cellfinder 1.4.0__tar.gz → 1.9.0__tar.gz

{cellfinder-1.4.0 → cellfinder-1.9.0}/.github/workflows/test_and_deploy.yml

@@ -50,15 +50,25 @@ jobs:
       matrix:
         # Run all supported Python versions on linux
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
         # Include one windows and one macOS (arm based) run
         include:
           - os: macos-latest
-            python-version: "3.12"
+            python-version: "3.13"
           - os: windows-latest
-            python-version: "3.12"
+            python-version: "3.13"
 
     steps:
+      # Free up disk space on ubuntu runners
+      - name: Free Disk Space
+        if: matrix.os == 'ubuntu-latest'
+        uses: endersonmenezes/free-disk-space@6c4664f43348c8c7011b53488d5ca65e9fc5cd1a # v3
+        with:
+          remove_android: true
+          remove_dotnet: true
+          rm_cmd: 'rmz'
+          rmz_version: '3.1.1'
+
       - uses: actions/checkout@v4
       - name: Cache pooch data
         uses: actions/cache@v4
@@ -86,6 +96,15 @@ jobs:
           secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
+      # Run tests on napari main if this is a scheduled run
+      - name: Run tests on napari main
+        if: github.event_name == 'schedule'
+        uses: neuroinformatics-unit/actions/test@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
+          tox-args: '-e napari-dev'
+
       - name: Notify slack on scheduled failure
         if: failure() && github.event_name == 'schedule'
         uses: ravsamhq/notify-slack-action@v2
@@ -107,6 +126,15 @@ jobs:
       BRAINGLOBE_TEST_DATA_DIR: "~/.pooch_cache"
 
     steps:
+      # Free up disk space on ubuntu runners
+      - name: Free Disk Space
+        uses: endersonmenezes/free-disk-space@6c4664f43348c8c7011b53488d5ca65e9fc5cd1a # v3
+        with:
+          remove_android: true
+          remove_dotnet: true
+          rm_cmd: 'rmz'
+          rmz_version: '3.1.1'
+
       - uses: actions/checkout@v4
       - name: Cache brainglobe directory
         uses: actions/cache@v3
@@ -154,6 +182,15 @@ jobs:
       KERAS_BACKEND: torch
       CELLFINDER_TEST_DEVICE: cpu
     steps:
+      # Free up disk space on ubuntu runners
+      - name: Free Disk Space
+        uses: endersonmenezes/free-disk-space@6c4664f43348c8c7011b53488d5ca65e9fc5cd1a # v3
+        with:
+          remove_android: true
+          remove_dotnet: true
+          rm_cmd: 'rmz'
+          rmz_version: '3.1.1'
+
       - name: Cache brainglobe directory
         uses: actions/cache@v3
         with:
@@ -199,6 +236,11 @@ jobs:
     if: github.event_name == 'push' && github.ref_type == 'tag'
     runs-on: ubuntu-latest
     steps:
-    - uses: neuroinformatics-unit/actions/upload_pypi@v2
+    - uses: actions/download-artifact@v4
+      with:
+        name: artifact
+        path: dist
+    - uses: pypa/gh-action-pypi-publish@release/v1
       with:
-        secret-pypi-key: ${{ secrets.TWINE_API_KEY }}
+        user: __token__
+        password: ${{ secrets.TWINE_API_KEY }}

{cellfinder-1.4.0 → cellfinder-1.9.0}/.github/workflows/test_include_guard.yaml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - name: Install cellfinder via pip
         run: python -m pip install -e "."

{cellfinder-1.4.0 → cellfinder-1.9.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: cellfinder
-Version: 1.4.0
+Version: 1.9.0
 Summary: Automated 3D cell detection in large microscopy images
 Author-email: "Adam Tyson, Christian Niedworok, Charly Rousseau" <code@adamltyson.com>
 License: BSD-3-Clause
@@ -16,26 +16,27 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Image Recognition
-Requires-Python: >=3.10
+Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: brainglobe-utils>=0.5.0
 Requires-Dist: brainglobe-napari-io>=0.3.4
 Requires-Dist: dask[array]
-Requires-Dist: fancylog>=0.0.7
+Requires-Dist: fancylog>=0.6.0
 Requires-Dist: natsort
 Requires-Dist: numba
 Requires-Dist: numpy
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: keras>=3.7.0
-Requires-Dist: torch!=2.4,>=2.1.0
+Requires-Dist: torch>=2.4.1
 Requires-Dist: tifffile
 Requires-Dist: tqdm
+Requires-Dist: qt-niu
 Provides-Extra: dev
 Requires-Dist: black; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
@@ -52,23 +53,26 @@ Requires-Dist: brainglobe-napari-io; extra == "napari"
 Requires-Dist: magicgui; extra == "napari"
 Requires-Dist: napari-ndtiffs; extra == "napari"
 Requires-Dist: napari-plugin-engine>=0.1.4; extra == "napari"
-Requires-Dist: napari[pyqt5]; extra == "napari"
+Requires-Dist: napari[pyqt5]>=0.6.5; extra == "napari"
 Requires-Dist: pooch>=1; extra == "napari"
 Requires-Dist: qtpy; extra == "napari"
+Dynamic: license-file
 
 [![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
 [![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)
-[![Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)
+[![Anaconda version](https://anaconda.org/conda-forge/cellfinder/badges/version.svg)](https://anaconda.org/conda-forge/cellfinder)
+[![Napari hub](https://img.shields.io/endpoint?url=https://npe2api-git-add-shields-napari.vercel.app/api/shields/cellfinder)](https://napari-hub.org/plugins/cellfinder.html)
+[![PyPI Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)
 [![Wheel](https://img.shields.io/pypi/wheel/cellfinder.svg)](https://pypi.org/project/cellfinder)
 [![Development Status](https://img.shields.io/pypi/status/cellfinder.svg)](https://github.com/brainglobe/cellfinder)
 [![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/cellfinder/test_and_deploy.yml?branch=main)](https://github.com/brainglobe/cellfinder/actions)
 [![codecov](https://codecov.io/gh/brainglobe/cellfinder/branch/main/graph/badge.svg?token=nx1lhNI7ox)](https://codecov.io/gh/brainglobe/cellfinder)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
-[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 [![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/community/developers/index.html)
-[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
-
+[![image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fbrainglobe.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/brainglobe)
+[![Bluesky](https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff)](https://bsky.app/profile/brainglobe.info)
+[![Mastodon](https://img.shields.io/badge/Mastodon-6364FF?logo=mastodon&logoColor=fff)](https://mastodon.online/@brainglobe)
 # cellfinder
 
 cellfinder is software for automated 3D cell detection in very large 3D images (e.g., serial two-photon or lightsheet volumes of whole mouse brains).

{cellfinder-1.4.0 → cellfinder-1.9.0}/README.md

@@ -1,16 +1,18 @@
 [![Python Version](https://img.shields.io/pypi/pyversions/cellfinder.svg)](https://pypi.org/project/cellfinder)
 [![PyPI](https://img.shields.io/pypi/v/cellfinder.svg)](https://pypi.org/project/cellfinder)
-[![Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)
+[![Anaconda version](https://anaconda.org/conda-forge/cellfinder/badges/version.svg)](https://anaconda.org/conda-forge/cellfinder)
+[![Napari hub](https://img.shields.io/endpoint?url=https://npe2api-git-add-shields-napari.vercel.app/api/shields/cellfinder)](https://napari-hub.org/plugins/cellfinder.html)
+[![PyPI Downloads](https://pepy.tech/badge/cellfinder)](https://pepy.tech/project/cellfinder)
 [![Wheel](https://img.shields.io/pypi/wheel/cellfinder.svg)](https://pypi.org/project/cellfinder)
 [![Development Status](https://img.shields.io/pypi/status/cellfinder.svg)](https://github.com/brainglobe/cellfinder)
 [![Tests](https://img.shields.io/github/actions/workflow/status/brainglobe/cellfinder/test_and_deploy.yml?branch=main)](https://github.com/brainglobe/cellfinder/actions)
 [![codecov](https://codecov.io/gh/brainglobe/cellfinder/branch/main/graph/badge.svg?token=nx1lhNI7ox)](https://codecov.io/gh/brainglobe/cellfinder)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
-[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
+[![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/format.json)](https://github.com/astral-sh/ruff)[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)
 [![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 [![Contributions](https://img.shields.io/badge/Contributions-Welcome-brightgreen.svg)](https://brainglobe.info/community/developers/index.html)
-[![Twitter](https://img.shields.io/twitter/follow/brain_globe?style=social)](https://twitter.com/brain_globe)
-
+[![image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fbrainglobe.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/brainglobe)
+[![Bluesky](https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky&logoColor=fff)](https://bsky.app/profile/brainglobe.info)
+[![Mastodon](https://img.shields.io/badge/Mastodon-6364FF?logo=mastodon&logoColor=fff)](https://mastodon.online/@brainglobe)
 # cellfinder
 
 cellfinder is software for automated 3D cell detection in very large 3D images (e.g., serial two-photon or lightsheet volumes of whole mouse brains).

{cellfinder-1.4.0 → cellfinder-1.9.0}/cellfinder/cli_migration_warning.py

@@ -1,5 +1,7 @@
 import argparse
 
+from cellfinder.core import logger
+
 BRAINGLOBE_WORKFLOWS = "https://github.com/brainglobe/brainglobe-workflows"
 NEW_NAME = "brainmapper"
 BLOG_POST = "https://brainglobe.info/blog/version1/core_and_napari_merge.html"
@@ -36,7 +38,7 @@ def cli_catch() -> None:
         ),
     )
 
-    print(
+    logger.warning(
         "Hey, it looks like you're trying to run the old command-line tool.",
         "This workflow has been renamed and moved -",
         " you can now find it in the brainglobe-workflows package:\n",

{cellfinder-1.4.0 → cellfinder-1.9.0}/cellfinder/core/classify/classify.py

@@ -11,7 +11,7 @@ from brainglobe_utils.general.system import get_num_processes
 from cellfinder.core import logger, types
 from cellfinder.core.classify.cube_generator import CubeGeneratorFromFile
 from cellfinder.core.classify.tools import get_model
-from cellfinder.core.train.train_yml import depth_type, models
+from cellfinder.core.train.train_yaml import depth_type, models
 
 
 def main(
@@ -19,8 +19,8 @@ def main(
     signal_array: types.array,
     background_array: types.array,
     n_free_cpus: int,
-    voxel_sizes: Tuple[int, int, int],
-    network_voxel_sizes: Tuple[int, int, int],
+    voxel_sizes: Tuple[float, float, float],
+    network_voxel_sizes: Tuple[float, float, float],
     batch_size: int,
     cube_height: int,
     cube_width: int,
@@ -29,12 +29,58 @@ def main(
     model_weights: Optional[os.PathLike],
     network_depth: depth_type,
     max_workers: int = 3,
+    pin_memory: bool = False,
     *,
     callback: Optional[Callable[[int], None]] = None,
 ) -> List[Cell]:
     """
     Parameters
     ----------
+
+    points: List of Cell objects
+        The potential cells to classify.
+    signal_array : numpy.ndarray or dask array
+        3D array representing the signal data in z, y, x order.
+    background_array : numpy.ndarray or dask array
+        3D array representing the signal data in z, y, x order.
+    n_free_cpus : int
+        How many CPU cores to leave free.
+    voxel_sizes : 3-tuple of floats
+        Size of your voxels in the z, y, and x dimensions.
+    network_voxel_sizes : 3-tuple of floats
+        Size of the pre-trained network's voxels in the z, y, and x dimensions.
+    batch_size : int
+        How many potential cells to classify at one time. The GPU/CPU
+        memory must be able to contain at once this many data cubes for
+        the models. For performance-critical applications, tune to maximize
+        memory usage without running out. Check your GPU/CPU memory to verify
+        it's not full.
+    cube_height: int
+        The height of the data cube centered on the cell used for
+        classification. Defaults to `50`.
+    cube_width: int
+        The width of the data cube centered on the cell used for
+        classification. Defaults to `50`.
+    cube_depth: int
+        The depth of the data cube centered on the cell used for
+        classification. Defaults to `20`.
+    trained_model : Optional[Path]
+        Trained model file path (home directory (default) -> pretrained
+        weights).
+    model_weights : Optional[Path]
+        Model weights path (home directory (default) -> pretrained
+        weights).
+    network_depth: str
+        The network depth to use during classification. Defaults to `"50"`.
+    max_workers: int
+        The number of sub-processes to use for data loading / processing.
+        Defaults to 8.
+    pin_memory: bool
+        Pins data to be sent to the GPU to the CPU memory. This allows faster
+        GPU data speeds, but can only be used if the data used by the GPU can
+        stay in the CPU RAM while the GPU uses it. I.e. there's enough RAM.
+        Otherwise, if there's a risk of the RAM being paged, it shouldn't be
+        used. Defaults to False.
     callback : Callable[int], optional
         A callback function that is called during classification. Called with
         the batch number once that batch has been classified.
@@ -70,7 +116,7 @@ def main(
     )
 
     if trained_model and Path(trained_model).suffix == ".h5":
-        print(
+        logger.warning(
             "Weights provided in place of the model, "
             "loading weights into default model."
         )
@@ -103,7 +149,7 @@ def main(
         points_list.append(cell)
 
     time_elapsed = datetime.now() - start_time
-    print(
+    logger.info(
         "Classfication complete - all points done in : {}".format(time_elapsed)
     )
 

{cellfinder-1.4.0 → cellfinder-1.9.0}/cellfinder/core/classify/tools.py

@@ -47,9 +47,19 @@ def get_model(
                 f"Setting model weights according to: {model_weights}",
             )
             if model_weights is None:
-                raise OSError("`model_weights` must be provided")
-            model.load_weights(model_weights)
-        return model
+                raise OSError(
+                    "`model_weights` must be provided for inference "
+                    "or continued training."
+                )
+            try:
+                model.load_weights(model_weights)
+            except (OSError, ValueError) as e:
+                raise ValueError(
+                    f"Error loading weights: {model_weights}.\n"
+                    "Provided weights don't match the model architecture.\n"
+                ) from e
+
+    return model
 
 
 def make_lists(

{cellfinder-1.4.0 → cellfinder-1.9.0}/cellfinder/core/detect/detect.py

@@ -48,12 +48,14 @@ def main(
     save_planes: bool = False,
     plane_directory: Optional[str] = None,
     batch_size: Optional[int] = None,
-    torch_device: str = "cpu",
-    use_scipy: bool = True,
-    split_ball_xy_size: int = 3,
-    split_ball_z_size: int = 3,
+    torch_device: Optional[str] = None,
+    pin_memory: bool = False,
+    split_ball_xy_size: float = 6,
+    split_ball_z_size: float = 15,
     split_ball_overlap_fraction: float = 0.8,
-    split_soma_diameter: int = 7,
+    n_splitting_iter: int = 10,
+    n_sds_above_mean_tiled_thresh: float = 10,
+    tiled_thresh_tile_size: float | None = None,
     *,
     callback: Optional[Callable[[int], None]] = None,
 ) -> List[Cell]:
@@ -62,69 +64,94 @@ def main(
 
     Parameters
     ----------
-    signal_array : numpy.ndarray
-        3D array representing the signal data.
-
+    signal_array : numpy.ndarray or dask array
+        3D array representing the signal data in z, y, x order.
     start_plane : int
-        Index of the starting plane for detection.
-
+        First plane index to process (inclusive, to process a subset of the
+        data).
     end_plane : int
-        Index of the ending plane for detection.
-
-    voxel_sizes : Tuple[float, float, float]
-        Tuple of voxel sizes in each dimension (z, y, x).
-
+        Last plane index to process (exclusive, to process a subset of the
+        data).
+    voxel_sizes : 3-tuple of floats
+        Size of your voxels in the z, y, and x dimensions (microns).
     soma_diameter : float
-        Diameter of the soma in physical units.
-
+        The expected in-plane (xy) soma diameter (microns).
     max_cluster_size : float
-        Maximum size of a cluster in physical units.
-
+        Largest detected cell cluster (in cubic um) where splitting
+        should be attempted. Clusters above this size will be labeled
+        as artifacts.
     ball_xy_size : float
-        Size of the XY ball used for filtering in physical units.
-
+        3d filter's in-plane (xy) filter ball size (microns).
     ball_z_size : float
-        Size of the Z ball used for filtering in physical units.
-
+        3d filter's axial (z) filter ball size (microns).
     ball_overlap_fraction : float
-        Fraction of overlap allowed between balls.
-
+        3d filter's fraction of the ball filter needed to be filled by
+        foreground voxels, centered on a voxel, to retain the voxel.
     soma_spread_factor : float
-        Spread factor for soma size.
-
+        Cell spread factor for determining the largest cell volume before
+        splitting up cell clusters. Structures with spherical volume of
+        diameter `soma_spread_factor * soma_diameter` or less will not be
+        split.
     n_free_cpus : int
-        Number of free CPU cores available for parallel processing.
-
+        How many CPU cores to leave free.
     log_sigma_size : float
-        Size of the sigma for the log filter.
-
+        Gaussian filter width (as a fraction of soma diameter) used during
+        2d in-plane Laplacian of Gaussian filtering.
     n_sds_above_mean_thresh : float
-        Number of standard deviations above the mean threshold.
-
+        Per-plane intensity threshold (the number of standard deviations
+        above the mean) of the filtered 2d planes used to mark pixels as
+        foreground or background.
     outlier_keep : bool, optional
         Whether to keep outliers during detection. Defaults to False.
-
     artifact_keep : bool, optional
         Whether to keep artifacts during detection. Defaults to False.
-
     save_planes : bool, optional
         Whether to save the planes during detection. Defaults to False.
-
     plane_directory : str, optional
         Directory path to save the planes. Defaults to None.
-
-    batch_size : int, optional
-        The number of planes to process in each batch. Defaults to 1.
-        For CPU, there's no benefit for a larger batch size. Only a memory
-        usage increase. For CUDA, the larger the batch size the better the
-        performance. Until it fills up the GPU memory - after which it
-        becomes slower.
-
+    batch_size: int
+        The number of planes of the original data volume to process at
+        once. The GPU/CPU memory must be able to contain this many planes
+        for all the filters. For performance-critical applications, tune to
+        maximize memory usage without running out. Check your GPU/CPU memory
+        to verify it's not full.
     torch_device : str, optional
-        The device on which to run the computation. By default, it's "cpu".
-        To run on a gpu, specify the PyTorch device name, such as "cuda" to
-        run on the first GPU.
-
+        The device on which to run the computation. If not specified (None),
+        "cuda" will be used if a GPU is available, otherwise "cpu".
+        You can also manually specify "cuda" or "cpu".
+    pin_memory: bool
+        Pins data to be sent to the GPU to the CPU memory. This allows faster
+        GPU data speeds, but can only be used if the data used by the GPU can
+        stay in the CPU RAM while the GPU uses it. I.e. there's enough RAM.
+        Otherwise, if there's a risk of the RAM being paged, it shouldn't be
+        used. Defaults to False.
+    split_ball_xy_size: float
+        Similar to `ball_xy_size`, except the value to use for the 3d
+        filter during cluster splitting.
+    split_ball_z_size: float
+        Similar to `ball_z_size`, except the value to use for the 3d filter
+        during cluster splitting.
+    split_ball_overlap_fraction: float
+        Similar to `ball_overlap_fraction`, except the value to use for the
+        3d filter during cluster splitting.
+    n_splitting_iter: int
+        The number of iterations to run the 3d filtering on a cluster. Each
+        iteration reduces the cluster size by the voxels not retained in
+        the previous iteration.
+    n_sds_above_mean_tiled_thresh : float
+        Per-plane, per-tile intensity threshold (the number of standard
+        deviations above the mean) for the filtered 2d planes used to mark
+        pixels as foreground or background. When used, (tile size is not zero)
+        a pixel is marked as foreground if its intensity is above both the
+        per-plane and per-tile threshold. I.e. it's above the set number of
+        standard deviations of the per-plane average and of the per-plane
+        per-tile average for the tile that contains it.
+    tiled_thresh_tile_size : float
+        The tile size used to tile the x, y plane to calculate the local
+        average intensity for the tiled threshold. The value is multiplied
+        by soma diameter (i.e. 1 means one soma diameter). If zero or None, the
+        tiled threshold is disabled and only the per-plane threshold is used.
+        Tiling is done with 50% overlap when striding.
     callback : Callable[int], optional
         A callback function that is called every time a plane has finished
         being processed. Called with the plane number that has finished.
@@ -132,9 +159,11 @@ def main(
     Returns
     -------
     List[Cell]
-        List of detected cells.
+        List of detected cell candidates.
     """
     start_time = datetime.now()
+    if torch_device is None:
+        torch_device = "cuda" if torch.cuda.is_available() else "cpu"
     if batch_size is None:
         if torch_device == "cpu":
             batch_size = 4
@@ -155,6 +184,12 @@ def main(
     end_plane = min(len(signal_array), end_plane)
 
     torch_device = torch_device.lower()
+    # Use SciPy filtering on CPU (better performance); use PyTorch on GPU
+    if torch_device != "cuda":
+        use_scipy = True
+    else:
+        use_scipy = False
+
     batch_size = max(batch_size, 1)
     # brainmapper can pass them in as str
     voxel_sizes = list(map(float, voxel_sizes))
@@ -174,25 +209,24 @@ def main(
         ball_overlap_fraction=ball_overlap_fraction,
         log_sigma_size=log_sigma_size,
         n_sds_above_mean_thresh=n_sds_above_mean_thresh,
+        n_sds_above_mean_tiled_thresh=n_sds_above_mean_tiled_thresh,
+        tiled_thresh_tile_size=tiled_thresh_tile_size,
         outlier_keep=outlier_keep,
         artifact_keep=artifact_keep,
         save_planes=save_planes,
         plane_directory=plane_directory,
         batch_size=batch_size,
         torch_device=torch_device,
+        pin_memory=pin_memory,
+        n_splitting_iter=n_splitting_iter,
     )
 
     # replicate the settings specific to splitting, before we access anything
     # of the original settings, causing cached properties
     kwargs = dataclasses.asdict(settings)
-    kwargs["ball_z_size_um"] = split_ball_z_size * settings.z_pixel_size
-    kwargs["ball_xy_size_um"] = (
-        split_ball_xy_size * settings.in_plane_pixel_size
-    )
+    kwargs["ball_z_size_um"] = split_ball_z_size
+    kwargs["ball_xy_size_um"] = split_ball_xy_size
     kwargs["ball_overlap_fraction"] = split_ball_overlap_fraction
-    kwargs["soma_diameter_um"] = (
-        split_soma_diameter * settings.in_plane_pixel_size
-    )
     # always run on cpu because copying to gpu overhead is likely slower than
     # any benefit for detection on smallish volumes
     kwargs["torch_device"] = "cpu"
@@ -212,7 +246,9 @@ def main(
         plane_shape=settings.plane_shape,
         clipping_value=settings.clipping_value,
         threshold_value=settings.threshold_value,
-        n_sds_above_mean_thresh=n_sds_above_mean_thresh,
+        n_sds_above_mean_thresh=settings.n_sds_above_mean_thresh,
+        n_sds_above_mean_tiled_thresh=settings.n_sds_above_mean_tiled_thresh,
+        tiled_thresh_tile_size=settings.tiled_thresh_tile_size,
         log_sigma_size=log_sigma_size,
         soma_diameter=settings.soma_diameter,
         torch_device=torch_device,
@@ -231,6 +267,5 @@ def main(
 
     time_elapsed = datetime.now() - start_time
     s = f"Detection complete. Found {len(cells)} cells in {time_elapsed}"
-    logger.debug(s)
-    print(s)
+    logger.info(s)
     return cells