lbm_suite2p_python 2.5.4__tar.gz → 2.5.7__tar.gz

{lbm_suite2p_python-2.5.4/lbm_suite2p_python.egg-info → lbm_suite2p_python-2.5.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lbm_suite2p_python
-Version: 2.5.4
+Version: 2.5.7
 Summary: Light Beads Microscopy Pipeline using Suite2p
 License-Expression: BSD-3-Clause
 Project-URL: homepage, https://github.com/MillerBrainObservatory/LBM-Suite2p-Python
@@ -8,12 +8,12 @@ Keywords: Pipeline,Numpy,Microscopy,ScanImage,Suite2p,tiff
 Classifier: Development Status :: 3 - Alpha
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: <3.12.10,>=3.12.7
+Requires-Python: <3.14,>=3.12.7
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: mbo_utilities>=2.6.0
-Provides-Extra: suite2p
-Requires-Dist: suite2p_mbo>=2.0.1; extra == "suite2p"
+Requires-Dist: mbo_utilities>=2.6.3
+Requires-Dist: suite2p_mbo>=2.0.1
+Requires-Dist: setuptools<81
 Provides-Extra: rastermap
 Requires-Dist: rastermap; extra == "rastermap"
 Provides-Extra: cellpose
@@ -22,7 +22,7 @@ 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,suite2p,torch]; extra == "all"
+Requires-Dist: lbm_suite2p_python[cellpose,rastermap,torch]; extra == "all"
 Dynamic: license-file
 
 <p align="center">

{lbm_suite2p_python-2.5.4 → lbm_suite2p_python-2.5.7}/lbm_suite2p_python/cellpose.py

@@ -37,9 +37,10 @@ def _compute_projection(
     Parameters
     ----------
     arr : array-like
-        Input array (T, Y, X) for 3D or (T, Z, Y, X) for 4D.
+        Input array. mbo_utilities arrays are 5D TCZYX.
+        Legacy 4D TZYX and 3D TYX inputs are also supported.
     plane_idx : int, optional
-        For 4D arrays, which z-plane to extract (0-indexed).
+        For volumetric arrays, which z-plane to extract (0-indexed).
         If None, uses all planes for 3D segmentation.
     method : str
         Projection method: 'max', 'mean', 'std', or 'percentile'.
@@ -53,19 +54,23 @@ def _compute_projection(
     """
     ndim = len(arr.shape)
 
-    if ndim == 4:
-        # (T, Z, Y, X)
+    if ndim == 5:
+        # 5D TCZYX: use channel 0
+        if plane_idx is not None:
+            data = arr[:, 0, plane_idx, :, :]  # (T, Y, X)
+        else:
+            data = arr[:, 0, :, :, :]  # (T, Z, Y, X)
+    elif ndim == 4:
+        # legacy 4D TZYX
         if plane_idx is not None:
-            # extract single plane -> (T, Y, X)
             data = arr[:, plane_idx, :, :]
         else:
-            # keep all planes -> (T, Z, Y, X)
             data = arr[:]
     elif ndim == 3:
-        # (T, Y, X)
+        # legacy 3D TYX
         data = arr[:]
     else:
-        raise ValueError(f"Expected 3D or 4D array, got {ndim}D")
+        raise ValueError(f"Expected 3D, 4D, or 5D array, got {ndim}D")
 
     # convert to numpy if lazy
     if hasattr(data, "compute"):
@@ -577,18 +582,18 @@ def cellpose(
 
     # get array info
     shape = arr.shape
-    ndim = len(shape)
     num_planes = _get_num_planes(arr)
     num_frames = shape[0]
+    is_volumetric = num_planes > 1
 
     print(f"\nDataset info:")
     print(f"  Shape: {shape}")
     print(f"  Frames: {num_frames}")
     print(f"  Planes: {num_planes}")
-    print(f"  Data type: {'4D volumetric' if ndim == 4 else '3D planar'}")
+    print(f"  Data type: {'volumetric' if is_volumetric else 'planar'}")
 
     # normalize planes to 0-indexed list
-    if ndim == 4:
+    if is_volumetric:
         planes_to_process = _normalize_planes(planes, num_planes)
     else:
         planes_to_process = [None]  # single plane data

{lbm_suite2p_python-2.5.4 → lbm_suite2p_python-2.5.7}/lbm_suite2p_python/grid_search.py

@@ -246,12 +246,15 @@ def grid_search(
         print(f"Processing plane {plane_num}")
         print(f"{'='*60}")
 
-        # get plane dimensions
-        if num_planes > 1:
-            sample_frame = arr[0, plane_idx]
+        # get plane spatial dimensions
+        # mbo_utilities arrays are 5D TCZYX; legacy 4D TZYX and 3D TYX still supported
+        ndim = len(arr.shape)
+        if ndim == 5:
+            plane_Ly, plane_Lx = arr.shape[3], arr.shape[4]
+        elif ndim == 4:
+            plane_Ly, plane_Lx = arr.shape[2], arr.shape[3]
         else:
-            sample_frame = arr[0] if arr.ndim == 3 else arr[0, 0]
-        plane_Ly, plane_Lx = sample_frame.shape[-2], sample_frame.shape[-1]
+            plane_Ly, plane_Lx = arr.shape[-2], arr.shape[-1]
 
         # create plane subdirectory
         plane_tag = f"plane{plane_num:02d}" if len(planes_to_process) > 1 else ""
@@ -300,18 +303,24 @@ def grid_search(
             else:
                 print(f"\nUsing existing base binary: {base_bin_file}")
 
-            # run registration once on base
+            # run registration once on base (or skip if user disabled it)
             base_reg_file = base_dir / "data.bin"
+            user_wants_reg = ops.get("do_registration", 1) not in (0, False)
+
             if not base_reg_file.exists() or force_reg:
-                print(f"Running registration on base...")
-                reg_ops = copy.deepcopy(default_ops())
-                if base_ops_file.exists():
-                    reg_ops.update(load_ops(base_ops_file))
-                reg_ops["do_registration"] = 1
-                reg_ops["roidetect"] = 0
-                np.save(base_ops_file, reg_ops)
-                run_plane_bin(base_ops_file)
-                print(f"Registration complete.")
+                if user_wants_reg:
+                    print(f"Running registration on base...")
+                    reg_ops = copy.deepcopy(default_ops())
+                    if base_ops_file.exists():
+                        reg_ops.update(load_ops(base_ops_file))
+                    reg_ops["do_registration"] = 1
+                    reg_ops["roidetect"] = 0
+                    np.save(base_ops_file, reg_ops)
+                    run_plane_bin(base_ops_file)
+                    print(f"Registration complete.")
+                else:
+                    print(f"Registration disabled, using raw binary as base.")
+                    shutil.copy2(base_bin_file, base_reg_file)
             else:
                 print(f"Using existing registered binary: {base_reg_file}")
 

{lbm_suite2p_python-2.5.4 → lbm_suite2p_python-2.5.7}/lbm_suite2p_python/postprocessing.py

@@ -77,8 +77,12 @@ def _save_filtered_iscell(plane_dir, iscell_filtered, iscell_original=None):
     iscell_path = plane_dir / "iscell.npy"
 
     # Load original to preserve probabilities
-    if iscell_original is None and iscell_path.exists():
-        iscell_original = np.load(iscell_path, allow_pickle=True)
+    if iscell_original is None:
+        backup_path = plane_dir / "iscell_suite2p.npy"
+        if backup_path.exists():
+            iscell_original = np.load(backup_path, allow_pickle=True)
+        elif iscell_path.exists():
+            iscell_original = np.load(iscell_path, allow_pickle=True)
 
     if iscell_original is not None and iscell_original.ndim == 2:
         # Preserve probability column
@@ -611,7 +615,7 @@ def apply_filters(
 
     # Save final result if requested
     if save and plane_dir is not None:
-        _save_filtered_iscell(plane_dir, iscell_current)
+        _save_filtered_iscell(plane_dir, iscell_current, iscell_original=iscell_orig)
 
     n_total = total_removed.sum()
     n_orig = iscell_orig.sum()
@@ -1031,13 +1035,14 @@ def compute_trace_quality_score(
 
     n_neurons = F.shape[0]
 
-    # Neuropil correction
+    # neuropil correction and rectification
     if Fneu is not None:
         F_corr = F - 0.7 * Fneu
     else:
         F_corr = F
+    F_corr = np.maximum(F_corr, 0)
 
-    # Compute baseline and dF/F
+    # compute baseline and dF/F
     baseline = np.percentile(F_corr, 20, axis=1, keepdims=True)
     baseline = np.maximum(baseline, 1e-6)
     dff = (F_corr - baseline) / baseline
@@ -1203,8 +1208,9 @@ def compute_roi_stats(plane_dir, fs=None):
 
     n_rois = F.shape[0]
 
-    # neuropil correction and dF/F
+    # neuropil correction, rectify negatives, and dF/F
     F_corr = F - 0.7 * Fneu
+    F_corr = np.maximum(F_corr, 0)
     baseline = np.percentile(F_corr, 20, axis=1, keepdims=True)
     baseline = np.maximum(baseline, 1e-6)
     dff = (F_corr - baseline) / baseline