sha256": "ca733be328ed5f1f033ee521fbf9bf0b088791bd19542f0071ddb01b4f2d3d9c",
+        "sha256": "843e994d7b16592f43a15ce36c33a51ead534cf22df792838ce2b800621114b7",
         "role": "PipelineOrchestrator configuration ownership, resolution, compiler setup, and executor lifecycle."
       },
       {
@@ -512,7 +512,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Pipeline, global, step, processing, and source configuration declarations."
       },
       {
@@ -572,7 +572,7 @@
       },
       {
         "path": "openhcs/core/context/processing_context.py",
-        "sha256": "9384fcc4d5ed7ea8607257ec448958f85a88a5caa6ae06f22142cc51b58b479e",
+        "sha256": "c7b79f50661c528261ce8c577fd67c753c84a5e499aa87cd5e540b53417351a2",
         "role": "Owns the compiled multiprocessing-axis identity carried by each runtime context."
       },
       {
@@ -822,7 +822,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Pipeline, global, step, processing, and source configuration declarations."
       },
       {
@@ -1020,7 +1020,7 @@
       },
       {
         "path": "openhcs/processing/materialization/core.py",
-        "sha256": "1372625f3d7dc04cf6822a1887871dfa9a149b2313df7d7acefd452a6ad0f932",
+        "sha256": "e79e734ce159f54eee10e7238b0b00a6a03e065af3c3c171e6934a3480a162fd",
         "role": "Nominal artifact materialisation and ROI projection strategies."
       },
       {
diff --git a/docs/audits/pr129_tiff_compression_review_20260924.md b/docs/audits/pr129_tiff_compression_review_20260924.md
new file mode 100644
index 0000000000..fa63778bd6
--- /dev/null
+++ b/docs/audits/pr129_tiff_compression_review_20260924.md
@@ -0,0 +1,30 @@
+# PR #129 TIFF compression authority-delta review
+
+Date: 2026-09-24
+
+The opt-in disk-TIFF writer change invalidated 34 recorded authority edges
+across 29 active documentation pages. I re-read each complete dependent page
+against the changed OpenHCS declarations, runtime path, and tests, and the
+PolyStore codec declaration. The generated configuration reference remains the
+authority for exact fields, accepted values, and defaults; it is not duplicated
+as a hand-maintained field table.
+
+Two pages needed prose changes. `concepts/storage_system.rst` now explains the
+separation of disk TIFF compression from Zarr compression and semantic
+materialization. `guide_for_biologists/configuration_reference.rst` now names
+the `TiffConfig` family and its scope in the practitioner mental model. Both
+remain explanations rather than becoming exhaustive field references. The
+other 27 pages retain their existing claims and Diátaxis purposes: the new
+config is resolved from the existing pipeline declaration, carried in the
+compiled processing context, and used only on disk TIFF writes, so their
+descriptions of inheritance, runtime ownership, ROI, MCP schema projection,
+analysis, and viewer behavior remain accurate.
+
+This is an editorial receipt, not product authority. The authoritative files
+are the declarations, implementations, and tests recorded in the JSON audit
+entries. The changed page and authority digests were refreshed only after this
+comparison. Documentation validation passed for 155 audited sources, the full
+Sphinx HTML build succeeded with warnings treated as errors, and 15 focused
+documentation, MCP, and TIFF-output tests passed. These checks do not waive
+the separate published-dependency readiness gate; PolyStore's new source has
+not been published as a new release.
diff --git a/docs/audits/user_docs.json b/docs/audits/user_docs.json
index cf587ac4db..66da81029c 100644
--- a/docs/audits/user_docs.json
+++ b/docs/audits/user_docs.json
@@ -11,7 +11,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -21,7 +21,7 @@
       },
       {
         "path": "openhcs/core/orchestrator/orchestrator.py",
-        "sha256": "ca733be328ed5f1f033ee521fbf9bf0b088791bd19542f0071ddb01b4f2d3d9c",
+        "sha256": "843e994d7b16592f43a15ce36c33a51ead534cf22df792838ce2b800621114b7",
         "role": "Owns execution orchestration, worker submission, progress handling, and cleanup of compiled bundles."
       },
       {
@@ -495,7 +495,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -674,7 +674,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -727,7 +727,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -843,7 +843,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -871,7 +871,7 @@
   },
   {
     "path": "docs/source/concepts/storage_system.rst",
-    "source_sha256": "fa377aa5280583609ca43d6190cc03aaabb1a7abed40dd4344d8e686866ce1f7",
+    "source_sha256": "e7e77ea48bfda5701e5c309561400ebc3d10a95aad8824c05c7561e7474882b4",
     "audience": [
       "pipeline authors",
       "storage integrators"
@@ -881,7 +881,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -891,7 +891,7 @@
       },
       {
         "path": "openhcs/core/steps/function_artifact_materialization.py",
-        "sha256": "5a219f74d1abfd59f915aae06cb3dc2befa1d1a83b82b59d6a8f98f3ac5865ba",
+        "sha256": "d25982897fb41b7bf392c3e85f4b5ac4f711c7219ead60833edd762e559cc8fb",
         "role": "Owns the rules that materialise function outputs through the configured storage backend."
       },
       {
@@ -899,14 +899,31 @@
         "sha256": "ae641affae21b61448816a14bd68b7f2f3fc0082f0f1fbe51079ed32520450b1",
         "role": "Declares the storage backend interface and lifecycle shared by local and remote materialisation backends."
       },
+      {
+        "path": "external/PolyStore/src/polystore/config.py",
+        "sha256": "62c8acad3da3abed8ccf7f1166fc6a0d094be1c3e842cec6446780541df292a0",
+        "role": "Declares lossless disk-TIFF codec settings, defaults, and path-specific batching."
+      },
+      {
+        "path": "external/PolyStore/src/polystore/disk.py",
+        "sha256": "cf089b8c79f86099a7cea1b6cbe43ceaec6331196a44b43183f2e64b7746c219",
+        "role": "Applies TIFF codec settings in the disk writer without changing other formats."
+      },
       {
         "path": "tests/unit/test_runtime_value_store.py",
         "sha256": "8900a7b83b59d0a40f9698dbafaaba778df982f9d7a0b628f80eab97335aeab0",
         "role": "Proves scoped typed runtime-value insertion, lookup, isolation, and cleanup."
+      },
+      {
+        "path": "tests/unit/test_tiff_output_compression.py",
+        "sha256": "458f576e545a033ed9e23b9dc349ab92c19d296ec7f0e269ea89884cd9b82942",
+        "role": "Proves configured main-flow and named-artifact disk-TIFF writes round-trip exactly."
       }
     ],
-    "findings": [],
-    "disposition": "keep",
+    "findings": [
+      "The storage explanation did not distinguish optional disk-TIFF compression from Zarr compression or semantic materialization."
+    ],
+    "disposition": "revise",
     "validation": [
       "Re-read docs/source/concepts/storage_system.rst in full against repository base bb4218fae and the current shared worktree; challenged its explanation user need for accuracy, freshness, duplication, owner boundaries, flow, and navigation.",
       "Compared every factual claim directly with the current hash-pinned authorities: openhcs/core/config.py; openhcs/core/runtime_stores.py; openhcs/core/steps/function_artifact_materialization.py; external/PolyStore/src/polystore/base.py; tests/unit/test_runtime_value_store.py.",
@@ -917,7 +934,8 @@
       "2026-09-09: Re-read this page against the changed source authorities for release 0.8.3; retained its Diataxis purpose and updated affected workflow claims.",
       "2026-09-16: Re-read the complete explanation against runtime artifact materialization changes. Added the semantic-versus-filename identity boundary and confirmed that path completion does not mutate artifact metadata; 249 focused materialization and adjacent runtime tests passed.",
       "2026-09-22 PR #126 targeted authority-delta review: re-read the complete page against `openhcs/core/config.py`; retained the supported claims, findings, and disposition, then refreshed only these compared evidence hashes. Review scope and the separate blocking runtime evidence are recorded in `docs/audits/pr126_authority_delta_review_20260922.md`.",
-      "2026-09-22 PR #126 integrated-repair follow-up: re-read the complete page and the final owner/test changes in `openhcs/core/steps/function_artifact_materialization.py`. Scalar image materialization now selects the execution scope matching the complete source address, deduplicates equivalent repeated group records, and rejects conflicts; the documented separation of semantic source identity, filename completion, runtime records, and persistence remains accurate. Refreshed only these compared evidence hashes; details are retained in `docs/audits/pr126_authority_delta_review_20260922.md`."
+      "2026-09-22 PR #126 integrated-repair follow-up: re-read the complete page and the final owner/test changes in `openhcs/core/steps/function_artifact_materialization.py`. Scalar image materialization now selects the execution scope matching the complete source address, deduplicates equivalent repeated group records, and rejects conflicts; the documented separation of semantic source identity, filename completion, runtime records, and persistence remains accurate. Refreshed only these compared evidence hashes; details are retained in `docs/audits/pr126_authority_delta_review_20260922.md`.",
+      "2026-09-24 PR #129: re-read the complete explanation against the changed config, materialization, PolyStore writer, and exact-roundtrip test authorities; added the disk-TIFF compression boundary without copying exact generated fields. Review scope is recorded in `docs/audits/pr129_tiff_compression_review_20260924.md`."
     ]
   },
   {
@@ -1264,7 +1282,7 @@
   },
   {
     "path": "docs/source/guide_for_biologists/configuration_reference.rst",
-    "source_sha256": "3a70946f59a595f5ebbdf4a176280d7ba497f630cec92c45cd2710d40a10f6f2",
+    "source_sha256": "ba3c4ef923c4f643c06accc8641c462b2f63a8e46694ef984dde96ef49a0d9c7",
     "audience": [
       "imaging scientists",
       "pipeline authors"
@@ -1274,7 +1292,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -1330,7 +1348,8 @@
     ],
     "findings": [
       "The configuration explanation now distinguishes source-document omission, which selects PipelineConfig(), from normal lazy-field inheritance.",
-      "The explanation did not tell agents that live field help projects accepted enum input strings, including member names for non-string values."
+      "The explanation did not tell agents that live field help projects accepted enum input strings, including member names for non-string values.",
+      "The practitioner configuration map did not name the new optional TIFF compression family or distinguish its output scope from Zarr and viewer streams."
     ],
     "disposition": "revise",
     "validation": [
@@ -1347,7 +1366,8 @@
       "2026-09-08: targeted 0.8.3 authority-delta review, retaining the earlier full-page review. Checked affected catalogue ownership, code round-trip, runtime-setting and endpoint lifecycle claims against the changed declarations. Updated the code-editing, dtype, callable-authoring and connection explanations where behaviour changed. Dependency and version changes do not alter the retained installation or package-ownership descriptions. Focused source/ObjectState round-trip and callable-contract checks passed 53 tests; this is not a new whole-document audit.",
       "2026-09-09: Re-read this page against the changed source authorities for release 0.8.3; retained its Diataxis purpose and updated affected workflow claims.",
       "2026-09-09: Reviewed the page sections affected by exact manager-item navigation, selection recovery guidance, and the pyqt-reactive dependency floor change from 0.3.20 to 0.3.21. Generic selection and deferred dispatch remain in pyqt-reactive; domain window identities stay in OpenHCS. Navigation acceptance does not replace action revision guards. Installation extras, Python support, code-document apply, and experimental/runtime semantics are unchanged by this batch. Updated the MCP architecture and basic-interface navigation explanations; retained existing setup/ownership links rather than duplicating a version catalogue. Only the reviewed navigation/dependency authorities were refreshed, excluding the scientific threshold patch. Final parent gates: 176 OpenHCS and 463 pyqt-reactive tests passed, including deferred target removal; full fresh-agent trial remains separate acceptance evidence.",
-      "2026-09-22 PR #126 targeted authority-delta review: re-read the complete page against `openhcs/core/config.py`, `tests/unit/pyqt_gui/test_ui_agent_bridge.py`; retained the supported claims, findings, and disposition, then refreshed only these compared evidence hashes. Review scope and the separate blocking runtime evidence are recorded in `docs/audits/pr126_authority_delta_review_20260922.md`."
+      "2026-09-22 PR #126 targeted authority-delta review: re-read the complete page against `openhcs/core/config.py`, `tests/unit/pyqt_gui/test_ui_agent_bridge.py`; retained the supported claims, findings, and disposition, then refreshed only these compared evidence hashes. Review scope and the separate blocking runtime evidence are recorded in `docs/audits/pr126_authority_delta_review_20260922.md`.",
+      "2026-09-24 PR #129: re-read the complete inheritance explanation against the new registered TIFF config and added its disk-output scope to the existing mental model; exact fields remain generated. Review scope is recorded in `docs/audits/pr129_tiff_compression_review_20260924.md`."
     ]
   },
   {
@@ -1461,7 +1481,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       }
     ],
@@ -1550,7 +1570,7 @@
       },
       {
         "path": "external/PolyStore/src/polystore/config.py",
-        "sha256": "241f728c991b9a4ac4d4440bba9bc08b5d89d23e7f8b3b9fcbdc18eb562a9bbc",
+        "sha256": "62c8acad3da3abed8ccf7f1166fc6a0d094be1c3e842cec6446780541df292a0",
         "role": "Owns the nominal Zarr compressor factories, Numcodecs creation, chunk strategy, and backend configuration."
       },
       {
@@ -2903,7 +2923,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -3085,7 +3105,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -3130,7 +3150,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -3240,7 +3260,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -3695,7 +3715,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
@@ -3755,7 +3775,7 @@
       },
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the default directory filenames and replicate-local normalization method."
       },
       {
@@ -4048,7 +4068,7 @@
     "authority": [
       {
         "path": "openhcs/core/config.py",
-        "sha256": "628b338097814f3d0297c28da8d016252214ff2253aee2e4946bad09f5890ea9",
+        "sha256": "ef81b50ee22b8da69513fd50d6e45a929117fa4bfaa62a20ef08a4c02531c043",
         "role": "Declares the supported OpenHCS configuration dataclasses, nested scopes, defaults, and field help metadata."
       },
       {
diff --git a/docs/source/concepts/storage_system.rst b/docs/source/concepts/storage_system.rst
index 23a0effbda..e788acf197 100644
--- a/docs/source/concepts/storage_system.rst
+++ b/docs/source/concepts/storage_system.rst
@@ -26,6 +26,18 @@ enum. OpenHCS contributes a fieldless registered subtype so those exact storage
 identities participate in global, pipeline, and step configuration without a
 second enum or field declaration.
 
+Disk TIFF compression
+---------------------
+
+``TiffConfig`` controls lossless compression for disk-backed TIFF outputs,
+including ordinary main-flow images and explicitly materialized named images.
+It is separate from Zarr compression and does not change non-TIFF artifacts or
+viewer streams. The default ``NONE`` retains uncompressed output; ``DEFLATE``
+uses the declared ``compression_level`` from 1 to 9. PolyStore owns the codec
+and writer behavior, while OpenHCS resolves the configuration for a pipeline
+and passes it to disk materialization. See :doc:`../reference/configuration`
+for exact fields and defaults.
+
 Artifacts first, paths second
 -----------------------------
 
diff --git a/docs/source/guide_for_biologists/configuration_reference.rst b/docs/source/guide_for_biologists/configuration_reference.rst
index 033b6a574e..801fbdeadf 100644
--- a/docs/source/guide_for_biologists/configuration_reference.rst
+++ b/docs/source/guide_for_biologists/configuration_reference.rst
@@ -120,6 +120,13 @@ Storage, paths, and persistence
   Read, intermediate, and persistent storage choices plus Zarr compression and
   chunking.
 
+``TiffConfig``
+  Optional lossless compression for disk-backed TIFF output, including saved
+  main-flow images and named image artifacts. The default is uncompressed;
+  enabling ``DEFLATE`` does not affect Zarr, other file formats, or viewer
+  streaming. The codec and level are resolved with the pipeline configuration
+  before execution.
+
 ``PathPlanningConfig``
   Output workspace/root placement, directory naming, and which processed wells
   seed the automatic main-flow output plate. ``well_filter=0`` keeps that
diff --git a/external/PolyStore b/external/PolyStore
index 9588e0c2cb..fc1d297dc4 160000
--- a/external/PolyStore
+++ b/external/PolyStore
@@ -1 +1 @@
-Subproject commit 9588e0c2cb76548fc4865a5670015a591223f284
+Subproject commit fc1d297dc45176057f420712aa616d11757be863

From 52b6cdb5d6515a585fb94a1d34beb829f69f98a6 Mon Sep 17 00:00:00 2001
From: Tristan Simas <tristan.simas@mail.mcgill.ca>
Date: Thu, 24 Sep 2026 01:18:32 -0400
Subject: [PATCH 3/6] Format TIFF materialization changes for CI

---
 docs/audits/architecture_a_m.json                           | 2 +-
 docs/audits/architecture_n_z_development.json               | 2 +-
 docs/audits/pr129_tiff_compression_review_20260924.md       | 6 ++++++
 docs/audits/user_docs.json                                  | 2 +-
 openhcs/core/steps/function_artifact_materialization.py     | 4 +---
 openhcs/processing/materialization/core.py                  | 4 +++-
 .../test_function_artifact_materialization_io_hotpath.py    | 3 ++-
 7 files changed, 15 insertions(+), 8 deletions(-)

diff --git a/docs/audits/architecture_a_m.json b/docs/audits/architecture_a_m.json
index fc58681038..fa97e154e7 100644
--- a/docs/audits/architecture_a_m.json
+++ b/docs/audits/architecture_a_m.json
@@ -188,7 +188,7 @@
       },
       {
         "path": "openhcs/processing/materialization/core.py",
-        "sha256": "e79e734ce159f54eee10e7238b0b00a6a03e065af3c3c171e6934a3480a162fd",
+        "sha256": "1f5a89a1eb50766ef093df3fece16d6bb03422b92d062fe8ae6471656b1ebd45",
         "role": "Owns writer runtime-path selection before rendering and the shared ROI target request."
       }
     ],
diff --git a/docs/audits/architecture_n_z_development.json b/docs/audits/architecture_n_z_development.json
index 2110b5c60d..3c9d55f196 100644
--- a/docs/audits/architecture_n_z_development.json
+++ b/docs/audits/architecture_n_z_development.json
@@ -1020,7 +1020,7 @@
       },
       {
         "path": "openhcs/processing/materialization/core.py",
-        "sha256": "e79e734ce159f54eee10e7238b0b00a6a03e065af3c3c171e6934a3480a162fd",
+        "sha256": "1f5a89a1eb50766ef093df3fece16d6bb03422b92d062fe8ae6471656b1ebd45",
         "role": "Nominal artifact materialisation and ROI projection strategies."
       },
       {
diff --git a/docs/audits/pr129_tiff_compression_review_20260924.md b/docs/audits/pr129_tiff_compression_review_20260924.md
index fa63778bd6..10342c0252 100644
--- a/docs/audits/pr129_tiff_compression_review_20260924.md
+++ b/docs/audits/pr129_tiff_compression_review_20260924.md
@@ -28,3 +28,9 @@ Sphinx HTML build succeeded with warnings treated as errors, and 15 focused
 documentation, MCP, and TIFF-output tests passed. These checks do not waive
 the separate published-dependency readiness gate; PolyStore's new source has
 not been published as a new release.
+
+The first CI pass found three Black-only formatting differences. After running
+the pinned formatter, the changed materialization owner files differ only in
+line wrapping. I rechecked the complete analysis-consolidation, ROI, and storage
+pages against those unchanged semantics before refreshing their three affected
+authority digests. The reformatted test file is not a recorded audit authority.
diff --git a/docs/audits/user_docs.json b/docs/audits/user_docs.json
index 66da81029c..9fc95f08c2 100644
--- a/docs/audits/user_docs.json
+++ b/docs/audits/user_docs.json
@@ -891,7 +891,7 @@
       },
       {
         "path": "openhcs/core/steps/function_artifact_materialization.py",
-        "sha256": "d25982897fb41b7bf392c3e85f4b5ac4f711c7219ead60833edd762e559cc8fb",
+        "sha256": "18c809a2d511501c4e308f6e92c18d5bb59744d4d3f59bb2bfc2507f2a2bdd03",
         "role": "Owns the rules that materialise function outputs through the configured storage backend."
       },
       {
diff --git a/openhcs/core/steps/function_artifact_materialization.py b/openhcs/core/steps/function_artifact_materialization.py
index e8923bb942..6bfc6e5b63 100644
--- a/openhcs/core/steps/function_artifact_materialization.py
+++ b/openhcs/core/steps/function_artifact_materialization.py
@@ -408,9 +408,7 @@ def backend_kwargs(
             result[backend] = RawBackendKwargs(
                 values,
                 tiff_config=(
-                    kwargs.tiff_config
-                    if isinstance(kwargs, RawBackendKwargs)
-                    else None
+                    kwargs.tiff_config if isinstance(kwargs, RawBackendKwargs) else None
                 ),
             )
 
diff --git a/openhcs/processing/materialization/core.py b/openhcs/processing/materialization/core.py
index 2dda9451a0..437f42ab19 100644
--- a/openhcs/processing/materialization/core.py
+++ b/openhcs/processing/materialization/core.py
@@ -175,7 +175,9 @@ def to_filemanager_kwargs(
         output: Output,
     ) -> dict:
         values = dict(self.values)
-        if self.tiff_config is not None and self.tiff_config.applies_to_path(output.path):
+        if self.tiff_config is not None and self.tiff_config.applies_to_path(
+            output.path
+        ):
             values["tiff_config"] = self.tiff_config
         return values
 
diff --git a/tests/unit/test_function_artifact_materialization_io_hotpath.py b/tests/unit/test_function_artifact_materialization_io_hotpath.py
index 3a046f5758..b6627f4cfa 100644
--- a/tests/unit/test_function_artifact_materialization_io_hotpath.py
+++ b/tests/unit/test_function_artifact_materialization_io_hotpath.py
@@ -54,7 +54,8 @@ def test_persistent_tiff_kwargs_apply_only_to_tiff_outputs() -> None:
     assert tuple(output.path for output in batches[0][0]) == ("/results/summary.csv",)
     assert batches[0][1] == {}
     assert tuple(output.path for output in batches[1][0]) == (
-        "/results/labels.tif", "/results/labels2.tiff"
+        "/results/labels.tif",
+        "/results/labels2.tiff",
     )
     assert batches[1][1] == {"tiff_config": config}
 

From cd86043c064a3c2f356e3006877aa070f15f0912 Mon Sep 17 00:00:00 2001
From: Tristan Simas <tristan.simas@mail.mcgill.ca>
Date: Thu, 24 Sep 2026 02:34:08 -0400
Subject: [PATCH 4/6] docs: explain per-callable 8-bit output versus TIFF
 compression

---
 docs/audits/user_docs.json                  | 36 +++++++++++++---
 docs/source/concepts/storage_system.rst     |  5 +++
 docs/source/user_guide/dtype_conversion.rst | 48 ++++++++++++++++++++-
 3 files changed, 82 insertions(+), 7 deletions(-)

diff --git a/docs/audits/user_docs.json b/docs/audits/user_docs.json
index 9fc95f08c2..228e84aa1e 100644
--- a/docs/audits/user_docs.json
+++ b/docs/audits/user_docs.json
@@ -871,7 +871,7 @@
   },
   {
     "path": "docs/source/concepts/storage_system.rst",
-    "source_sha256": "e7e77ea48bfda5701e5c309561400ebc3d10a95aad8824c05c7561e7474882b4",
+    "source_sha256": "6457c0c132bd45f195274e51b255f45713b5efda9ee7ada352de556ac4aa1dde",
     "audience": [
       "pipeline authors",
       "storage integrators"
@@ -909,6 +909,11 @@
         "sha256": "cf089b8c79f86099a7cea1b6cbe43ceaec6331196a44b43183f2e64b7746c219",
         "role": "Applies TIFF codec settings in the disk writer without changing other formats."
       },
+      {
+        "path": "external/arraybridge/src/arraybridge/decorators.py",
+        "sha256": "99823105b0ae59054df1d84013633b8b6628d0a6dc3326383199ac7c65c69bed",
+        "role": "Applies declared dtype conversion to a callable result before materialisation can persist it."
+      },
       {
         "path": "tests/unit/test_runtime_value_store.py",
         "sha256": "8900a7b83b59d0a40f9698dbafaaba778df982f9d7a0b628f80eab97335aeab0",
@@ -921,7 +926,8 @@
       }
     ],
     "findings": [
-      "The storage explanation did not distinguish optional disk-TIFF compression from Zarr compression or semantic materialization."
+      "The storage explanation did not distinguish optional disk-TIFF compression from Zarr compression or semantic materialization.",
+      "The compression explanation did not contrast lossless codec selection with the existing value-changing callable dtype policy."
     ],
     "disposition": "revise",
     "validation": [
@@ -935,7 +941,8 @@
       "2026-09-16: Re-read the complete explanation against runtime artifact materialization changes. Added the semantic-versus-filename identity boundary and confirmed that path completion does not mutate artifact metadata; 249 focused materialization and adjacent runtime tests passed.",
       "2026-09-22 PR #126 targeted authority-delta review: re-read the complete page against `openhcs/core/config.py`; retained the supported claims, findings, and disposition, then refreshed only these compared evidence hashes. Review scope and the separate blocking runtime evidence are recorded in `docs/audits/pr126_authority_delta_review_20260922.md`.",
       "2026-09-22 PR #126 integrated-repair follow-up: re-read the complete page and the final owner/test changes in `openhcs/core/steps/function_artifact_materialization.py`. Scalar image materialization now selects the execution scope matching the complete source address, deduplicates equivalent repeated group records, and rejects conflicts; the documented separation of semantic source identity, filename completion, runtime records, and persistence remains accurate. Refreshed only these compared evidence hashes; details are retained in `docs/audits/pr126_authority_delta_review_20260922.md`.",
-      "2026-09-24 PR #129: re-read the complete explanation against the changed config, materialization, PolyStore writer, and exact-roundtrip test authorities; added the disk-TIFF compression boundary without copying exact generated fields. Review scope is recorded in `docs/audits/pr129_tiff_compression_review_20260924.md`."
+      "2026-09-24 PR #129: re-read the complete explanation against the changed config, materialization, PolyStore writer, and exact-roundtrip test authorities; added the disk-TIFF compression boundary without copying exact generated fields. Review scope is recorded in `docs/audits/pr129_tiff_compression_review_20260924.md`.",
+      "2026-09-24: re-read the complete explanation and checked the ArrayBridge dtype wrapper against the PolyStore TIFF writer; documented that the codec preserves the callable-produced dtype, while a callable-level conversion changes it before persistence."
     ]
   },
   {
@@ -3706,7 +3713,7 @@
   },
   {
     "path": "docs/source/user_guide/dtype_conversion.rst",
-    "source_sha256": "15887645e3b1f7ffc098364060108c42fcd72f2be9de9968ece8f3610ed74bd1",
+    "source_sha256": "c95144eee07fe4134768fd2e839cb25dfaa9d61e9794332c8481ccfc39a95d4c",
     "audience": [
       "pipeline authors"
     ],
@@ -3728,6 +3735,21 @@
         "sha256": "99823105b0ae59054df1d84013633b8b6628d0a6dc3326383199ac7c65c69bed",
         "role": "Declares decorators that write independent input, output, and execution memory roles plus dtype policy."
       },
+      {
+        "path": "external/arraybridge/src/arraybridge/array_operations.py",
+        "sha256": "7e9ebda3d058702cdf8662dc5ab1faf1254649f3cbde76fa0adcbe02677fa103",
+        "role": "Defines NumPy float-to-integer scaling and integer-to-integer casting at the callable dtype boundary."
+      },
+      {
+        "path": "openhcs/processing/backends/processors/numpy_processor.py",
+        "sha256": "311634ec55ec8ddefe05118329d208e4b33df86f81d54ca4e258e7f4d2dbc980",
+        "role": "Declares the decorated projection function used in the 8-bit materialisation example."
+      },
+      {
+        "path": "external/PolyStore/src/polystore/disk.py",
+        "sha256": "cf089b8c79f86099a7cea1b6cbe43ceaec6331196a44b43183f2e64b7746c219",
+        "role": "Writes materialised TIFF pixels at the dtype supplied by the processing result."
+      },
       {
         "path": "tests/unit/test_callable_contract.py",
         "sha256": "493f76a54f5fe024ca8f10c53b1f810b8c369626ad7141205b42ef3a78282137",
@@ -3740,7 +3762,8 @@
       }
     ],
     "findings": [
-      "The task guide told users to change a desktop or step setting without naming the control or showing an executable override."
+      "The task guide told users to change a desktop or step setting without naming the control or showing an executable override.",
+      "The callable override lacked a concrete 8-bit materialisation example and warnings about NumPy scaling, integer wrapping, downstream values, and auxiliary outputs."
     ],
     "disposition": "revise",
     "validation": [
@@ -3751,7 +3774,8 @@
       "Passed ./.venv/bin/python -m sphinx -E -W --keep-going -b html docs/source <temporary-build-directory>: 153 source files rendered without warnings.",
       "On 2026-08-24, re-read the complete page against the changed declaration, dependency, UI state, knowledge, and test authorities named by this record; the documented behavior and ownership boundaries remain accurate.",
       "2026-09-08: targeted 0.8.3 authority-delta review, retaining the earlier full-page review. Checked affected catalogue ownership, code round-trip, runtime-setting and endpoint lifecycle claims against the changed declarations. Updated the code-editing, dtype, callable-authoring and connection explanations where behaviour changed. Dependency and version changes do not alter the retained installation or package-ownership descriptions. Focused source/ObjectState round-trip and callable-contract checks passed 53 tests; this is not a new whole-document audit.",
-      "2026-09-22 PR #126 targeted authority-delta review: re-read the complete page against `openhcs/core/config.py`; retained the supported claims, findings, and disposition, then refreshed only these compared evidence hashes. Review scope and the separate blocking runtime evidence are recorded in `docs/audits/pr126_authority_delta_review_20260922.md`."
+      "2026-09-22 PR #126 targeted authority-delta review: re-read the complete page against `openhcs/core/config.py`; retained the supported claims, findings, and disposition, then refreshed only these compared evidence hashes. Review scope and the separate blocking runtime evidence are recorded in `docs/audits/pr126_authority_delta_review_20260922.md`.",
+      "2026-09-24: re-read the full how-to and verified the new callable-level UINT8 materialisation example instantiates in the source checkout; direct NumPy-backed projection checks confirmed float scaling and integer wrapping. Reviewed ArrayBridge wrapper, NumPy scaling, the example callable, and the disk TIFF writer."
     ]
   },
   {
diff --git a/docs/source/concepts/storage_system.rst b/docs/source/concepts/storage_system.rst
index e788acf197..66f05d5944 100644
--- a/docs/source/concepts/storage_system.rst
+++ b/docs/source/concepts/storage_system.rst
@@ -38,6 +38,11 @@ and writer behavior, while OpenHCS resolves the configuration for a pipeline
 and passes it to disk materialization. See :doc:`../reference/configuration`
 for exact fields and defaults.
 
+Compression preserves the dtype and pixel values produced by the callable.
+For a smaller 8-bit display image, set the existing callable-level dtype policy
+on the image-producing function instead; this changes values before storage.
+See :doc:`../user_guide/dtype_conversion` for the conversion boundaries.
+
 Artifacts first, paths second
 -----------------------------
 
diff --git a/docs/source/user_guide/dtype_conversion.rst b/docs/source/user_guide/dtype_conversion.rst
index 0f020902d6..a410a1cb63 100644
--- a/docs/source/user_guide/dtype_conversion.rst
+++ b/docs/source/user_guide/dtype_conversion.rst
@@ -27,13 +27,59 @@ The equivalent step declaration is:
 
 .. code-block:: python
 
-   from arraybridge.decorators import DtypeConversion
    from openhcs.core.config import LazyDtypeConfig
+   from arraybridge.decorators import DtypeConversion
 
    step.dtype_config = LazyDtypeConfig(
        default_dtype_conversion=DtypeConversion.PRESERVE_INPUT,
    )
 
+Save an 8-bit visualisation
+---------------------------
+
+For a display image that does not need its original precision, set ``UINT8``
+on the image-producing callable in the function pattern and materialise that
+step's result:
+
+.. code-block:: python
+
+   from openhcs.core.config import LazyDtypeConfig, LazyStepMaterializationConfig
+   from openhcs.core.steps.function_step import FunctionStep
+   from openhcs.processing.backends.processors.numpy_processor import create_projection
+   from arraybridge.decorators import DtypeConversion
+
+   preview_step = FunctionStep(
+       func=(
+           create_projection,
+           {
+               "dtype_config": LazyDtypeConfig(
+                   default_dtype_conversion=DtypeConversion.UINT8,
+               ),
+           },
+       ),
+       name="8-bit projection for review",
+       step_materialization_config=LazyStepMaterializationConfig(enabled=True),
+   )
+
+Use this example with a floating-point image stack. The callable-level policy
+converts the main result before materialisation. When TIFF is the selected
+output format, the disk file therefore contains 8-bit pixels.
+The policy belongs to this callable occurrence, not to every function in the
+pipeline. Later steps using this result also receive its 8-bit values, so keep
+the conversion on a terminal review route if analysis still needs full
+precision.
+
+Check the values before choosing this policy. For NumPy-backed callables,
+float-to-``UINT8`` conversion scales the minimum and maximum of each
+non-constant callable result to the 8-bit range. Integer-to-``UINT8``
+conversion casts instead: values outside 0--255 can wrap. Neither is suitable
+for preserving quantitative intensities or object-label identities. A
+tuple-returning callable converts only its first, main result; it does not
+convert auxiliary named outputs.
+
+To save space without changing pixel values, use lossless disk TIFF compression
+instead. See :doc:`../concepts/storage_system` for the separate storage policy.
+
 Compile again after changing the policy. Do not cast merely to cross
 NumPy/CuPy/Torch boundaries; memory conversion and dtype policy are separate
 declarations.

From f2310ebc2f127e8af58f445b56188c06ec32e8a8 Mon Sep 17 00:00:00 2001
From: Tristan Simas <tristan.simas@mail.mcgill.ca>
Date: Thu, 24 Sep 2026 02:58:46 -0400
Subject: [PATCH 5/6] Require published PolyStore TIFF compression release

---
 docs/audits/architecture_a_m.json                |  2 +-
 docs/audits/architecture_n_z_development.json    | 16 ++++++++--------
 .../pr129_tiff_compression_review_20260924.md    | 16 +++++++++++++---
 docs/audits/project_surface.json                 |  2 +-
 docs/audits/user_docs.json                       | 14 +++++++-------
 external/PolyStore                               |  2 +-
 pyproject.toml                                   |  2 +-
 7 files changed, 32 insertions(+), 22 deletions(-)

diff --git a/docs/audits/architecture_a_m.json b/docs/audits/architecture_a_m.json
index fa97e154e7..a4e273211a 100644
--- a/docs/audits/architecture_a_m.json
+++ b/docs/audits/architecture_a_m.json
@@ -1198,7 +1198,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Pins the eight first-party package constraints and documents their installed integration surface."
       },
       {
diff --git a/docs/audits/architecture_n_z_development.json b/docs/audits/architecture_n_z_development.json
index 3c9d55f196..b73c6fe04f 100644
--- a/docs/audits/architecture_n_z_development.json
+++ b/docs/audits/architecture_n_z_development.json
@@ -1408,7 +1408,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       }
     ],
@@ -1646,7 +1646,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       },
       {
@@ -1719,7 +1719,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package-discovery, and installed entry-point authority."
       },
       {
@@ -2659,7 +2659,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       },
       {
@@ -2763,7 +2763,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       },
       {
@@ -2811,7 +2811,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       },
       {
@@ -3521,7 +3521,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       },
       {
@@ -3712,7 +3712,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Current Python support, dependency, package discovery, and entry-point authority."
       }
     ],
diff --git a/docs/audits/pr129_tiff_compression_review_20260924.md b/docs/audits/pr129_tiff_compression_review_20260924.md
index 10342c0252..652e74423a 100644
--- a/docs/audits/pr129_tiff_compression_review_20260924.md
+++ b/docs/audits/pr129_tiff_compression_review_20260924.md
@@ -25,12 +25,22 @@ are the declarations, implementations, and tests recorded in the JSON audit
 entries. The changed page and authority digests were refreshed only after this
 comparison. Documentation validation passed for 155 audited sources, the full
 Sphinx HTML build succeeded with warnings treated as errors, and 15 focused
-documentation, MCP, and TIFF-output tests passed. These checks do not waive
-the separate published-dependency readiness gate; PolyStore's new source has
-not been published as a new release.
+documentation, MCP, and TIFF-output tests passed. At this initial review,
+the separate published-dependency readiness gate remained open because the
+PolyStore change had not yet been released.
 
 The first CI pass found three Black-only formatting differences. After running
 the pinned formatter, the changed materialization owner files differ only in
 line wrapping. I rechecked the complete analysis-consolidation, ROI, and storage
 pages against those unchanged semantics before refreshing their three affected
 authority digests. The reformatted test file is not a recorded audit authority.
+
+## Published-dependency follow-up
+
+PolyStore PR #11 was merged and released as v0.2.19. Its publish workflow
+passed, and both the wheel and source distribution are present on PyPI.
+OpenHCS now requires `polystore>=0.2.19,<0.3` and pins the PolyStore
+submodule to release commit `0efe67fdd14985bf90cee6e0f0c4735d41d265d1`.
+The 17 documentation audit entries that depend on `pyproject.toml` were
+rechecked against the new dependency floor and their authority digests
+refreshed. No affected explanatory page asserted the prior floor.
diff --git a/docs/audits/project_surface.json b/docs/audits/project_surface.json
index 5f0ca69728..ab29a11a7f 100644
--- a/docs/audits/project_surface.json
+++ b/docs/audits/project_surface.json
@@ -12,7 +12,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the published README, Python range, package dependencies, optional surfaces, console commands, and project links."
       },
       {
diff --git a/docs/audits/user_docs.json b/docs/audits/user_docs.json
index 228e84aa1e..e94402a95d 100644
--- a/docs/audits/user_docs.json
+++ b/docs/audits/user_docs.json
@@ -171,7 +171,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the package version, Python requirement, dependency extras, scripts, and distribution metadata."
       },
       {
@@ -707,7 +707,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the package version, Python requirement, dependency extras, scripts, and distribution metadata."
       },
       {
@@ -957,7 +957,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the package version, Python requirement, dependency extras, scripts, and distribution metadata."
       },
       {
@@ -1676,7 +1676,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the package version, Python requirement, dependency extras, scripts, and distribution metadata."
       },
       {
@@ -2350,7 +2350,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Includes the complete openhcs/omero deployment and plugin bundle in installed distributions."
       },
       {
@@ -2863,7 +2863,7 @@
     "authority": [
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the package version, Python requirement, dependency extras, scripts, and distribution metadata."
       },
       {
@@ -3496,7 +3496,7 @@
       },
       {
         "path": "pyproject.toml",
-        "sha256": "61621859d0f780d2d3e004782f242ef923d6cd1e83bb3bbc9761197ba33a4165",
+        "sha256": "6217b5f029796edcd83aa47fb8632d37aa7552344755c578fa4f181a6b23282d",
         "role": "Declares the package version, Python requirement, dependency extras, scripts, and distribution metadata."
       }
     ],
diff --git a/external/PolyStore b/external/PolyStore
index fc1d297dc4..0efe67fdd1 160000
--- a/external/PolyStore
+++ b/external/PolyStore
@@ -1 +1 @@
-Subproject commit fc1d297dc45176057f420712aa616d11757be863
+Subproject commit 0efe67fdd14985bf90cee6e0f0c4735d41d265d1
diff --git a/pyproject.toml b/pyproject.toml
index b20d05c0c7..cede0e82e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -102,7 +102,7 @@ dependencies = [
     "python-introspect>=0.1.14,<0.2",
     "metaclass-registry>=0.2.1,<0.3",
     "arraybridge>=0.3.4,<0.4",
-    "polystore>=0.2.18,<0.3",
+    "polystore>=0.2.19,<0.3",
     "pyqt-reactive>=0.3.24,<0.4",
 ]
 

From 612f59309cbfb5f0d476b3fee8867c7c95b41291 Mon Sep 17 00:00:00 2001
From: Tristan Simas <tristan.simas@mail.mcgill.ca>
Date: Thu, 24 Sep 2026 03:04:02 -0400
Subject: [PATCH 6/6] Keep gallery type-only execution DTO out of website
 runtime

---
 docs/audits/architecture_n_z_development.json |  4 ++--
 .../pr129_tiff_compression_review_20260924.md |  9 ++++++++
 docs/audits/user_docs.json                    | 22 +++++++++----------
 scripts/gallery_catalog.py                    |  2 +-
 4 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/docs/audits/architecture_n_z_development.json b/docs/audits/architecture_n_z_development.json
index b73c6fe04f..78b0415766 100644
--- a/docs/audits/architecture_n_z_development.json
+++ b/docs/audits/architecture_n_z_development.json
@@ -2612,7 +2612,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns nominal gallery scenario identity, publication targets, representative images, copy, accessibility text, dimensions, contextual and stable-window capture targets, and derivative contracts."
       },
       {
@@ -2869,7 +2869,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the nominal gallery scenario lattice, stable-window and contextual capture targets, publication targets, derivative inventory, source evidence, card rendering, and generated release record."
       },
       {
diff --git a/docs/audits/pr129_tiff_compression_review_20260924.md b/docs/audits/pr129_tiff_compression_review_20260924.md
index 652e74423a..a38b161206 100644
--- a/docs/audits/pr129_tiff_compression_review_20260924.md
+++ b/docs/audits/pr129_tiff_compression_review_20260924.md
@@ -44,3 +44,12 @@ submodule to release commit `0efe67fdd14985bf90cee6e0f0c4735d41d265d1`.
 The 17 documentation audit entries that depend on `pyproject.toml` were
 rechecked against the new dependency floor and their authority digests
 refreshed. No affected explanatory page asserted the prior floor.
+
+The subsequent website CI run exposed an eager import in the gallery catalog:
+its source-capture request used `ExecutionConnectionSpec` only as a postponed
+type annotation, but importing that DTO loaded the scientific runtime into
+the deliberately minimal website environment. The import is now restricted to
+type checking. The gallery's runtime declarations, capture behavior, and
+published projections are unchanged. The 13 audited pages referencing the
+gallery catalog were checked for claims about those surfaces, and their
+authority digests were refreshed.
diff --git a/docs/audits/user_docs.json b/docs/audits/user_docs.json
index e94402a95d..79b610ca7a 100644
--- a/docs/audits/user_docs.json
+++ b/docs/audits/user_docs.json
@@ -1192,7 +1192,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the documentation-enabled Function Selector capture declaration, accessibility text, capture target, and generated visual projection."
       },
       {
@@ -1349,7 +1349,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the documentation-enabled global, pipeline, step, and nested function configuration capture declarations, accessibility text, capture targets, and generated visual projections."
       }
     ],
@@ -1557,7 +1557,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the documentation-enabled source-image browser capture, caption, accessibility text, dimensions, and source evidence."
       },
       {
@@ -1808,7 +1808,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the documentation-enabled synthetic generator, plate metadata, and live measurement result capture declarations used by the first-workflow tutorial."
       }
     ],
@@ -2832,7 +2832,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the landing-page workspace scenario, representative image, caption, description, alt text, dimensions, and release evidence."
       }
     ],
@@ -3219,7 +3219,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Projects every registered stable-window identity into its documentation scenario, capture target, filename, and accessibility text."
       },
       {
@@ -3396,7 +3396,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the lazy-inheritance scenario, representative poster, caption, description, alt text, dimensions, and release evidence."
       },
       {
@@ -3594,7 +3594,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the documentation-enabled Custom Function Manager capture declaration, accessibility text, capture target, and generated visual projection."
       },
       {
@@ -3922,7 +3922,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the documentation-enabled execution-log capture, caption, accessibility text, dimensions, and source evidence."
       }
     ],
@@ -3994,7 +3994,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the local-MCP endpoint-startup scenario, representative poster, caption, description, alt text, dimensions, and release evidence."
       },
       {
@@ -4142,7 +4142,7 @@
       },
       {
         "path": "scripts/gallery_catalog.py",
-        "sha256": "e6516488d7024771c35faf1a25d3ec3abc3b2f21830a8b318c9665d9469c5c0a",
+        "sha256": "bda42a36c1c510af7ac587dc2642548758d28c4a0061d581ebe38a5be4fb3743",
         "role": "Owns the Napari ROI-navigation and Fiji ROI-review scenarios, representative images, captions, descriptions, alt text, dimensions, and release evidence."
       }
     ],
diff --git a/scripts/gallery_catalog.py b/scripts/gallery_catalog.py
index c445344ca6..701d45636b 100644
--- a/scripts/gallery_catalog.py
+++ b/scripts/gallery_catalog.py
@@ -25,7 +25,6 @@
 from pyqt_reactive.services.system_monitor_actions import SystemMonitorAction
 from python_introspect import dataclass_from_mapping
 
-from openhcs.agent.dto.execution import ExecutionConnectionSpec
 from openhcs.agent.ui_bridge_actions import PlateManagerAction
 from openhcs.agent.ui_bridge_identities import (
     GlobalConfigWindowIdentity,
@@ -41,6 +40,7 @@
 from openhcs.serialization.json import JsonValue, to_jsonable
 
 if TYPE_CHECKING:
+    from openhcs.agent.dto.execution import ExecutionConnectionSpec
     from openhcs.pyqt_gui.services.step_scope_identity import StepEditorScope
 
 RELEASE_MEDIA_SCHEMA_VERSION = "openhcs.release-media.v7"