patchworks 1.2.0__tar.gz → 1.2.2__tar.gz

{patchworks-1.2.0 → patchworks-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: patchworks
-Version: 1.2.0
+Version: 1.2.2
 Summary: Tiled processing of arbitrarily large images with globally consistent labels
 Project-URL: Homepage, https://github.com/imcf/patchworks
 Project-URL: Issues, https://github.com/imcf/patchworks/issues
@@ -39,6 +39,7 @@ Requires-Dist: napari[all]>=0.7.1; extra == 'all'
 Requires-Dist: numpy<2.5; extra == 'all'
 Requires-Dist: nvidia-ml-py; extra == 'all'
 Requires-Dist: psutil; extra == 'all'
+Requires-Dist: pyqt6<6.10; extra == 'all'
 Requires-Dist: scikit-image; extra == 'all'
 Requires-Dist: tqdm; extra == 'all'
 Provides-Extra: bioio
@@ -80,6 +81,7 @@ Requires-Dist: lxml-html-clean; extra == 'napari'
 Requires-Dist: napari-chunked-regionprops>=0.1.0; extra == 'napari'
 Requires-Dist: napari[all]>=0.7.1; extra == 'napari'
 Requires-Dist: numpy<2.5; extra == 'napari'
+Requires-Dist: pyqt6<6.10; extra == 'napari'
 Provides-Extra: workflow
 Requires-Dist: openpyxl; extra == 'workflow'
 Requires-Dist: snakemake-executor-plugin-slurm; extra == 'workflow'

{patchworks-1.2.0 → patchworks-1.2.2}/cliff.toml

@@ -8,11 +8,13 @@ body = """
 - {% if commit.scope %}**{{ commit.scope }}**: {% endif %}{{ commit.message | split(pat="\n") | first }}
 {% endfor %}
 {% endfor %}\
-{% if github.contributors | length > 0 %}
+{% set contributor_commits = commits | unique(attribute="author.name") %}
+{% if contributor_commits | length > 0 %}
 ### 👥 Contributors
 
-{% for contributor in github.contributors %}\
-{% if contributor.username %}* @{{ contributor.username }}
+{% for c in contributor_commits %}\
+{% if c.github.username %}* @{{ c.github.username }}
+{% else %}* {{ c.author.name }}
 {% endif %}\
 {% endfor %}
 {% endif %}\

{patchworks-1.2.0 → patchworks-1.2.2}/docs/examples/dog.md

@@ -101,6 +101,68 @@ custom:
 See `workflow/config/config_cilia.yaml` for a full example, including
 deconvolution.
 
+### With deconvolution, on SLURM
+
+Add `decon_kwargs` under `custom.kwargs` — same keys as the plain-Python
+example above — and the segment job deconvolves each tile with
+`pycudadecon` before running the DoG detector:
+
+```yaml
+# config/config_cilia.yaml (excerpt)
+channel: 2
+tile_shape: [16, 1024, 1024]
+overlap: 30 # cover the PSF support (decon) + the DoG's high_sigma
+skip_empty: true
+
+method: "custom"
+label_name: "cilia_labels"
+custom:
+  module: "patchworks.plugins.dog"
+  function: "segment"
+  kwargs:
+    low_sigma: 1.0
+    high_sigma: 3.0
+    threshold: 0.02
+    decon_kwargs:
+      psf: "/path/to/psf.tif"
+      dxpsf: 0.1
+      dxdata: 0.1
+      dzpsf: 0.2
+      dzdata: 0.2
+      wavelength: 525
+      na: 1.4
+      nimm: 1.515
+```
+
+Run it exactly like a Cellpose config:
+
+```bash
+python -m snakemake --workflow-profile profile/slurm \
+                    --configfile config/config_cilia.yaml
+```
+
+Checklist specific to this config:
+
+- **Env:** the segment job's environment needs `patchworks[dog]`
+  (`pip install "patchworks[dog]"`) on top of whatever else it uses — plain
+  `dog_label_fn` only needs scipy, but `decon_kwargs` pulls in
+  `pycudadecon`.
+- **GPU always required:** `pycudadecon` is CUDA-only regardless of the
+  detector's own `use_gpu` flag, so `set-resources: segment:` in
+  `profile/slurm/config.yaml` must request a GPU (`slurm_extra:
+  "'--gres=gpu:1'"`) the same as for Cellpose.
+- **`overlap`:** widen it past the PSF support, not just past `high_sigma` —
+  a thin intensity/threshold halo isn't enough once deconvolution is in the
+  loop.
+- **`skip_empty`:** the `prepare` rule (`workflow/scripts/prepare_tiles.py`)
+  calls `estimate_empty_tiles()` before submitting any `segment` jobs,
+  regardless of `method`, so cilia/DoG runs skip background tiles exactly
+  like Cellpose runs — no extra config needed beyond `skip_empty: true`
+  (the default).
+- Run alongside `config_cyto.yaml`/`config_nuclei.yaml` via `config/multi.yaml`
+  to also get the cilia→cell/nucleus relation — see *Relating cilia to their
+  cell*, below.
+
 ## Relating cilia to their cell
 
 Segment the cell body with Cellpose and the cilia with `dog_label_fn` as two

{patchworks-1.2.0 → patchworks-1.2.2}/docs/guide/ome_zarr_napari.md

@@ -136,13 +136,18 @@ image found under `scan.zarr/labels/`:
 ```python
 from patchworks.plugins.napari import view_in_napari
 
-# auto-loads scan.zarr/labels/* as Labels layers:
+# auto-loads scan.zarr/labels/* as Labels layers, all image channels shown:
 view_in_napari("scan.zarr")
 
 # or point at a separate plain label store written with write_to=:
 view_in_napari("scan.zarr", labels="labels.zarr")
 ```
 
+By default every channel of the image is shown (`channel=None`), independent
+of which one you segmented on — Cellpose might run on channel 0 while you
+still want to see the whole multi-channel acquisition. Pass an int to view
+just one channel instead: `view_in_napari("scan.zarr", channel=0)`.
+
 !!! note
     napari ships in `patchworks[all]`, or install just it with
     `pip install "patchworks[napari]"`.

{patchworks-1.2.0 → patchworks-1.2.2}/pyproject.toml

@@ -77,6 +77,11 @@ imaris = ["imaris-ims-file-reader"]
 #   their backing dask/zarr arrays — the "Measure" dock widget. Formerly
 #   napari-dask-ndmeasure; renamed when its engine dropped dask_image.ndmeasure
 #   for a chunk-local map/merge that scales with chunk count, not object count.
+# - pyqt6 < 6.10: PyQt6-Qt6 6.10.2's Windows wheel fails to import (`DLL load
+#   failed while importing QtWidgets: The specified procedure could not be
+#   found`) — confirmed unrelated to napari/qtpy, reproduces on a bare
+#   `from PyQt6.QtWidgets import QApplication`. 6.9.1 works; excluding the
+#   whole 6.10.x line until a fixed release is confirmed.
 napari = [
     "napari[all]>=0.7.1",
     "numpy<2.5",
@@ -84,6 +89,7 @@ napari = [
     "lxml-html-clean",
     "glasbey",
     "napari-chunked-regionprops>=0.1.0",
+    "pyqt6<6.10",
 ]
 # workflow runs the Snakemake pipeline (per-tile SLURM jobs across GPUs).
 # openpyxl -> scripts/run_multi.py writes label_relations() output as an

{patchworks-1.2.0 → patchworks-1.2.2}/src/patchworks/plugins/napari.py

@@ -267,7 +267,7 @@ def view_in_napari(
     image: Union[da.Array, str, Path],
     labels: Union[da.Array, str, Path, None] = None,
     *,
-    channel: int | None = 0,
+    channel: int | None = None,
     labels_component: str = "labels",
     image_name: str = "image",
     labels_name: str = "labels",
@@ -290,7 +290,9 @@ def view_in_napari(
         place ``tile_process`` writes them by default — each as its own Labels
         layer. (Falls back to image-only if there are none.)
     channel : int or None, optional
-        Channel to display from the image (``None`` keeps all channels).
+        Channel to display from the image. ``None`` (default) shows every
+        channel — the segmentation channel doesn't need to match what you
+        view. Pass an int to show just that one.
     labels_component : str, optional
         Array name inside a plain-zarr label store (default ``"labels"``,
         matching ``tile_process``'s ``output_component``).