cellfinder 1.4.1__py3-none-any.whl → 1.9.0__py3-none-any.whl

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/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/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/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

cellfinder/core/detect/filters/plane/plane_filter.py

@@ -1,13 +1,12 @@
-from dataclasses import dataclass, field
 from typing import Tuple
 
 import torch
+import torch.nn.functional as F
 
 from cellfinder.core.detect.filters.plane.classical_filter import PeakEnhancer
 from cellfinder.core.detect.filters.plane.tile_walker import TileWalker
 
 
-@dataclass
 class TileProcessor:
     """
     Processor that filters each plane to highlight the peaks and also
@@ -39,7 +38,7 @@ class TileProcessor:
         Number of standard deviations above the mean threshold to use for
         determining whether a voxel is bright.
     log_sigma_size : float
-        Size of the sigma for the gaussian filter.
+        Size of the Gaussian sigma for the Laplacian of Gaussian filtering.
     soma_diameter : float
         Diameter of the soma in voxels.
     torch_device: str
@@ -63,12 +62,22 @@ class TileProcessor:
     # voxels who are this many std above mean or more are set to
     # threshold_value
     n_sds_above_mean_thresh: float
+    # If used, voxels who are this many or more std above mean of the
+    # containing tile as well as above n_sds_above_mean_thresh for the plane
+    # average are set to threshold_value.
+    n_sds_above_mean_tiled_thresh: float
+    # the tile size, in pixels, that will be used to tile the x, y plane when
+    # we calculate the per-tile mean / std for use with
+    # n_sds_above_mean_tiled_thresh. We use 50% overlap when tiling.
+    local_threshold_tile_size_px: int = 0
+    # the torch device name
+    torch_device: str = ""
 
     # filter that finds the peaks in the planes
-    peak_enhancer: PeakEnhancer = field(init=False)
+    peak_enhancer: PeakEnhancer = None
     # generates tiles of the planes, with each tile marked as being inside
     # or outside the brain based on brightness
-    tile_walker: TileWalker = field(init=False)
+    tile_walker: TileWalker = None
 
     def __init__(
         self,
@@ -76,6 +85,8 @@ class TileProcessor:
         clipping_value: int,
         threshold_value: int,
         n_sds_above_mean_thresh: float,
+        n_sds_above_mean_tiled_thresh: float,
+        tiled_thresh_tile_size: float | None,
         log_sigma_size: float,
         soma_diameter: int,
         torch_device: str,
@@ -85,6 +96,12 @@ class TileProcessor:
         self.clipping_value = clipping_value
         self.threshold_value = threshold_value
         self.n_sds_above_mean_thresh = n_sds_above_mean_thresh
+        self.n_sds_above_mean_tiled_thresh = n_sds_above_mean_tiled_thresh
+        if tiled_thresh_tile_size:
+            self.local_threshold_tile_size_px = int(
+                round(soma_diameter * tiled_thresh_tile_size)
+            )
+        self.torch_device = torch_device
 
         laplace_gaussian_sigma = log_sigma_size * soma_diameter
         self.peak_enhancer = PeakEnhancer(
@@ -131,7 +148,10 @@ class TileProcessor:
             planes,
             enhanced_planes,
             self.n_sds_above_mean_thresh,
+            self.n_sds_above_mean_tiled_thresh,
+            self.local_threshold_tile_size_px,
             self.threshold_value,
+            self.torch_device,
         )
 
         return planes, inside_brain_tiles
@@ -145,21 +165,98 @@ def _threshold_planes(
     planes: torch.Tensor,
     enhanced_planes: torch.Tensor,
     n_sds_above_mean_thresh: float,
+    n_sds_above_mean_tiled_thresh: float,
+    local_threshold_tile_size_px: int,
     threshold_value: int,
+    torch_device: str,
 ) -> None:
     """
     Sets each plane (in-place) to threshold_value, where the corresponding
     enhanced_plane > mean + n_sds_above_mean_thresh*std. Each plane will be
     set to zero elsewhere.
     """
-    planes_1d = enhanced_planes.view(enhanced_planes.shape[0], -1)
+    z, y, x = enhanced_planes.shape
 
+    # ---- get per-plane global threshold ----
+    planes_1d = enhanced_planes.view(z, -1)
     # add back last dim
-    avg = torch.mean(planes_1d, dim=1, keepdim=True).unsqueeze(2)
-    sd = torch.std(planes_1d, dim=1, keepdim=True).unsqueeze(2)
-    threshold = avg + n_sds_above_mean_thresh * sd
+    std, mean = torch.std_mean(planes_1d, dim=1, keepdim=True)
+    threshold = mean.unsqueeze(2) + n_sds_above_mean_thresh * std.unsqueeze(2)
+    above_global = enhanced_planes > threshold
+
+    # ---- calculate the local tiled threshold ----
+    # we do 50% overlap so there's no jumps at boundaries
+    stride = local_threshold_tile_size_px // 2
+    # make tile even for ease of computation
+    tile_size = stride * 2
+    # Due to 50% overlap, to get tiles we move the tile by half tile (stride).
+    # Total moves will be y // stride - 2 (we start already with mask on first
+    # tile). So add back 1 for the first tile. Partial tiles are dropped
+    n_y_tiles = max(y // stride - 1, 1) if stride else 1
+    n_x_tiles = max(x // stride - 1, 1) if stride else 1
+    do_tile_y = n_y_tiles >= 2
+    do_tile_x = n_x_tiles >= 2
+    # we want at least one axis to have at least two tiles
+    if local_threshold_tile_size_px >= 2 and (do_tile_y or do_tile_x):
+        # num edge pixels dropped b/c moving by stride would move tile off edge
+        y_rem = y % stride
+        x_rem = x % stride
+        enhanced_planes_raw = enhanced_planes
+        if do_tile_y:
+            enhanced_planes = enhanced_planes[:, y_rem // 2 :, :]
+        if do_tile_x:
+            enhanced_planes = enhanced_planes[:, :, x_rem // 2 :]
+
+        # add empty channel dim after z "batch" dim -> zcyx
+        enhanced_planes = enhanced_planes.unsqueeze(1)
+        # unfold makes it 3 dim, z, M, L. L is number of tiles, M is tile area
+        unfolded = F.unfold(
+            enhanced_planes,
+            (tile_size if do_tile_y else y, tile_size if do_tile_x else x),
+            stride=stride,
+        )
+        # average the tile areas, for each tile
+        std, mean = torch.std_mean(unfolded, dim=1, keepdim=True)
+        threshold = mean + n_sds_above_mean_tiled_thresh * std
+
+        # reshape it back into Y by X tiles, instead of YX being one dim
+        threshold = threshold.reshape((z, n_y_tiles, n_x_tiles))
+
+        # we need total size of n_tiles * stride + stride + rem for the
+        # original size. So we add 2 strides and then chop off the excess above
+        # rem. We center it because of 50% overlap, the first tile is actually
+        # centered in between the first two strides
+        offsets = [(0, y), (0, x)]
+        for dim, do_tile, n_tiles, n, rem in [
+            (1, do_tile_y, n_y_tiles, y, y_rem),
+            (2, do_tile_x, n_x_tiles, x, x_rem),
+        ]:
+            if do_tile:
+                repeats = (
+                    torch.ones(n_tiles, dtype=torch.int, device=torch_device)
+                    * stride
+                )
+                # add total of 2 additional strides
+                repeats[0] = 2 * stride
+                repeats[-1] = 2 * stride
+                output_size = (n_tiles + 2) * stride
+
+                threshold = threshold.repeat_interleave(
+                    repeats, dim=dim, output_size=output_size
+                )
+                # drop the excess we gained from padding rem to whole stride
+                offset = (stride - rem) // 2
+                offsets[dim - 1] = offset, n + offset
+
+        # can't use slice(...) objects in jit code so use actual indices
+        (a, b), (c, d) = offsets
+        threshold = threshold[:, a:b, c:d]
+
+        above_local = enhanced_planes_raw > threshold
+        above = torch.logical_and(above_global, above_local)
+    else:
+        above = above_global
 
-    above = enhanced_planes > threshold
     planes[above] = threshold_value
     # subsequent steps only care about the values that are set to threshold or
     # above in planes. We set values in *planes* to threshold based on the

cellfinder/core/detect/filters/setup_filters.py

@@ -80,23 +80,28 @@ class DetectionSettings:
 
     voxel_sizes: Tuple[float, float, float] = (1.0, 1.0, 1.0)
     """
-    Tuple of voxel sizes in each dimension (z, y, x). We use this to convert
-    from `um` to pixel sizes.
+    Tuple of voxel sizes (microns) in each dimension (z, y, x). We use this
+    to convert from `um` to pixel sizes.
     """
 
     soma_spread_factor: float = 1.4
-    """Spread factor for soma size - how much it may stretch in the images."""
+    """
+    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.
+    """
 
     soma_diameter_um: float = 16
     """
-    Diameter of a typical soma in um. Bright areas larger than this will be
-    split.
+    Diameter of a typical soma in-plane (xy) in microns.
     """
 
     max_cluster_size_um3: float = 100_000
     """
-    Maximum size of a cluster (bright area) that will be processed, in um.
-    Larger bright areas are skipped as artifacts.
+    Largest detected cell cluster (in cubic um) where splitting
+    should be attempted. Clusters above this size will be labeled
+    as artifacts.
     """
 
     ball_xy_size_um: float = 6
@@ -116,17 +121,41 @@ class DetectionSettings:
 
     ball_overlap_fraction: float = 0.6
     """
-    Fraction of overlap between a bright area and the spherical kernel,
-    for the area to be considered a single ball.
+    Fraction of the 3d ball filter needed to be filled by foreground voxels,
+    centered on a voxel, to retain the voxel.
     """
 
     log_sigma_size: float = 0.2
-    """Size of the sigma for the 2d Gaussian 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 = 10
     """
-    Number of standard deviations above the mean intensity to use for a
-    threshold to define bright areas. Below it, it's not considered bright.
+    Per-plane intensity threshold (the number of standard deviations
+    above the mean) of the 2d filtered planes used to mark pixels as
+    foreground or background.
+    """
+
+    n_sds_above_mean_tiled_thresh: float = 10
+    """
+    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 | None = None
+    """
+    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.
     """
 
     outlier_keep: bool = False
@@ -180,6 +209,14 @@ class DetectionSettings:
     to run on the first GPU.
     """
 
+    pin_memory: bool = False
+    """
+    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.
+    """
+
     n_free_cpus: int = 2
     """
     Number of free CPU cores to keep available and not use during parallel
@@ -191,6 +228,8 @@ class DetectionSettings:
     """
     During the structure splitting phase we iteratively shrink the bright areas
     and re-filter with the 3d filter. This is the number of iterations to do.
+    Each iteration reduces the cluster size by the voxels not retained in the
+    previous iteration.
 
     This is a maximum because we also stop if there are no more structures left
     during any iteration.