lbm_suite2p_python 2.3.0__tar.gz → 2.3.1__tar.gz

{lbm_suite2p_python-2.3.0/lbm_suite2p_python.egg-info → lbm_suite2p_python-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 2.3.0
+Version: 2.3.1
 Summary: Light Beads Microscopy Pipeline using Suite2p
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
@@ -12,15 +12,18 @@ Requires-Python: <3.12.10,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 Requires-Dist: mbo_utilities>=2.3.0
-Requires-Dist: suite2p_mbo>=2.0.0
+Requires-Dist: fastplotlib
+Provides-Extra: suite2p
+Requires-Dist: suite2p_mbo>=2.0.0; extra == "suite2p"
 Provides-Extra: rastermap
 Requires-Dist: rastermap; extra == "rastermap"
 Provides-Extra: cellpose
-Requires-Dist: cellpose==4.0.6; extra == "cellpose"
-Requires-Dist: torch>=2.7.0; extra == "cellpose"
-Requires-Dist: torchvision>=0.22.0; extra == "cellpose"
+Requires-Dist: cellpose>=4.0.6; extra == "cellpose"
+Provides-Extra: torch
+Requires-Dist: torch>=2.7.0; extra == "torch"
+Requires-Dist: torchvision>=0.22.0; extra == "torch"
 Provides-Extra: all
-Requires-Dist: lbm_suite2p_python[cellpose,rastermap]; extra == "all"
+Requires-Dist: lbm_suite2p_python[cellpose,rastermap,suite2p,torch]; extra == "all"
 Dynamic: license-file
 
 # LBM-Suite2p-Python

{lbm_suite2p_python-2.3.0 → lbm_suite2p_python-2.3.1}/lbm_suite2p_python/__init__.py

@@ -19,6 +19,7 @@ __all__ = [
     "run_plane",
     "grid_search",
     "consolidate_volume",
+    "add_processing_step",
     "plot_traces",
     "plot_masks",
     "plot_rastermap",
@@ -36,6 +37,7 @@ __all__ = [
     "plot_plane_diagnostics",
     "plot_trace_analysis",
     "plot_zplane_figures",
+    "plot_mask_comparison",
     "create_volume_summary_table",
     "dff_rolling_percentile",
     "dff_median_filter",
@@ -45,4 +47,21 @@ __all__ = [
     "load_ops",
     "load_planar_results",
     "default_ops",
+    # Image processing utilities
+    "normalize99",
+    "apply_hp_filter",
+    "random_colors_for_mask",
+    "mask_overlay",
+    "stat_to_mask",
+    # Filtering utilities
+    "filter_by_max_diameter",
+    "filter_by_diameter",
+    "filter_by_area",
+    "filter_by_eccentricity",
+    "plot_regional_zoom",
+    "plot_filtered_cells",
+    "plot_diameter_histogram",
 ]
+
+# Re-export with public name
+from lbm_suite2p_python.run_lsp import _add_processing_step as add_processing_step

{lbm_suite2p_python-2.3.0 → lbm_suite2p_python-2.3.1}/lbm_suite2p_python/default_ops.py

@@ -130,8 +130,7 @@ def s2p_ops():
         "cellprob_threshold": -6,  # cellprob_threshold for cellpose
         "flow_threshold": 0,  # flow_threshold for cellpose
         "spatial_hp_cp": 0.5,  # high-pass image spatially by a multiple of the diameter
-        "pretrained_model":
-            "cpsam",  # path to pretrained model or model type string in Cellpose (can be user model)
+        "pretrained_model": "cpsam",  # cellpose model to use for anatomical detection
 
         # classification parameters
         "soma_crop":

{lbm_suite2p_python-2.3.0 → lbm_suite2p_python-2.3.1}/lbm_suite2p_python/postprocessing.py

@@ -39,6 +39,121 @@ def filter_by_diameter(iscell, stat, ops, min_mult=0.3, max_mult=3.0):
     return iscell
 
 
+def filter_by_max_diameter(
+    iscell,
+    stat,
+    max_diameter_um: float = None,
+    max_diameter_px: float = None,
+    pixel_size_um: float = None,
+    ops: dict = None,
+):
+    """
+    Filter cells by maximum diameter in microns or pixels.
+
+    Sets iscell=False for ROIs whose diameter exceeds the specified threshold.
+    Diameter is computed as 2 * radius from the ellipse fit.
+
+    Parameters
+    ----------
+    iscell : np.ndarray
+        Cell classification array (n_rois,) or (n_rois, 2).
+    stat : np.ndarray or list
+        Suite2p stat array with ROI statistics.
+    max_diameter_um : float, optional
+        Maximum allowed diameter in microns. Requires pixel_size_um or ops
+        with pixel resolution info.
+    max_diameter_px : float, optional
+        Maximum allowed diameter in pixels. Used if max_diameter_um not given.
+    pixel_size_um : float, optional
+        Pixel size in microns. If None, attempts to read from ops.
+    ops : dict, optional
+        Suite2p ops dictionary. Used to get pixel resolution if pixel_size_um
+        not provided. Looks for 'umPerPix' or 'diameter' keys.
+
+    Returns
+    -------
+    iscell_filtered : np.ndarray
+        Updated iscell array with large ROIs marked as rejected.
+    removed_mask : np.ndarray
+        Boolean mask of ROIs that were removed (True = removed).
+    diameters_px : np.ndarray
+        Diameter of each ROI in pixels.
+    threshold_px : float
+        The threshold used in pixels.
+
+    Examples
+    --------
+    >>> # Filter by max 22 microns diameter
+    >>> iscell_filtered, removed, diameters, thresh = filter_by_max_diameter(
+    ...     iscell, stat, max_diameter_um=22, ops=ops
+    ... )
+
+    >>> # Filter by max 15 pixels diameter
+    >>> iscell_filtered, removed, diameters, thresh = filter_by_max_diameter(
+    ...     iscell, stat, max_diameter_px=15
+    ... )
+
+    >>> # Plot the removed cells
+    >>> from lbm_suite2p_python import plot_filtered_cells
+    >>> fig = plot_filtered_cells(stat, iscell_filtered, removed, ops=ops)
+    """
+    iscell = _normalize_iscell(iscell)
+
+    if max_diameter_um is None and max_diameter_px is None:
+        raise ValueError("Must specify either max_diameter_um or max_diameter_px")
+
+    # Get radii from stat
+    if "radius" not in stat[0]:
+        # Compute radius if not present
+        radii = []
+        for s in stat:
+            npix = len(s["xpix"])
+            # Approximate radius from area: r = sqrt(npix / pi)
+            radii.append(np.sqrt(npix / np.pi))
+        radii = np.array(radii)
+    else:
+        radii = np.array([s["radius"] for s in stat])
+
+    diameters_px = 2 * radii
+
+    # Convert to pixels if given in microns
+    if max_diameter_um is not None:
+        # Get pixel size
+        if pixel_size_um is None and ops is not None:
+            # Try various keys for pixel resolution
+            if "umPerPix" in ops:
+                pixel_size_um = ops["umPerPix"]
+            elif "um_per_pixel" in ops:
+                pixel_size_um = ops["um_per_pixel"]
+            elif "pixel_resolution" in ops and ops["pixel_resolution"]:
+                pr = ops["pixel_resolution"]
+                if isinstance(pr, (list, tuple)) and len(pr) >= 2:
+                    pixel_size_um = np.mean([pr[0], pr[1]])
+                else:
+                    pixel_size_um = float(pr)
+            elif "umPerPixX" in ops and "umPerPixY" in ops:
+                pixel_size_um = np.mean([ops["umPerPixX"], ops["umPerPixY"]])
+
+        if pixel_size_um is None:
+            raise ValueError(
+                "Cannot convert microns to pixels: pixel_size_um not provided "
+                "and could not be found in ops. Use max_diameter_px instead."
+            )
+
+        max_diameter_px = max_diameter_um / pixel_size_um
+
+    # Apply filter
+    valid = diameters_px <= max_diameter_px
+    removed_mask = ~valid & iscell  # ROIs that were cells but got filtered out
+    n_rejected = removed_mask.sum()
+
+    if n_rejected > 0:
+        print(f"Filtered {n_rejected} ROIs with diameter > {max_diameter_px:.1f} px")
+
+    iscell_filtered = iscell & valid
+    return iscell_filtered, removed_mask, diameters_px, max_diameter_px
+
+
 def filter_by_area(iscell, stat, min_mult=0.25, max_mult=4.0):
     """
     Filter cells by total area (in pixels).